Survival analysis: Part I — analysis of time-to-event

PubMed Central

2018-01-01

Length of time is a variable often encountered during data analysis. Survival analysis provides simple, intuitive results concerning time-to-event for events of interest, which are not confined to death. This review introduces methods of analyzing time-to-event. The Kaplan-Meier survival analysis, log-rank test, and Cox proportional hazards regression modeling method are described with examples of hypothetical data. PMID:29768911

Competency-based residency training and the web log: modeling practice-based learning and enhancing medical knowledge†

PubMed Central

Hollon, Matthew F.

2015-01-01

Background By using web-based tools in medical education, there are opportunities to innovatively teach important principles from the general competencies of graduate medical education. Objectives Postulating that faculty transparency in learning from uncertainties in clinical work could help residents to incorporate the principles of practice-based learning and improvement (PBLI) in their professional development, faculty in this community-based residency program modeled the steps of PBLI on a weekly basis through the use of a web log. Method The program confidentially surveyed residents before and after this project about actions consistent with PBLI and knowledge acquired through reading the web log. Results The frequency that residents encountered clinical situations where they felt uncertain declined over the course of the 24 weeks of the project from a mean frequency of uncertainty of 36% to 28% (Wilcoxon signed rank test, p=0.008); however, the frequency with which residents sought answers when faced with uncertainty did not change (Wilcoxon signed rank test, p=0.39), remaining high at approximately 80%. Residents answered a mean of 52% of knowledge questions correct when tested prior to faculty posts to the blog, rising to a mean of 65% of questions correct when tested at the end of the project (paired t-test, p=0.001). Conclusions Faculty role modeling of PBLI behaviors and posting clinical questions and answers to a web log led to modest improvements in medical knowledge but did not alter behavior that was already taking place frequently among residents. PMID:26653701

Functional form and risk adjustment of hospital costs: Bayesian analysis of a Box-Cox random coefficients model.

PubMed

Hollenbeak, Christopher S

2005-10-15

While risk-adjusted outcomes are often used to compare the performance of hospitals and physicians, the most appropriate functional form for the risk adjustment process is not always obvious for continuous outcomes such as costs. Semi-log models are used most often to correct skewness in cost data, but there has been limited research to determine whether the log transformation is sufficient or whether another transformation is more appropriate. This study explores the most appropriate functional form for risk-adjusting the cost of coronary artery bypass graft (CABG) surgery. Data included patients undergoing CABG surgery at four hospitals in the midwest and were fit to a Box-Cox model with random coefficients (BCRC) using Markov chain Monte Carlo methods. Marginal likelihoods and Bayes factors were computed to perform model comparison of alternative model specifications. Rankings of hospital performance were created from the simulation output and the rankings produced by Bayesian estimates were compared to rankings produced by standard models fit using classical methods. Results suggest that, for these data, the most appropriate functional form is not logarithmic, but corresponds to a Box-Cox transformation of -1. Furthermore, Bayes factors overwhelmingly rejected the natural log transformation. However, the hospital ranking induced by the BCRC model was not different from the ranking produced by maximum likelihood estimates of either the linear or semi-log model. Copyright (c) 2005 John Wiley & Sons, Ltd.

A novel sample size formula for the weighted log-rank test under the proportional hazards cure model.

PubMed

Xiong, Xiaoping; Wu, Jianrong

2017-01-01

The treatment of cancer has progressed dramatically in recent decades, such that it is no longer uncommon to see a cure or log-term survival in a significant proportion of patients with various types of cancer. To adequately account for the cure fraction when designing clinical trials, the cure models should be used. In this article, a sample size formula for the weighted log-rank test is derived under the fixed alternative hypothesis for the proportional hazards cure models. Simulation showed that the proposed sample size formula provides an accurate estimation of sample size for designing clinical trials under the proportional hazards cure models. Copyright © 2016 John Wiley & Sons, Ltd.

Outcome prediction in patients with glioblastoma by using imaging, clinical, and genomic biomarkers: focus on the nonenhancing component of the tumor.

PubMed

Jain, Rajan; Poisson, Laila M; Gutman, David; Scarpace, Lisa; Hwang, Scott N; Holder, Chad A; Wintermark, Max; Rao, Arvind; Colen, Rivka R; Kirby, Justin; Freymann, John; Jaffe, C Carl; Mikkelsen, Tom; Flanders, Adam

2014-08-01

To correlate patient survival with morphologic imaging features and hemodynamic parameters obtained from the nonenhancing region (NER) of glioblastoma (GBM), along with clinical and genomic markers. An institutional review board waiver was obtained for this HIPAA-compliant retrospective study. Forty-five patients with GBM underwent baseline imaging with contrast material-enhanced magnetic resonance (MR) imaging and dynamic susceptibility contrast-enhanced T2*-weighted perfusion MR imaging. Molecular and clinical predictors of survival were obtained. Single and multivariable models of overall survival (OS) and progression-free survival (PFS) were explored with Kaplan-Meier estimates, Cox regression, and random survival forests. Worsening OS (log-rank test, P = .0103) and PFS (log-rank test, P = .0223) were associated with increasing relative cerebral blood volume of NER (rCBVNER), which was higher with deep white matter involvement (t test, P = .0482) and poor NER margin definition (t test, P = .0147). NER crossing the midline was the only morphologic feature of NER associated with poor survival (log-rank test, P = .0125). Preoperative Karnofsky performance score (KPS) and resection extent (n = 30) were clinically significant OS predictors (log-rank test, P = .0176 and P = .0038, respectively). No genomic alterations were associated with survival, except patients with high rCBVNER and wild-type epidermal growth factor receptor (EGFR) mutation had significantly poor survival (log-rank test, P = .0306; area under the receiver operating characteristic curve = 0.62). Combining resection extent with rCBVNER marginally improved prognostic ability (permutation, P = .084). Random forest models of presurgical predictors indicated rCBVNER as the top predictor; also important were KPS, age at diagnosis, and NER crossing the midline. A multivariable model containing rCBVNER, age at diagnosis, and KPS can be used to group patients with more than 1 year of difference in observed median survival (0.49-1.79 years). Patients with high rCBVNER and NER crossing the midline and those with high rCBVNER and wild-type EGFR mutation showed poor survival. In multivariable survival models, however, rCBVNER provided unique prognostic information that went above and beyond the assessment of all NER imaging features, as well as clinical and genomic features.

Estimating survival of radio-tagged birds

USGS Publications Warehouse

Bunck, C.M.; Pollock, K.H.; Lebreton, J.-D.; North, P.M.

1993-01-01

Parametric and nonparametric methods for estimating survival of radio-tagged birds are described. The general assumptions of these methods are reviewed. An estimate based on the assumption of constant survival throughout the period is emphasized in the overview of parametric methods. Two nonparametric methods, the Kaplan-Meier estimate of the survival funcrion and the log rank test, are explained in detail The link between these nonparametric methods and traditional capture-recapture models is discussed aloag with considerations in designing studies that use telemetry techniques to estimate survival.

Low-rank structure learning via nonconvex heuristic recovery.

PubMed

Deng, Yue; Dai, Qionghai; Liu, Risheng; Zhang, Zengke; Hu, Sanqing

2013-03-01

In this paper, we propose a nonconvex framework to learn the essential low-rank structure from corrupted data. Different from traditional approaches, which directly utilizes convex norms to measure the sparseness, our method introduces more reasonable nonconvex measurements to enhance the sparsity in both the intrinsic low-rank structure and the sparse corruptions. We will, respectively, introduce how to combine the widely used ℓp norm (0 < p < 1) and log-sum term into the framework of low-rank structure learning. Although the proposed optimization is no longer convex, it still can be effectively solved by a majorization-minimization (MM)-type algorithm, with which the nonconvex objective function is iteratively replaced by its convex surrogate and the nonconvex problem finally falls into the general framework of reweighed approaches. We prove that the MM-type algorithm can converge to a stationary point after successive iterations. The proposed model is applied to solve two typical problems: robust principal component analysis and low-rank representation. Experimental results on low-rank structure learning demonstrate that our nonconvex heuristic methods, especially the log-sum heuristic recovery algorithm, generally perform much better than the convex-norm-based method (0 < p < 1) for both data with higher rank and with denser corruptions.

Effect of different mixing methods on the bacterial microleakage of calcium-enriched mixture cement.

PubMed

Shahi, Shahriar; Jeddi Khajeh, Soniya; Rahimi, Saeed; Yavari, Hamid R; Jafari, Farnaz; Samiei, Mohammad; Ghasemi, Negin; Milani, Amin S

2016-10-01

Calcium-enriched mixture (CEM) cement is used in the field of endodontics. It is similar to mineral trioxide aggregate in its main ingredients. The present study investigated the effect of different mixing methods on the bacterial microleakage of CEM cement. A total of 55 human single-rooted human permanent teeth were decoronated so that 14-mm-long samples were obtained and obturated with AH26 sealer and gutta-percha using lateral condensation technique. Three millimeters of the root end were cut off and randomly divided into 3 groups of 15 each (3 mixing methods of amalgamator, ultrasonic and conventional) and 2 negative and positive control groups (each containing 5 samples). BHI (brain-heart infusion agar) suspension containing Enterococcus faecalis was used for bacterial leakage assessment. Statistical analysis was carried out using descriptive statistics, Kaplan-Meier survival analysis with censored data and log rank test. Statistical significance was set at P<0.05. The survival means for conventional, amalgamator and ultrasonic methods were 62.13±12.44, 68.87±12.79 and 77.53±12.52 days, respectively. The log rank test showed no significant differences between the groups. Based on the results of the present study it can be concluded that different mixing methods had no significant effect on the bacterial microleakage of CEM cement.

Survival analysis using inverse probability of treatment weighted methods based on the generalized propensity score.

PubMed

Sugihara, Masahiro

2010-01-01

In survival analysis, treatment effects are commonly evaluated based on survival curves and hazard ratios as causal treatment effects. In observational studies, these estimates may be biased due to confounding factors. The inverse probability of treatment weighted (IPTW) method based on the propensity score is one of the approaches utilized to adjust for confounding factors between binary treatment groups. As a generalization of this methodology, we developed an exact formula for an IPTW log-rank test based on the generalized propensity score for survival data. This makes it possible to compare the group differences of IPTW Kaplan-Meier estimators of survival curves using an IPTW log-rank test for multi-valued treatments. As causal treatment effects, the hazard ratio can be estimated using the IPTW approach. If the treatments correspond to ordered levels of a treatment, the proposed method can be easily extended to the analysis of treatment effect patterns with contrast statistics. In this paper, the proposed method is illustrated with data from the Kyushu Lipid Intervention Study (KLIS), which investigated the primary preventive effects of pravastatin on coronary heart disease (CHD). The results of the proposed method suggested that pravastatin treatment reduces the risk of CHD and that compliance to pravastatin treatment is important for the prevention of CHD. (c) 2009 John Wiley & Sons, Ltd.

rpsftm: An R Package for Rank Preserving Structural Failure Time Models

PubMed Central

Allison, Annabel; White, Ian R; Bond, Simon

2018-01-01

Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999). The method is randomisation based and uses only the randomised treatment group, observed event times, and treatment history in order to estimate a causal treatment effect. The treatment effect, ψ, is estimated by balancing counter-factual event times (that would be observed if no treatment were received) between treatment groups. G-estimation is used to find the value of ψ such that a test statistic Z(ψ) = 0. This is usually the test statistic used in the intention-to-treat analysis, for example, the log rank test statistic. We present an R package that implements the method of rpsftm. PMID:29564164

rpsftm: An R Package for Rank Preserving Structural Failure Time Models.

PubMed

Allison, Annabel; White, Ian R; Bond, Simon

2017-12-04

Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999). The method is randomisation based and uses only the randomised treatment group, observed event times, and treatment history in order to estimate a causal treatment effect. The treatment effect, ψ , is estimated by balancing counter-factual event times (that would be observed if no treatment were received) between treatment groups. G-estimation is used to find the value of ψ such that a test statistic Z ( ψ ) = 0. This is usually the test statistic used in the intention-to-treat analysis, for example, the log rank test statistic. We present an R package that implements the method of rpsftm.

Subclassification of Barcelona Clinic Liver Cancer B and C hepatocellular carcinoma: A cohort study of the multicenter registry database.

PubMed

Lee, Sangheun; Kim, Beom Kyung; Song, Kijun; Park, Jun Yong; Ahn, Sang Hoon; Kim, Seung Up; Han, Kwang-Hyub; Kim, Do Young

2016-04-01

We aimed to subclassify hepatocellular carcinoma (HCC) using Barcelona Clinic Liver Cancer intermediate and advanced stages, which include a highly heterogeneous population. From two registries ("random" and "voluntary" cohorts in the Korean Liver Cancer Study Group), patients who were newly diagnosed as HCC with intermediate or advanced stage between 2003 and 2005 were considered eligible. Overall survival (OS) was analyzed using Kaplan-Meier method with comparison by log-rank test. Patients with intermediate-stage HCC (n = 994) were subclassified according to tumor size and Child-Pugh class. Patients with tumor size < 5 cm (B1), those with tumor size ≥ 5 cm and Child-Pugh A (B2), and those with tumor size ≥ 5 cm and Child-Pugh B (B3) had median OS of 30.73, 20.60, and 9.23 months, respectively (P < 0.001 by log-rank test). Among patients with advanced stage HCC (n = 1746), patients were subclassified according to presence of significant portal vein invasion (sPVI; defined as portal vein invasion in lobar, main, or contralateral branch) and extrahepatic spread (EHS). Patients with neither sPVI nor EHS (C1), those with either sPVI or EHS (C2), and those with both sPVI and EHS (C3) had median OS of 8.43, 4.63, and 3.63 months, respectively (P < 0.001 by log-rank test). Subclassification of Barcelona Clinic Liver Cancer intermediate and advanced stages might be useful for determining patient prognosis and guiding treatment strategies for HCC. © 2015 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Heart Rate Recovery After 6-Min Walk Test Predicts Survival in Patients With Idiopathic Pulmonary Fibrosis

PubMed Central

Swigris, Jeffrey J.; Swick, Jeff; Wamboldt, Frederick S.; Sprunger, David; du Bois, Roland; Fischer, Aryeh; Cosgrove, Gregory P.; Frankel, Stephen K.; Fernandez-Perez, Evans R.; Kervitsky, Dolly; Brown, Kevin K.

2009-01-01

Background: In patients with idiopathic pulmonary fibrosis (IPF), our objectives were to identify predictors of abnormal heart rate recovery (HRR) at 1 min after completion of a 6-min walk test (6MWT) [HRR1] and 2 min after completion of a 6MWT (HRR2), and to determine whether abnormal HRR predicts mortality. Methods: From 2003 to 2008, we identified IPF patients who had been evaluated at our center (n = 76) with a pulmonary physiologic examination and the 6MWT. We used logistic regression to identify predictors of abnormal HRR, the product-limit method to compare survival in the sample stratified on HRR, and Cox proportional hazards analysis to estimate the prognostic capability of abnormal HRR. Results: Cutoff values were 13 beats for abnormal HRR1 and 22 beats for HRR2. In a multivariable model, predictors of abnormal HRR1 were diffusing capacity of the lung for carbon monoxide (odds ratio [OR], 0.4 per 10% predicted; 95% confidence interval [CI], 0.2 to 0.7; p = 0.003), change in heart rate from baseline to maximum (OR, 0.9; 95% CI, 0.8 to 0.97; p = 0.01), and having a right ventricular systolic pressure > 35 mm Hg as determined by transthoracic echocardiogram (OR, 12.7; 95% CI, 2.0 to 79.7; p = 0.01). Subjects with an abnormal HRR had significantly worse survival than subjects with a normal HRR (for HRR1, p = 0.0007 [log-rank test]; for HRR2, p = 0.03 [log-rank test]); these results held for the subgroup of 30 subjects without resting pulmonary hypertension (HRR1, p = 0.04 [log-rank test]). Among several candidate variables, abnormal HRR1 appeared to be the most potent predictor of mortality (hazard ratio, 5.2; 95% CI, 1.8 to 15.2; p = 0.004). Conclusion: Abnormal HRR after 6MWT predicts mortality in IPF patients. Research is needed to confirm these findings prospectively and to examine the mechanisms of HRR in IPF patients. PMID:19395579

Group sequential monitoring based on the weighted log-rank test statistic with the Fleming-Harrington class of weights in cancer vaccine studies.

PubMed

Hasegawa, Takahiro

2016-09-01

In recent years, immunological science has evolved, and cancer vaccines are now approved and available for treating existing cancers. Because cancer vaccines require time to elicit an immune response, a delayed treatment effect is expected and is actually observed in drug approval studies. Accordingly, we propose the evaluation of survival endpoints by weighted log-rank tests with the Fleming-Harrington class of weights. We consider group sequential monitoring, which allows early efficacy stopping, and determine a semiparametric information fraction for the Fleming-Harrington family of weights, which is necessary for the error spending function. Moreover, we give a flexible survival model in cancer vaccine studies that considers not only the delayed treatment effect but also the long-term survivors. In a Monte Carlo simulation study, we illustrate that when the primary analysis is a weighted log-rank test emphasizing the late differences, the proposed information fraction can be a useful alternative to the surrogate information fraction, which is proportional to the number of events. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Microbial ranking of porous packaging materials (exposure chamber method), ASTM method: collaborative study.

PubMed

Placencia, A M; Peeler, J T

1999-01-01

A collaborative study involving 11 laboratories was conducted to measure the microbial barrier effectiveness of porous medical packaging. Two randomly cut samples from each of 6 commercially available porous materials and one positive and one negative control were tested by one operator in each of 11 laboratories. Microbial barrier effectiveness was measured in terms of logarithm reduction value (LRV), which reflects the log10 microbial penetration of the material being tested. The logarithm of the final concentration is subtracted from that of the initial concentration to obtain the LRV. Thus the higher the LRV, the better the barrier. Repeatability standard deviations ranged from 6.42 to 16.40; reproducibility standard deviations ranged from 15.50 to 22.70. Materials B(53), C(50), D(CT), and E(45MF) differ significantly from the positive control. The microbial ranking of porous packaging materials (exposure chamber method), ASTM method, has been adopted First Action by AOAC INTERNATIONAL.

Overall Survival and Updated Results for Sunitinib Compared With Interferon Alfa in Patients With Metastatic Renal Cell Carcinoma

PubMed Central

Motzer, Robert J.; Hutson, Thomas E.; Tomczak, Piotr; Michaelson, M. Dror; Bukowski, Ronald M.; Oudard, Stéphane; Negrier, Sylvie; Szczylik, Cezary; Pili, Roberto; Bjarnason, Georg A.; Garcia-del-Muro, Xavier; Sosman, Jeffrey A.; Solska, Ewa; Wilding, George; Thompson, John A.; Kim, Sindy T.; Chen, Isan; Huang, Xin; Figlin, Robert A.

2009-01-01

Purpose A randomized, phase III trial demonstrated superiority of sunitinib over interferon alfa (IFN-α) in progression-free survival (primary end point) as first-line treatment for metastatic renal cell carcinoma (RCC). Final survival analyses and updated results are reported. Patients and Methods Seven hundred fifty treatment-naïve patients with metastatic clear cell RCC were randomly assigned to sunitinib 50 mg orally once daily on a 4 weeks on, 2 weeks off dosing schedule or to IFN-α 9 MU subcutaneously thrice weekly. Overall survival was compared by two-sided log-rank and Wilcoxon tests. Progression-free survival, response, and safety end points were assessed with updated follow-up. Results Median overall survival was greater in the sunitinib group than in the IFN-α group (26.4 v 21.8 months, respectively; hazard ratio [HR] = 0.821; 95% CI, 0.673 to 1.001; P = .051) per the primary analysis of unstratified log-rank test (P = .013 per unstratified Wilcoxon test). By stratified log-rank test, the HR was 0.818 (95% CI, 0.669 to 0.999; P = .049). Within the IFN-α group, 33% of patients received sunitinib, and 32% received other vascular endothelial growth factor–signaling inhibitors after discontinuation from the trial. Median progression-free survival was 11 months for sunitinib compared with 5 months for IFN-α (P < .001). Objective response rate was 47% for sunitinib compared with 12% for IFN-α (P < .001). The most commonly reported sunitinib-related grade 3 adverse events included hypertension (12%), fatigue (11%), diarrhea (9%), and hand-foot syndrome (9%). Conclusion Sunitinib demonstrates longer overall survival compared with IFN-α plus improvement in response and progression-free survival in the first-line treatment of patients with metastatic RCC. The overall survival highlights an improved prognosis in patients with RCC in the era of targeted therapy. PMID:19487381

Comparison of sampling methods to measure HIV RNA viral load in female genital tract secretions.

PubMed

Jaumdally, Shameem Z; Jones, Heidi E; Hoover, Donald R; Gamieldien, Hoyam; Kriek, Jean-Mari; Langwenya, Nontokozo; Myer, Landon; Passmore, Jo-Ann S; Todd, Catherine S

2017-03-01

How does menstrual cup (MC) compare to other genital sampling methods for HIV RNA recovery? We compared HIV RNA levels between MC, endocervical swab (ECS), and ECS-enriched cervicovaginal lavage (eCVL) specimens in 51 HIV-positive, antiretroviral therapy-naive women at enrollment, 3 and 6 months, with order rotated by visit. Paired comparisons were analyzed with McNemar's exact tests, signed-rank tests, and an extension of Somer's D for pooled analyses across visits. MC specimens had the highest proportion of quantifiable HIV VL at enrollment and month 3, but more MC specimens (n=12.8%) were insufficient for testing, compared with ECS (2%, P=0.006) and eCVL (0%, P<0.001). Among sufficient specimens, median VL was significantly higher for MC (2.62 log 10 copies/mL) compared to ECS (1.30 log 10 copies/mL, P<0.001) and eCVL (1.60 log 10 copies/mL, P<0.001) across visits. MC may be more sensitive than eCVL and CVS, provided insufficient specimens are reduced. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

CHEK2*1100delC Heterozygosity in Women With Breast Cancer Associated With Early Death, Breast Cancer–Specific Death, and Increased Risk of a Second Breast Cancer

PubMed Central

Weischer, Maren; Nordestgaard, Børge G.; Pharoah, Paul; Bolla, Manjeet K.; Nevanlinna, Heli; van't Veer, Laura J.; Garcia-Closas, Montserrat; Hopper, John L.; Hall, Per; Andrulis, Irene L.; Devilee, Peter; Fasching, Peter A.; Anton-Culver, Hoda; Lambrechts, Diether; Hooning, Maartje; Cox, Angela; Giles, Graham G.; Burwinkel, Barbara; Lindblom, Annika; Couch, Fergus J.; Mannermaa, Arto; Grenaker Alnæs, Grethe; John, Esther M.; Dörk, Thilo; Flyger, Henrik; Dunning, Alison M.; Wang, Qin; Muranen, Taru A.; van Hien, Richard; Figueroa, Jonine; Southey, Melissa C.; Czene, Kamila; Knight, Julia A.; Tollenaar, Rob A.E.M.; Beckmann, Matthias W.; Ziogas, Argyrios; Christiaens, Marie-Rose; Collée, Johanna Margriet; Reed, Malcolm W.R.; Severi, Gianluca; Marme, Frederik; Margolin, Sara; Olson, Janet E.; Kosma, Veli-Matti; Kristensen, Vessela N.; Miron, Alexander; Bogdanova, Natalia; Shah, Mitul; Blomqvist, Carl; Broeks, Annegien; Sherman, Mark; Phillips, Kelly-Anne; Li, Jingmei; Liu, Jianjun; Glendon, Gord; Seynaeve, Caroline; Ekici, Arif B.; Leunen, Karin; Kriege, Mieke; Cross, Simon S.; Baglietto, Laura; Sohn, Christof; Wang, Xianshu; Kataja, Vesa; Børresen-Dale, Anne-Lise; Meyer, Andreas; Easton, Douglas F.; Schmidt, Marjanka K.; Bojesen, Stig E.

2012-01-01

Purpose We tested the hypotheses that CHEK2*1100delC heterozygosity is associated with increased risk of early death, breast cancer–specific death, and risk of a second breast cancer in women with a first breast cancer. Patients and Methods From 22 studies participating in the Breast Cancer Association Consortium, 25,571 white women with invasive breast cancer were genotyped for CHEK2*1100delC and observed for up to 20 years (median, 6.6 years). We examined risk of early death and breast cancer–specific death by estrogen receptor status and risk of a second breast cancer after a first breast cancer in prospective studies. Results CHEK2*1100delC heterozygosity was found in 459 patients (1.8%). In women with estrogen receptor–positive breast cancer, multifactorially adjusted hazard ratios for heterozygotes versus noncarriers were 1.43 (95% CI, 1.12 to 1.82; log-rank P = .004) for early death and 1.63 (95% CI, 1.24 to 2.15; log-rank P < .001) for breast cancer–specific death. In all women, hazard ratio for a second breast cancer was 2.77 (95% CI, 2.00 to 3.83; log-rank P < .001) increasing to 3.52 (95% CI, 2.35 to 5.27; log-rank P < .001) in women with estrogen receptor–positive first breast cancer only. Conclusion Among women with estrogen receptor–positive breast cancer, CHEK2*1100delC heterozygosity was associated with a 1.4-fold risk of early death, a 1.6-fold risk of breast cancer–specific death, and a 3.5-fold risk of a second breast cancer. This is one of the few examples of a genetic factor that influences long-term prognosis being documented in an extensive series of women with breast cancer. PMID:23109706

Analysis of censored data.

PubMed

Lucijanic, Marko; Petrovecki, Mladen

2012-01-01

Analyzing events over time is often complicated by incomplete, or censored, observations. Special non-parametric statistical methods were developed to overcome difficulties in summarizing and comparing censored data. Life-table (actuarial) method and Kaplan-Meier method are described with an explanation of survival curves. For the didactic purpose authors prepared a workbook based on most widely used Kaplan-Meier method. It should help the reader understand how Kaplan-Meier method is conceptualized and how it can be used to obtain statistics and survival curves needed to completely describe a sample of patients. Log-rank test and hazard ratio are also discussed.

Application of Poisson random effect models for highway network screening.

PubMed

Jiang, Ximiao; Abdel-Aty, Mohamed; Alamili, Samer

2014-02-01

In recent years, Bayesian random effect models that account for the temporal and spatial correlations of crash data became popular in traffic safety research. This study employs random effect Poisson Log-Normal models for crash risk hotspot identification. Both the temporal and spatial correlations of crash data were considered. Potential for Safety Improvement (PSI) were adopted as a measure of the crash risk. Using the fatal and injury crashes that occurred on urban 4-lane divided arterials from 2006 to 2009 in the Central Florida area, the random effect approaches were compared to the traditional Empirical Bayesian (EB) method and the conventional Bayesian Poisson Log-Normal model. A series of method examination tests were conducted to evaluate the performance of different approaches. These tests include the previously developed site consistence test, method consistence test, total rank difference test, and the modified total score test, as well as the newly proposed total safety performance measure difference test. Results show that the Bayesian Poisson model accounting for both temporal and spatial random effects (PTSRE) outperforms the model that with only temporal random effect, and both are superior to the conventional Poisson Log-Normal model (PLN) and the EB model in the fitting of crash data. Additionally, the method evaluation tests indicate that the PTSRE model is significantly superior to the PLN model and the EB model in consistently identifying hotspots during successive time periods. The results suggest that the PTSRE model is a superior alternative for road site crash risk hotspot identification. Copyright © 2013 Elsevier Ltd. All rights reserved.

Effectiveness of platinum-based adjuvant chemotherapy for muscle-invasive bladder cancer: A weighted propensity score analysis.

PubMed

Shimizu, Fumitaka; Muto, Satoru; Taguri, Masataka; Ieda, Takeshi; Tsujimura, Akira; Sakamoto, Yoshiro; Fujita, Kazuhiko; Okegawa, Takatsugu; Yamaguchi, Raizo; Horie, Shigeo

2017-05-01

To evaluate the clinical benefit of adjuvant platinum-based chemotherapy after radical cystectomy for muscle-invasive bladder cancer in routine clinical practice. The present observational study was carried out to compare the effectiveness of adjuvant chemotherapy versus observation post-radical cystectomy in patients with clinically muscle-invasive bladder cancer. Cancer-specific survival and overall survival between the adjuvant chemotherapy group and radical cystectomy alone group were compared using Kaplan-Meier method and log-rank test. After adjusting for background factors using propensity score weighting, differences in cancer-specific survival and overall survival between these two groups were compared. Subgroup analyses by the pathological characteristics were carried out. In total, 322 patients were included in the present study. Of these, 23% received adjuvant chemotherapy post-radical cystectomy. Clinicopathological characteristics showed that patients in the adjuvant chemotherapy group were pathologically more advanced and were at higher risk than the radical cystectomy alone group. In the unadjusted population, although it is not significant, the adjuvant chemotherapy group had lower overall survival (3-year overall survival; 61.5% vs 73.6%, HR 1.33, P = 0.243, log-rank test, adjuvant chemotherapy vs radical cystectomy alone). In the weighted propensity score analysis, although it is not significant, the adjuvant chemotherapy group were superior to radical cystectomy alone groups (overall survival: HR 0.65, 95% CI 0.39-1.09, P = 0.099, log-rank test, adjuvant chemotherapy vs radical cystectomy alone). Subgroup analyses showed that adjuvant chemotherapy significantly reduced the hazard ratio of overall survival and cancer-specific survival in the ≥pT3, pN+, ly+ and v+ subgroups. Platinum-based adjuvant chemotherapy might be associated with increased cancer-specific survival and overall survival in patients with high-risk invasive bladder cancer. © 2017 The Japanese Urological Association.

Environmental influences on antibody-enhanced dengue disease outcomes.

PubMed

Diniz, Daniel Guerreiro; Fôro, César Augusto Raiol; Turiel, Maíra C Pereira; Sosthenes, Marcia C K; Demachki, Sâmia; Gomes, Giovanni Freitas; Rego, Carla M Damasceno; Magalhães, Marina Cutrim; Pinho, Brunno Gomes; Ramos, Juliana Pastana; Casseb, Samir M Moraes; Brito, Maysa de Vasconcelos; da Silva, Eliana Vieira Pinto; Nunes, Marcio Roberto Teixeira; Diniz, José Antonio Picanço; Cunningham, Colm; Perry, Victor Hugh; Vasconcelos, Pedro F Costa; Diniz, Cristovam W Picanço

2012-12-01

Because an enriched environment (EE) enhances T-cell activity and T-lymphocytes contribute to immunopathogenesis during heterologous dengue virus (DENV) infections, we hypothesised that an EE increases dengue severity. To compare single serotype (SS) and antibody-enhanced disease (AED) infections regimens, serial intraperitoneal were performed with DENV3 (genotype III) infected brain homogenate or anti-DENV2 hyperimmune serum followed 24 h later by DENV3 (genotype III) infected brain homogenate. Compared AED for which significant differences were detected between the EE and impoverished environmental (IE) groups (Kaplan-Meyer log-rank test, p = 0.0025), no significant differences were detected between the SS experimental groups (Kaplan-Meyer log-rank test, p = 0.089). Survival curves from EE and IE animals infected with the AED regimen were extended after corticoid injection and this effect was greater in the EE than in the IE group (Kaplan-Meyer log-rank test, p = 0.0162). Under the AED regimen the EE group showed more intense clinical signs than the IE group. Dyspnoea, tremor, hunched posture, ruffled fur, immobility, pre-terminal paralysis, shock and death were associated with dominant T-lymphocytic hyperplasia and presence of viral antigens in the liver and lungs. We propose that the increased expansion of these memory T-cells and serotype cross-reactive antibodies facilitates the infection of these cells by DENV and that these events correlate with disease severity in an EE.

The Wilcoxon signed rank test for paired comparisons of clustered data.

PubMed

Rosner, Bernard; Glynn, Robert J; Lee, Mei-Ling T

2006-03-01

The Wilcoxon signed rank test is a frequently used nonparametric test for paired data (e.g., consisting of pre- and posttreatment measurements) based on independent units of analysis. This test cannot be used for paired comparisons arising from clustered data (e.g., if paired comparisons are available for each of two eyes of an individual). To incorporate clustering, a generalization of the randomization test formulation for the signed rank test is proposed, where the unit of randomization is at the cluster level (e.g., person), while the individual paired units of analysis are at the subunit within cluster level (e.g., eye within person). An adjusted variance estimate of the signed rank test statistic is then derived, which can be used for either balanced (same number of subunits per cluster) or unbalanced (different number of subunits per cluster) data, with an exchangeable correlation structure, with or without tied values. The resulting test statistic is shown to be asymptotically normal as the number of clusters becomes large, if the cluster size is bounded. Simulation studies are performed based on simulating correlated ranked data from a signed log-normal distribution. These studies indicate appropriate type I error for data sets with > or =20 clusters and a superior power profile compared with either the ordinary signed rank test based on the average cluster difference score or the multivariate signed rank test of Puri and Sen. Finally, the methods are illustrated with two data sets, (i) an ophthalmologic data set involving a comparison of electroretinogram (ERG) data in retinitis pigmentosa (RP) patients before and after undergoing an experimental surgical procedure, and (ii) a nutritional data set based on a randomized prospective study of nutritional supplements in RP patients where vitamin E intake outside of study capsules is compared before and after randomization to monitor compliance with nutritional protocols.

Statistical methods of fracture characterization using acoustic borehole televiewer log interpretation

NASA Astrophysics Data System (ADS)

Massiot, Cécile; Townend, John; Nicol, Andrew; McNamara, David D.

2017-08-01

Acoustic borehole televiewer (BHTV) logs provide measurements of fracture attributes (orientations, thickness, and spacing) at depth. Orientation, censoring, and truncation sampling biases similar to those described for one-dimensional outcrop scanlines, and other logging or drilling artifacts specific to BHTV logs, can affect the interpretation of fracture attributes from BHTV logs. K-means, fuzzy K-means, and agglomerative clustering methods provide transparent means of separating fracture groups on the basis of their orientation. Fracture spacing is calculated for each of these fracture sets. Maximum likelihood estimation using truncated distributions permits the fitting of several probability distributions to the fracture attribute data sets within truncation limits, which can then be extrapolated over the entire range where they naturally occur. Akaike Information Criterion (AIC) and Schwartz Bayesian Criterion (SBC) statistical information criteria rank the distributions by how well they fit the data. We demonstrate these attribute analysis methods with a data set derived from three BHTV logs acquired from the high-temperature Rotokawa geothermal field, New Zealand. Varying BHTV log quality reduces the number of input data points, but careful selection of the quality levels where fractures are deemed fully sampled increases the reliability of the analysis. Spacing data analysis comprising up to 300 data points and spanning three orders of magnitude can be approximated similarly well (similar AIC rankings) with several distributions. Several clustering configurations and probability distributions can often characterize the data at similar levels of statistical criteria. Thus, several scenarios should be considered when using BHTV log data to constrain numerical fracture models.

A new modeling and inference approach for the Systolic Blood Pressure Intervention Trial outcomes.

PubMed

Yang, Song; Ambrosius, Walter T; Fine, Lawrence J; Bress, Adam P; Cushman, William C; Raj, Dominic S; Rehman, Shakaib; Tamariz, Leonardo

2018-06-01

Background/aims In clinical trials with time-to-event outcomes, usually the significance tests and confidence intervals are based on a proportional hazards model. Thus, the temporal pattern of the treatment effect is not directly considered. This could be problematic if the proportional hazards assumption is violated, as such violation could impact both interim and final estimates of the treatment effect. Methods We describe the application of inference procedures developed recently in the literature for time-to-event outcomes when the treatment effect may or may not be time-dependent. The inference procedures are based on a new model which contains the proportional hazards model as a sub-model. The temporal pattern of the treatment effect can then be expressed and displayed. The average hazard ratio is used as the summary measure of the treatment effect. The test of the null hypothesis uses adaptive weights that often lead to improvement in power over the log-rank test. Results Without needing to assume proportional hazards, the new approach yields results consistent with previously published findings in the Systolic Blood Pressure Intervention Trial. It provides a visual display of the time course of the treatment effect. At four of the five scheduled interim looks, the new approach yields smaller p values than the log-rank test. The average hazard ratio and its confidence interval indicates a treatment effect nearly a year earlier than a restricted mean survival time-based approach. Conclusion When the hazards are proportional between the comparison groups, the new methods yield results very close to the traditional approaches. When the proportional hazards assumption is violated, the new methods continue to be applicable and can potentially be more sensitive to departure from the null hypothesis.

Converging or Crossing Curves: Untie the Gordian Knot or Cut it? Appropriate Statistics for Non-Proportional Hazards in Decitabine DACO-016 Study (AML).

PubMed

Tomeczkowski, Jörg; Lange, Ansgar; Güntert, Andreas; Thilakarathne, Pushpike; Diels, Joris; Xiu, Liang; De Porre, Peter; Tapprich, Christoph

2015-09-01

Among patients with acute myeloid leukemia (AML), the DACO-016 randomized study showed reduction in mortality for decitabine [Dacogen(®) (DAC), Eisai Inc., Woodcliff Lake, NJ, USA] compared with treatment choice (TC): at primary analysis the hazard ratio (HR) was 0.85 (95% confidence interval 0.69-1.04; stratified log-rank P = 0.108). With two interim analyses, two-sided alpha was adjusted to 0.0462. With 1-year additional follow-up the HR reached 0.82 (nominal P = 0.0373). These data resulted in approval of DAC in the European Union, though not in the United States. Though pre-specified, the log-rank test could be considered not optimal to assess the observed survival difference because of the non-proportional hazard nature of the survival curves. We applied the Wilcoxon test as a sensitivity analysis. Patients were randomized to DAC (N = 242) or TC (N = 243). One-hundred and eight (44.4%) patients in the TC arm and 91 (37.6%) patients in the DAC arm selectively crossed over to subsequent disease modifying therapies at progression, which might impact the survival beyond the median with resultant converging curves (and disproportional hazards). The stratified Wilcoxon test showed a significant improvement in median (CI 95%) overall survival with DAC [7.7 (6.2; 9.2) months] versus TC [5.0 (4.3; 6.3) months; P = 0.0458]. Wilcoxon test indicated significant increase in survival for DAC versus TC compared to log-rank test. Janssen-Cilag GmbH.

VALORATE: fast and accurate log-rank test in balanced and unbalanced comparisons of survival curves and cancer genomics.

PubMed

Treviño, Victor; Tamez-Pena, Jose

2017-06-15

The association of genomic alterations to outcomes in cancer is affected by a problem of unbalanced groups generated by the low frequency of alterations. For this, an R package (VALORATE) that estimates the null distribution and the P -value of the log-rank based on a recent reformulation is presented. For a given number of alterations that define the size of survival groups, the log-rank density is estimated by a weighted sum of conditional distributions depending on a co-occurrence term of mutations and events. The estimations are accurately accelerated by sampling across co-occurrences allowing the analysis of large genomic datasets in few minutes. In conclusion, the proposed VALORATE R package is a valuable tool for survival analysis. The R package is available in CRAN at https://cran.r-project.org and in http://bioinformatica.mty.itesm.mx/valorateR . vtrevino@itesm.mx. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Sustained Benefit at 2 Years for Covered Stents Versus Bare-Metal Stents in Long SFA Lesions: The VIASTAR Trial

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lammer, Johannes, E-mail: jlammer@gmx.at, E-mail: johannes.lammer@meduniwien.ac.at; Zeller, Thomas, E-mail: thomas.zeller@universitaets-herzzentrum.de; Hausegger, Klaus A., E-mail: klaus.hausegger@lkh-klu.at

PurposeThe hypothesis that covered stents are superior to bare-metal stents (BMS) in long femoropopliteal artery disease was tested. The one-year results of the VIASTAR trial revealed a patency benefit of covered stents in the treatment-per-protocol (TPP) analysis only.MethodsA prospective, randomized, single-blind, multicenter study evaluated 141 patients with symptomatic peripheral arterial disease (PAD) after treatment with heparin-bonded covered stents (VIABAHN{sup ®} Endoprosthesis) or BMS. Clinical outcomes and patency rates were assessed at 1, 6, 12, and 24 months. Mean lesion length was 19.0 ± 6.3 cm in the VIABAHN{sup ®} versus 17.3 ± 6.6 cm in the BMS group.ResultsThe 24-month primary patency rates in the VIABAHN{sup ®} andmore » BMS group were: intention-to-treat 63.1 (95 % CI 0.52–0.76) versus 41.2 % (95 % CI 0.29–0.57; log rank p = 0.04) and TPP 69.4 (95 % CI 0.58–0.83) versus 40.0 % (95 % CI 0.28–0.56; log rank p = 0.004). Freedom from target-lesion-revascularization (TLR) was 79.4 (95 % CI 0.70–0.90) versus 73.0 % (95 % CI 0.63–0.85) for VIABAHN{sup ®} versus BMS (log rank p = 0.37). For the TPP group in lesions ≥20 cm, the 24-month patency rates were 65.2 (95 % CI 0.50–0.85) versus 26.7 % (95 % CI 0.12–0.59; log rank p = 0.004) for VIABAHN{sup ®} versus BMS, and freedom from TLR was 80.0 (95 % CI 0.68–0.94) versus 61.9 % (95 % CI 0.44–0.87; log rank p = 0.13). The ankle brachial index was 0.89 ± 0.18 versus 0.91 ± 0.17 (p = 0.76) at 24-month in the VIABAHN{sup ®} versus the BMS group, respectively.ConclusionAt 24-month, this trial in PAD patients with long femoropopliteal lesions demonstrated a significantly improved primary patency rate for heparin-bonded covered stents compared to BMS, however, without a significant impact on clinical outcomes and TLR rate (Reg. Nr. ISRCTN48164244)« less

Competency-based residency training and the web log: modeling practice-based learning and enhancing medical knowledge.

PubMed

Hollon, Matthew F

2015-01-01

By using web-based tools in medical education, there are opportunities to innovatively teach important principles from the general competencies of graduate medical education. Postulating that faculty transparency in learning from uncertainties in clinical work could help residents to incorporate the principles of practice-based learning and improvement (PBLI) in their professional development, faculty in this community-based residency program modeled the steps of PBLI on a weekly basis through the use of a web log. The program confidentially surveyed residents before and after this project about actions consistent with PBLI and knowledge acquired through reading the web log. The frequency that residents encountered clinical situations where they felt uncertain declined over the course of the 24 weeks of the project from a mean frequency of uncertainty of 36% to 28% (Wilcoxon signed rank test, p=0.008); however, the frequency with which residents sought answers when faced with uncertainty did not change (Wilcoxon signed rank test, p=0.39), remaining high at approximately 80%. Residents answered a mean of 52% of knowledge questions correct when tested prior to faculty posts to the blog, rising to a mean of 65% of questions correct when tested at the end of the project (paired t-test, p=0.001). Faculty role modeling of PBLI behaviors and posting clinical questions and answers to a web log led to modest improvements in medical knowledge but did not alter behavior that was already taking place frequently among residents.

ROLE OF PARENTERAL NUTRITION IN ONCOLOGIC PATIENTS WITH INTESTINAL OCCLUSION AND PERITONEAL CARCINOMATOSIS.

PubMed

Aría Guerra, Eva; Cortés-Salgado, Alfonso; Mateo-Lobo, Raquel; Nattero, Lía; Riveiro, Javier; Vega-Piñero, Belén; Valbuena, Beatriz; Carabaña, Fátima; Carrero, Carmen; Grande, Enrique; Carrato, Alfredo; Botella-Carretero, José Ignacio

2015-09-01

the precise role of parenteral nutrition in the management of oncologic patients with intestinal occlusion is not well defined yet. We aimed to identify the effects of parenteral nutrition in these patients regarding prognosis. 55 patients with intestinal occlusion and peritoneal carcinomatosis were included. Parenteral nutrition aimed at 20-35 kcal/Kg/day, and 1.0 g/kg/day of amino-acids. Weight, body mass index, type of tumor, type of chemotherapy, and ECOG among others were recorded and analyzed. 69.1% of the patients had gastrointestinal tumors, 18.2% gynecologic and 12.7% others. Age was 60 ± 13y, baseline ECOG 1.5 ± 0.5 and body mass index 21.6 ± 4.3. Malnutrition was present in 85%. Survival from the start of parenteral nutrition was not significant when considering baseline ECOG (log rank = 0.593, p = 0.743), previous lines of chemotherapy (log rank = 2.117, p = 0.548), baseline BMI (log rank = 2.686, p = 0.261), or type of tumor (log rank = 2.066, p = 0.356). Survival in patients who received home parenteral nutrition after hospital discharge was higher than those who stayed in-hospital (log rank = 7.090, p = 0.008). Survival in patients who started chemotherapy during or after parenteral nutrition was higher than those who did not so (log rank = 17.316, p < 0.001). A total of 3.6% of patients presented catheter related infection without affecting survival (log rank = 0.061, p = 0.804). Parenteral nutrition in patients with advanced cancer and intestinal occlusion is safe, and in tho se who respond to chemotherapy, further administration of home parenteral nutrition together with chemotherapy may enhance prolonged survival. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Long-term Results of the UCSF-LBNL Randomized Trial: Charged Particle With Helium Ion Versus Iodine-125 Plaque Therapy for Choroidal and Ciliary Body Melanoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Kavita K., E-mail: Kavita.mishra@ucsf.edu; Quivey, Jeanne M.; Daftari, Inder K.

Purpose: Relevant clinical data are needed given the increasing national interest in charged particle radiation therapy (CPT) programs. Here we report long-term outcomes from the only randomized, stratified trial comparing CPT with iodine-125 plaque therapy for choroidal and ciliary body melanoma. Methods and Materials: From 1985 to 1991, 184 patients met eligibility criteria and were randomized to receive particle (86 patients) or plaque therapy (98 patients). Patients were stratified by tumor diameter, thickness, distance to disc/fovea, anterior extension, and visual acuity. Tumors close to the optic disc were included. Local tumor control, as well as eye preservation, metastases due tomore » melanoma, and survival were evaluated. Results: Median follow-up times for particle and plaque arm patients were 14.6 years and 12.3 years, respectively (P=.22), and for those alive at last follow-up, 18.5 and 16.5 years, respectively (P=.81). Local control (LC) for particle versus plaque treatment was 100% versus 84% at 5 years, and 98% versus 79% at 12 years, respectively (log rank: P=.0006). If patients with tumors close to the disc (<2 mm) were excluded, CPT still resulted in significantly improved LC: 100% versus 90% at 5 years and 98% versus 86% at 12 years, respectively (log rank: P=.048). Enucleation rate was lower after CPT: 11% versus 22% at 5 years and 17% versus 37% at 12 years, respectively (log rank: P=.01). Using Cox regression model, likelihood ratio test, treatment was the most important predictor of LC (P=.0002) and eye preservation (P=.01). CPT was a significant predictor of prolonged disease-free survival (log rank: P=.001). Conclusions: Particle therapy resulted in significantly improved local control, eye preservation, and disease-free survival as confirmed by long-term outcomes from the only randomized study available to date comparing radiation modalities in choroidal and ciliary body melanoma.« less

A Recursive Partitioning Method for the Prediction of Preference Rankings Based Upon Kemeny Distances.

PubMed

D'Ambrosio, Antonio; Heiser, Willem J

2016-09-01

Preference rankings usually depend on the characteristics of both the individuals judging a set of objects and the objects being judged. This topic has been handled in the literature with log-linear representations of the generalized Bradley-Terry model and, recently, with distance-based tree models for rankings. A limitation of these approaches is that they only work with full rankings or with a pre-specified pattern governing the presence of ties, and/or they are based on quite strict distributional assumptions. To overcome these limitations, we propose a new prediction tree method for ranking data that is totally distribution-free. It combines Kemeny's axiomatic approach to define a unique distance between rankings with the CART approach to find a stable prediction tree. Furthermore, our method is not limited by any particular design of the pattern of ties. The method is evaluated in an extensive full-factorial Monte Carlo study with a new simulation design.

Grid-based lattice summation of electrostatic potentials by assembled rank-structured tensor approximation

NASA Astrophysics Data System (ADS)

Khoromskaia, Venera; Khoromskij, Boris N.

2014-12-01

Our recent method for low-rank tensor representation of sums of the arbitrarily positioned electrostatic potentials discretized on a 3D Cartesian grid reduces the 3D tensor summation to operations involving only 1D vectors however retaining the linear complexity scaling in the number of potentials. Here, we introduce and study a novel tensor approach for fast and accurate assembled summation of a large number of lattice-allocated potentials represented on 3D N × N × N grid with the computational requirements only weakly dependent on the number of summed potentials. It is based on the assembled low-rank canonical tensor representations of the collected potentials using pointwise sums of shifted canonical vectors representing the single generating function, say the Newton kernel. For a sum of electrostatic potentials over L × L × L lattice embedded in a box the required storage scales linearly in the 1D grid-size, O(N) , while the numerical cost is estimated by O(NL) . For periodic boundary conditions, the storage demand remains proportional to the 1D grid-size of a unit cell, n = N / L, while the numerical cost reduces to O(N) , that outperforms the FFT-based Ewald-type summation algorithms of complexity O(N3 log N) . The complexity in the grid parameter N can be reduced even to the logarithmic scale O(log N) by using data-sparse representation of canonical N-vectors via the quantics tensor approximation. For justification, we prove an upper bound on the quantics ranks for the canonical vectors in the overall lattice sum. The presented approach is beneficial in applications which require further functional calculus with the lattice potential, say, scalar product with a function, integration or differentiation, which can be performed easily in tensor arithmetics on large 3D grids with 1D cost. Numerical tests illustrate the performance of the tensor summation method and confirm the estimated bounds on the tensor ranks.

Phase II Trials for Heterogeneous Patient Populations with a Time-to-Event Endpoint.

PubMed

Jung, Sin-Ho

2017-07-01

In this paper, we consider a single-arm phase II trial with a time-to-event end-point. We assume that the study population has multiple subpopulations with different prognosis, but the study treatment is expected to be similarly efficacious across the subpopulations. We review a stratified one-sample log-rank test and present its sample size calculation method under some practical design settings. Our sample size method requires specification of the prevalence of subpopulations. We observe that the power of the resulting sample size is not very sensitive to misspecification of the prevalence.

5-Fluorouracil Adjuvant Chemotherapy Does Not Increase Survival in Patients with CpG Island Methylator Phenotype Colorectal Cancer

PubMed Central

Jover, Rodrigo; Nguyen, Thuy-Phuong; Pérez-Carbonell, Lucía; Zapater, Pedro; Payá, Artemio; Alenda, Cristina; Rojas, Estefanía; Cubiella, Joaquín; Balaguer, Francesc; Morillas, Juan D.; Clofent, Juan; Bujanda, Luis; Reñé, Josep M; Bessa, Xavier; Xicola, Rosa M.; Nicolás-Pérez, David; Castells, Antoni; Andreu, Montserrat; Llor, Xavier; Boland, C. Richard; Goel, Ajay

2011-01-01

Background & Aims 5-FU-based adjuvant chemotherapy does not increase survival times of patients with colorectal tumors with microsatellite instability. We determined the response of patients with colorectal tumors with the CpG island methylator phenotype (CIMP) to 5-FU-based therapy. Methods We analyzed a population-based cohort of 302 patients with colorectal cancer (CRC) for a median follow-up time of 50.7 months. CIMP status was determined by analysis of the CACNAG1, SOCS1, RUNX3, NEUROG1, and MLH1 promoters; tumors were considered to be CIMP-positive (CIMP+) if at least 3 promoters were methylated. Results Tumors from 29.5% (89/302) of patients were CIMP+; this did not influence disease-free survival (log rank=.26). Of tumors of TNM stages II–III (n=196), 32.7% were CIMP+. Among patients with CRC stages II–III who did not receive adjuvant 5-FU chemotherapy, those with CIMP+ tumors had longest times of disease-free survival (log rank=.04); patients with CIMP+ tumors who received chemotherapy had shorter times of disease-free survival (log rank=0.02). In patients with CIMP-negative tumors, adjuvant 5-FU chemotherapy significantly increased time of disease-free survival (log-rank=.00001). However, in patients with CIMP+ tumors, adjuvant 5-FU chemotherapy did not affect time of disease-free survival (log rank=.7). Multivariate analysis showed a significant, independent interaction between 5-FU treatment and CIMP status (hazard ratio [HR]=0.6; 95% confidence interval [CI], .5–.8). Among patients with CIMP+ tumors, adjuvant chemotherapy was not an independent predictor of outcome (HR=0.8; 95% CI, 0.3–2.0). In patients who did not receive adjuvant 5-FU chemotherapy, CIMP status was the only independent predictor of survival (HR=2.0; 95% CI, 1.1–3.8) Conclusion Patients with CIMP+ colorectal tumors do not benefit from 5-FU–based adjuvant chemotherapy. PMID:21185836

Cross-validation and Peeling Strategies for Survival Bump Hunting using Recursive Peeling Methods

PubMed Central

Dazard, Jean-Eudes; Choe, Michael; LeBlanc, Michael; Rao, J. Sunil

2015-01-01

We introduce a framework to build a survival/risk bump hunting model with a censored time-to-event response. Our Survival Bump Hunting (SBH) method is based on a recursive peeling procedure that uses a specific survival peeling criterion derived from non/semi-parametric statistics such as the hazards-ratio, the log-rank test or the Nelson--Aalen estimator. To optimize the tuning parameter of the model and validate it, we introduce an objective function based on survival or prediction-error statistics, such as the log-rank test and the concordance error rate. We also describe two alternative cross-validation techniques adapted to the joint task of decision-rule making by recursive peeling and survival estimation. Numerical analyses show the importance of replicated cross-validation and the differences between criteria and techniques in both low and high-dimensional settings. Although several non-parametric survival models exist, none addresses the problem of directly identifying local extrema. We show how SBH efficiently estimates extreme survival/risk subgroups unlike other models. This provides an insight into the behavior of commonly used models and suggests alternatives to be adopted in practice. Finally, our SBH framework was applied to a clinical dataset. In it, we identified subsets of patients characterized by clinical and demographic covariates with a distinct extreme survival outcome, for which tailored medical interventions could be made. An R package PRIMsrc (Patient Rule Induction Method in Survival, Regression and Classification settings) is available on CRAN (Comprehensive R Archive Network) and GitHub. PMID:27034730

SCD-HeFT: Use of RR Interval Statistics for Long-term Risk Stratification for Arrhythmic Sudden Cardiac Death

PubMed Central

Au-yeung, Wan-tai M.; Reinhall, Per; Poole, Jeanne E.; Anderson, Jill; Johnson, George; Fletcher, Ross D.; Moore, Hans J.; Mark, Daniel B.; Lee, Kerry L.; Bardy, Gust H.

2015-01-01

Background In the SCD-HeFT a significant fraction of the congestive heart failure (CHF) patients ultimately did not die suddenly from arrhythmic causes. CHF patients will benefit from better tools to identify if ICD therapy is needed. Objective To identify predictor variables from baseline SCD-HeFT patients’ RR intervals that correlate to arrhythmic sudden cardiac death (SCD) and mortality and to design an ICD therapy screening test. Methods Ten predictor variables were extracted from pre-randomization Holter data from 475 patients enrolled in the SCD-HeFT ICD arm using novel and traditional heart rate variability methods. All variables were correlated to SCD using Mann Whitney-Wilcoxon test and receiver operating characteristic analysis. ICD therapy screening tests were designed by minimizing the cost of false classifications. Survival analysis, including log-rank test and Cox models, was also performed. Results α1 and α2 from detrended fluctuation analysis, the ratio of low to high frequency power, the number of PVCs per hour and heart rate turbulence slope are all statistically significant for predicting the occurrences of SCD (p<0.001) and survival (log-rank p<0.01). The most powerful multivariate predictor tool using the Cox Proportional Hazards was α2 with a hazard ratio of 0.0465 (95% CI: 0.00528 – 0.409, p<0.01). Conclusion Predictor variables from RR intervals correlate to the occurrences of SCD and distinguish survival among SCD-HeFT ICD patients. We believe SCD prediction models should incorporate Holter based RR interval analysis to refine ICD patient selection especially in removing patients who are unlikely to benefit from ICD therapy. PMID:26096609

Prognostic value of alcohol dehydrogenase mRNA expression in gastric cancer.

PubMed

Guo, Erna; Wei, Haotang; Liao, Xiwen; Xu, Yang; Li, Shu; Zeng, Xiaoyun

2018-04-01

Previous studies have reported that alcohol dehydrogenase (ADH) isoenzymes possess diagnostic value in gastric cancer (GC). However, the prognostic value of ADH isoenzymes in GC remains unclear. The aim of the present study was to identify the prognostic value of ADH genes in patients with GC. The prognostic value of ADH genes was investigated in patients with GC using the Kaplan-Meier plotter tool. Kaplan-Meier plots were used to assess the difference between groups of patients with GC with different prognoses. Hazard ratios (HR) and 95% confidence intervals (CI) were used to assess the relative risk of GC survival. Overall, 593 patients with GC and 7 ADH genes were included in the survival analysis. High expression of ADH 1A (class 1), α polypeptide ( ADH1A; log-rank P=0.043; HR=0.79; 95% CI: 0.64-0.99), ADH 1B (class 1), β polypeptide ( ADH1B ; log-rank P=1.9×10 -05 ; HR=0.65; 95% CI: 0.53-0.79) and ADH 5 (class III), χ polypeptide ( ADH5 ; log-rank P=0.0011; HR=0.73; 95% CI: 0.6-0.88) resulted in a significantly decreased risk of mortality in all patients with GC compared with patients with low expression of those genes. Furthermore, protective effects may additionally be observed in patients with intestinal-type GC with high expression of ADH1B (log-rank P=0.031; HR=0.64; 95% CI: 0.43-0.96) and patients with diffuse-type GC with high expression of ADH1A (log-rank P=0.014; HR=0.51; 95% CI: 0.3-0.88), ADH1B (log-rank P=0.04; HR=0.53; 95% CI: 0.29-0.98), ADH 4 (class II), π polypeptide (log-rank P=0.033; HR=0.58; 95% CI: 0.35-0.96) and ADH 6 (class V) (log-rank P=0.037; HR=0.59; 95% CI: 0.35-0.97) resulting in a significantly decreased risk of mortality compared with patients with low expression of those genes. In contrast, patients with diffuse-type GC with high expression of ADH5 (log-rank P=0.044; HR=1.66; 95% CI: 1.01-2.74) were significantly correlated with a poor prognosis. The results of the present study suggest that ADH1A and ADH1B may be potential prognostic biomarkers of GC, whereas the prognostic value of other ADH genes requires further investigation.

Prognostic value of alcohol dehydrogenase mRNA expression in gastric cancer

PubMed Central

Guo, Erna; Wei, Haotang; Liao, Xiwen; Xu, Yang; Li, Shu; Zeng, Xiaoyun

2018-01-01

Previous studies have reported that alcohol dehydrogenase (ADH) isoenzymes possess diagnostic value in gastric cancer (GC). However, the prognostic value of ADH isoenzymes in GC remains unclear. The aim of the present study was to identify the prognostic value of ADH genes in patients with GC. The prognostic value of ADH genes was investigated in patients with GC using the Kaplan-Meier plotter tool. Kaplan-Meier plots were used to assess the difference between groups of patients with GC with different prognoses. Hazard ratios (HR) and 95% confidence intervals (CI) were used to assess the relative risk of GC survival. Overall, 593 patients with GC and 7 ADH genes were included in the survival analysis. High expression of ADH 1A (class 1), α polypeptide (ADH1A; log-rank P=0.043; HR=0.79; 95% CI: 0.64–0.99), ADH 1B (class 1), β polypeptide (ADH1B; log-rank P=1.9×10−05; HR=0.65; 95% CI: 0.53–0.79) and ADH 5 (class III), χ polypeptide (ADH5; log-rank P=0.0011; HR=0.73; 95% CI: 0.6–0.88) resulted in a significantly decreased risk of mortality in all patients with GC compared with patients with low expression of those genes. Furthermore, protective effects may additionally be observed in patients with intestinal-type GC with high expression of ADH1B (log-rank P=0.031; HR=0.64; 95% CI: 0.43–0.96) and patients with diffuse-type GC with high expression of ADH1A (log-rank P=0.014; HR=0.51; 95% CI: 0.3–0.88), ADH1B (log-rank P=0.04; HR=0.53; 95% CI: 0.29–0.98), ADH 4 (class II), π polypeptide (log-rank P=0.033; HR=0.58; 95% CI: 0.35–0.96) and ADH 6 (class V) (log-rank P=0.037; HR=0.59; 95% CI: 0.35–0.97) resulting in a significantly decreased risk of mortality compared with patients with low expression of those genes. In contrast, patients with diffuse-type GC with high expression of ADH5 (log-rank P=0.044; HR=1.66; 95% CI: 1.01–2.74) were significantly correlated with a poor prognosis. The results of the present study suggest that ADH1A and ADH1B may be potential prognostic biomarkers of GC, whereas the prognostic value of other ADH genes requires further investigation. PMID:29552190

Sentiment analysis of feature ranking methods for classification accuracy

NASA Astrophysics Data System (ADS)

Joseph, Shashank; Mugauri, Calvin; Sumathy, S.

2017-11-01

Text pre-processing and feature selection are important and critical steps in text mining. Text pre-processing of large volumes of datasets is a difficult task as unstructured raw data is converted into structured format. Traditional methods of processing and weighing took much time and were less accurate. To overcome this challenge, feature ranking techniques have been devised. A feature set from text preprocessing is fed as input for feature selection. Feature selection helps improve text classification accuracy. Of the three feature selection categories available, the filter category will be the focus. Five feature ranking methods namely: document frequency, standard deviation information gain, CHI-SQUARE, and weighted-log likelihood -ratio is analyzed.

Prognostic Factors for Survival in Patients with Gastric Cancer using a Random Survival Forest

PubMed

Adham, Davoud; Abbasgholizadeh, Nategh; Abazari, Malek

2017-01-01

Background: Gastric cancer is the fifth most common cancer and the third top cause of cancer related death with about 1 million new cases and 700,000 deaths in 2012. The aim of this investigation was to identify important factors for outcome using a random survival forest (RSF) approach. Materials and Methods: Data were collected from 128 gastric cancer patients through a historical cohort study in Hamedan-Iran from 2007 to 2013. The event under consideration was death due to gastric cancer. The random survival forest model in R software was applied to determine the key factors affecting survival. Four split criteria were used to determine importance of the variables in the model including log-rank, conversation?? of events, log-rank score, and randomization. Efficiency of the model was confirmed in terms of Harrell’s concordance index. Results: The mean age of diagnosis was 63 ±12.57 and mean and median survival times were 15.2 (95%CI: 13.3, 17.0) and 12.3 (95%CI: 11.0, 13.4) months, respectively. The one-year, two-year, and three-year rates for survival were 51%, 13%, and 5%, respectively. Each RSF approach showed a slightly different ranking order. Very important covariates in nearly all the 4 RSF approaches were metastatic status, age at diagnosis and tumor size. The performance of each RSF approach was in the range of 0.29-0.32 and the best error rate was obtained by the log-rank splitting rule; second, third, and fourth ranks were log-rank score, conservation of events, and the random splitting rule, respectively. Conclusion: Low survival rate of gastric cancer patients is an indication of absence of a screening program for early diagnosis of the disease. Timely diagnosis in early phases increases survival and decreases mortality. Creative Commons Attribution License

Linear modeling of the soil-water partition coefficient normalized to organic carbon content by reversed-phase thin-layer chromatography.

PubMed

Andrić, Filip; Šegan, Sandra; Dramićanin, Aleksandra; Majstorović, Helena; Milojković-Opsenica, Dušanka

2016-08-05

Soil-water partition coefficient normalized to the organic carbon content (KOC) is one of the crucial properties influencing the fate of organic compounds in the environment. Chromatographic methods are well established alternative for direct sorption techniques used for KOC determination. The present work proposes reversed-phase thin-layer chromatography (RP-TLC) as a simpler, yet equally accurate method as officially recommended HPLC technique. Several TLC systems were studied including octadecyl-(RP18) and cyano-(CN) modified silica layers in combination with methanol-water and acetonitrile-water mixtures as mobile phases. In total 50 compounds of different molecular shape, size, and various ability to establish specific interactions were selected (phenols, beznodiazepines, triazine herbicides, and polyaromatic hydrocarbons). Calibration set of 29 compounds with known logKOC values determined by sorption experiments was used to build simple univariate calibrations, Principal Component Regression (PCR) and Partial Least Squares (PLS) models between logKOC and TLC retention parameters. Models exhibit good statistical performance, indicating that CN-layers contribute better to logKOC modeling than RP18-silica. The most promising TLC methods, officially recommended HPLC method, and four in silico estimation approaches have been compared by non-parametric Sum of Ranking Differences approach (SRD). The best estimations of logKOC values were achieved by simple univariate calibration of TLC retention data involving CN-silica layers and moderate content of methanol (40-50%v/v). They were ranked far well compared to the officially recommended HPLC method which was ranked in the middle. The worst estimates have been obtained from in silico computations based on octanol-water partition coefficient. Linear Solvation Energy Relationship study revealed that increased polarity of CN-layers over RP18 in combination with methanol-water mixtures is the key to better modeling of logKOC through significant diminishing of dipolar and proton accepting influence of the mobile phase as well as enhancing molar refractivity in excess of the chromatographic systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Association of day 4 cumulative fluid balance with mortality in critically ill patients with influenza: A multicenter retrospective cohort study in Taiwan

PubMed Central

Chien, Ying-Chun; Sheu, Chau-Chyun; Tsai, Ming-Ju; Fang, Wen-Feng; Chen, Yu-Mu; Kao, Kuo-Chin; Hu, Han-Chung; Perng, Wann-Cherng; Yang, Kuang-Yao; Chen, Wei-Chih; Liang, Shinn-Jye; Wu, Chieh-Liang; Wang, Hao-Chien; Chan, Ming-Cheng

2018-01-01

Background Fluid balance is a fundamental management of patients with sepsis, and this study aimed to investigate the impact of cumulative fluid balance on critically ill patients with influenza admitted to an intensive care unit (ICU). Methods This multicenter retrospective cohort study was conducted by the Taiwan Severe Influenza Research Consortium (TSIRC) which includes eight medical centers. Patients with virology-proven influenza infection admitted to ICUs between October 2015 and March 2016 were included for analysis. Results A total of 296 patients were enrolled (mean age: 61.4±15.6 years; 62.8% men), and 92.2% (273/296) of them required mechanical ventilation. In the survivors, the daily fluid balance was positive from day 1 to day 3, and then gradually became negative from day 4 to day 7, whereas daily fluid balance was continuously positive in the non-survivors. Using the cumulative fluid balance from day 1–4 as a cut-off point, we found that a negative cumulative day 1–4 fluid balance was associated with a lower 30-day mortality rate (log-rank test, P = 0.003). To evaluate the impact of shock on this association, we divided the patients into shock and non-shock groups. The positive correlation between negative day 1–4 fluid balance and mortality was significant in the non-shock group (log-rank test, P = 0.008), but not in the shock group (log-rank test, P = 0.396). In a multivariate Cox proportional hazard regression model adjusted for age, sex, cerebrovascular disease, and PaO2/FiO2, day 1–4 fluid balance was independently associated with a higher 30-day mortality rate (aHR 1.088, 95% CI: 1.007–1.174). Conclusions A negative day 1–4 cumulative fluid balance was associated with a lower mortality rate in critically ill patients with influenza. Our findings indicate the critical role of conservative fluid strategy in the management of patients with complicated influenza. PMID:29315320

A Gene Signature to Determine Metastatic Behavior in Thymomas

PubMed Central

Gökmen-Polar, Yesim; Wilkinson, Jeff; Maetzold, Derek; Stone, John F.; Oelschlager, Kristen M.; Vladislav, Ioan Tudor; Shirar, Kristen L.; Kesler, Kenneth A.; Loehrer, Patrick J.; Badve, Sunil

2013-01-01

Purpose Thymoma represents one of the rarest of all malignancies. Stage and completeness of resection have been used to ascertain postoperative therapeutic strategies albeit with limited prognostic accuracy. A molecular classifier would be useful to improve the assessment of metastatic behaviour and optimize patient management. Methods qRT-PCR assay for 23 genes (19 test and four reference genes) was performed on multi-institutional archival primary thymomas (n = 36). Gene expression levels were used to compute a signature, classifying tumors into classes 1 and 2, corresponding to low or high likelihood for metastases. The signature was validated in an independent multi-institutional cohort of patients (n = 75). Results A nine-gene signature that can predict metastatic behavior of thymomas was developed and validated. Using radial basis machine modeling in the training set, 5-year and 10-year metastasis-free survival rates were 77% and 26% for predicted low (class 1) and high (class 2) risk of metastasis (P = 0.0047, log-rank), respectively. For the validation set, 5-year metastasis-free survival rates were 97% and 30% for predicted low- and high-risk patients (P = 0.0004, log-rank), respectively. The 5-year metastasis-free survival rates for the validation set were 49% and 41% for Masaoka stages I/II and III/IV (P = 0.0537, log-rank), respectively. In univariate and multivariate Cox models evaluating common prognostic factors for thymoma metastasis, the nine-gene signature was the only independent indicator of metastases (P = 0.036). Conclusion A nine-gene signature was established and validated which predicts the likelihood of metastasis more accurately than traditional staging. This further underscores the biologic determinants of the clinical course of thymoma and may improve patient management. PMID:23894276

Increased orosomucoid in urine is an independent predictor of cardiovascular and all-cause mortality in patients with type 2 diabetes at 10 years of follow-up.

PubMed

Svendstrup, Mathilde; Christiansen, Merete Skovdal; Magid, Erik; Hommel, Eva; Feldt-Rasmussen, Bo

2013-01-01

To evaluate whether increased urinary orosomucoid excretion rate (UOER) is an independent predictor of cardiovascular and all-cause mortality in type 2 diabetes (T2DM) and type 1 diabetes (T1DM) at 10years of follow-up. We followed 430 patients with T2DM and 148 patients with T1DM until emigration, death or November 2011. We measured UOER levels in overnight urine samples. Descriptive data are given in the article. In patients with T2DM and T1DM, all-cause mortality (log-rank test, p<0.01 for both types) and cardiovascular mortality (log-rank test, p<0.01 for T2DM and p=0.04 for T1DM) were significantly higher in patients with increased UOER. Normoalbuminuric patients with T2DM and increased UOER levels had higher all-cause and cardiovascular mortality (log-rank test, p<0.01 for both types). UOER was independently predictive of all-cause (HR 1.52; 95% CI 1.10-2.09; p=0.01) and cardiovascular (HR 2.31; 95% CI 1.46-3.66; p<0.01) mortality in patients with T2DM, but not in patients with T1DM. UOER is an independent predictor of all-cause and cardiovascular mortality even in normoalbuminuric patients with T2DM at 10years of follow-up. Further studies are needed in order to evaluate the prognostic and clinical relevance. Copyright © 2013 Elsevier Inc. All rights reserved.

Coexpression of aPKCλ/ι and IL-6 in prostate cancer tissue correlates with biochemical recurrence.

PubMed

Ishiguro, Hitoshi; Akimoto, Kazunori; Nagashima, Yoji; Kagawa, Eriko; Sasaki, Takeshi; Sano, Jin-yu; Takagawa, Ryo; Fujinami, Kiyoshi; Sasaki, Kazunori; Aoki, Ichiro; Ohno, Shigeo; Kubota, Yoshinobu; Uemura, Hiroji

2011-08-01

Atypical protein kinase C λ/ι (aPKCλ/ι) and interleukin-6 (IL-6) have been implicated in prostate cancer progression, the mechanisms of which have been demonstrated both in vitro and in vivo. However, the clinical significance of the correlation between the expressions of these factors remains to be clarified. In the present study, we report a significant correlation between aPKCλ/ι and IL-6 proteins in prostate cancer tissue by immunohistochemical staining. We evaluated the association of both proteins by analyzing clinicopathological parameters using chi-square test, Kaplan-Meier with log-rank test, and a Cox proportional hazard regression model in univariate and multivariate analyses. The results again showed that the expression of aPKCλ/ι and IL-6 correlates in prostate cancer tissue (P < 0.001). Atypical protein kinase C λ/ι was also found to correlate with the Gleason score (P < 0.001) and with biochemical recurrence after prostatectomy (P = 0.02). Furthermore, aPKCλ/ι correlated with biochemical recurrence in a Kaplan-Meier and log-rank test (P = 0.01) and Cox analysis (P = 0.02 in the univariate analysis, P = 0.02 in the multivariate analysis). The coexpression of aPKCλ/ι and IL-6 also correlated with biochemical recurrence by Kaplan-Meier and log-rank test (P = 0.005) and Cox analysis (P = 0.01 in the univariate analysis, P = 0.03 in the multivariate analysis). These results indicate a strong correlation between aPKCλ/ι and IL-6 in prostate tumors, and that the aPKCλ/ι-IL-6 axis is a reliable prognostic factor for the biochemical recurrence of this cancer. © 2011 Japanese Cancer Association.

Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data.

PubMed

Tekwe, Carmen D; Carroll, Raymond J; Dabney, Alan R

2012-08-01

Protein abundance in quantitative proteomics is often based on observed spectral features derived from liquid chromatography mass spectrometry (LC-MS) or LC-MS/MS experiments. Peak intensities are largely non-normal in distribution. Furthermore, LC-MS-based proteomics data frequently have large proportions of missing peak intensities due to censoring mechanisms on low-abundance spectral features. Recognizing that the observed peak intensities detected with the LC-MS method are all positive, skewed and often left-censored, we propose using survival methodology to carry out differential expression analysis of proteins. Various standard statistical techniques including non-parametric tests such as the Kolmogorov-Smirnov and Wilcoxon-Mann-Whitney rank sum tests, and the parametric survival model and accelerated failure time-model with log-normal, log-logistic and Weibull distributions were used to detect any differentially expressed proteins. The statistical operating characteristics of each method are explored using both real and simulated datasets. Survival methods generally have greater statistical power than standard differential expression methods when the proportion of missing protein level data is 5% or more. In particular, the AFT models we consider consistently achieve greater statistical power than standard testing procedures, with the discrepancy widening with increasing missingness in the proportions. The testing procedures discussed in this article can all be performed using readily available software such as R. The R codes are provided as supplemental materials. ctekwe@stat.tamu.edu.

Robust Intratumor Partitioning to Identify High-Risk Subregions in Lung Cancer: A Pilot Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Jia; Gensheimer, Michael F.; Dong, Xinzhe

2016-08-01

Purpose: To develop an intratumor partitioning framework for identifying high-risk subregions from {sup 18}F-fluorodeoxyglucose positron emission tomography (FDG-PET) and computed tomography (CT) imaging and to test whether tumor burden associated with the high-risk subregions is prognostic of outcomes in lung cancer. Methods and Materials: In this institutional review board–approved retrospective study, we analyzed the pretreatment FDG-PET and CT scans of 44 lung cancer patients treated with radiation therapy. A novel, intratumor partitioning method was developed, based on a 2-stage clustering process: first at the patient level, each tumor was over-segmented into many superpixels by k-means clustering of integrated PET andmore » CT images; next, tumor subregions were identified by merging previously defined superpixels via population-level hierarchical clustering. The volume associated with each of the subregions was evaluated using Kaplan-Meier analysis regarding its prognostic capability in predicting overall survival (OS) and out-of-field progression (OFP). Results: Three spatially distinct subregions were identified within each tumor that were highly robust to uncertainty in PET/CT co-registration. Among these, the volume of the most metabolically active and metabolically heterogeneous solid component of the tumor was predictive of OS and OFP on the entire cohort, with a concordance index or CI of 0.66-0.67. When restricting the analysis to patients with stage III disease (n=32), the same subregion achieved an even higher CI of 0.75 (hazard ratio 3.93, log-rank P=.002) for predicting OS, and a CI of 0.76 (hazard ratio 4.84, log-rank P=.002) for predicting OFP. In comparison, conventional imaging markers, including tumor volume, maximum standardized uptake value, and metabolic tumor volume using threshold of 50% standardized uptake value maximum, were not predictive of OS or OFP, with CI mostly below 0.60 (log-rank P>.05). Conclusion: We propose a robust intratumor partitioning method to identify clinically relevant, high-risk subregions in lung cancer. We envision that this approach will be applicable to identifying useful imaging biomarkers in many cancer types.« less

Practical application of cure mixture model for long-term censored survivor data from a withdrawal clinical trial of patients with major depressive disorder.

PubMed

Arano, Ichiro; Sugimoto, Tomoyuki; Hamasaki, Toshimitsu; Ohno, Yuko

2010-04-23

Survival analysis methods such as the Kaplan-Meier method, log-rank test, and Cox proportional hazards regression (Cox regression) are commonly used to analyze data from randomized withdrawal studies in patients with major depressive disorder. However, unfortunately, such common methods may be inappropriate when a long-term censored relapse-free time appears in data as the methods assume that if complete follow-up were possible for all individuals, each would eventually experience the event of interest. In this paper, to analyse data including such a long-term censored relapse-free time, we discuss a semi-parametric cure regression (Cox cure regression), which combines a logistic formulation for the probability of occurrence of an event with a Cox proportional hazards specification for the time of occurrence of the event. In specifying the treatment's effect on disease-free survival, we consider the fraction of long-term survivors and the risks associated with a relapse of the disease. In addition, we develop a tree-based method for the time to event data to identify groups of patients with differing prognoses (cure survival CART). Although analysis methods typically adapt the log-rank statistic for recursive partitioning procedures, the method applied here used a likelihood ratio (LR) test statistic from a fitting of cure survival regression assuming exponential and Weibull distributions for the latency time of relapse. The method is illustrated using data from a sertraline randomized withdrawal study in patients with major depressive disorder. We concluded that Cox cure regression reveals facts on who may be cured, and how the treatment and other factors effect on the cured incidence and on the relapse time of uncured patients, and that cure survival CART output provides easily understandable and interpretable information, useful both in identifying groups of patients with differing prognoses and in utilizing Cox cure regression models leading to meaningful interpretations.

Polypropylene vs silicone Ahmed valve with adjunctive mitomycin C in paediatric age group: a prospective controlled study

PubMed Central

El Sayed, Y; Awadein, A

2013-01-01

Purpose To compare the results of silicone and polypropylene Ahmed glaucoma valves (AGV) implanted during the first 10 years of life. Methods A prospective study was performed on 50 eyes of 33 patients with paediatric glaucoma. Eyes were matched to either polypropylene or silicone AGV. In eyes with bilateral glaucoma, one eye was implanted with polypropylene and the other eye was implanted with silicone AGV. Results Fifty eyes of 33 children were reviewed. Twenty five eyes received a polypropylene valve, and 25 eyes received a silicone valve. Eyes implanted with silicone valves achieved a significantly lower intraocular pressure (IOP) compared with the polypropylene group at 6 months, 1 year, and 2 years postoperatively. The average survival time was significantly longer (P=0.001 by the log-rank test) for the silicone group than for the polypropylene group and the cumulative probability of survival by the log-rank test at the end of the second year was 80% (SE: 8.0, 95% confidence interval (CI): 64–96%) in the silicone group and 56% (SE: 9.8, 95% CI: 40–90%) in the polypropylene group. The difference in the number of postoperative interventions and complications between both groups was statistically insignificant. Conclusion Silicone AGVs can achieve better IOP control, and longer survival with less antiglaucoma drops compared with polypropylene valves in children younger than 10 years. PMID:23579403

Ranking of stopping criteria for log domain diffeomorphic demons application in clinical radiation therapy.

PubMed

Peroni, M; Golland, P; Sharp, G C; Baroni, G

2011-01-01

Deformable Image Registration is a complex optimization algorithm with the goal of modeling a non-rigid transformation between two images. A crucial issue in this field is guaranteeing the user a robust but computationally reasonable algorithm. We rank the performances of four stopping criteria and six stopping value computation strategies for a log domain deformable registration. The stopping criteria we test are: (a) velocity field update magnitude, (b) vector field Jacobian, (c) mean squared error, and (d) harmonic energy. Experiments demonstrate that comparing the metric value over the last three iterations with the metric minimum of between four and six previous iterations is a robust and appropriate strategy. The harmonic energy and vector field update magnitude metrics give the best results in terms of robustness and speed of convergence.

Using volcano plots and regularized-chi statistics in genetic association studies.

PubMed

Li, Wentian; Freudenberg, Jan; Suh, Young Ju; Yang, Yaning

2014-02-01

Labor intensive experiments are typically required to identify the causal disease variants from a list of disease associated variants in the genome. For designing such experiments, candidate variants are ranked by their strength of genetic association with the disease. However, the two commonly used measures of genetic association, the odds-ratio (OR) and p-value may rank variants in different order. To integrate these two measures into a single analysis, here we transfer the volcano plot methodology from gene expression analysis to genetic association studies. In its original setting, volcano plots are scatter plots of fold-change and t-test statistic (or -log of the p-value), with the latter being more sensitive to sample size. In genetic association studies, the OR and Pearson's chi-square statistic (or equivalently its square root, chi; or the standardized log(OR)) can be analogously used in a volcano plot, allowing for their visual inspection. Moreover, the geometric interpretation of these plots leads to an intuitive method for filtering results by a combination of both OR and chi-square statistic, which we term "regularized-chi". This method selects associated markers by a smooth curve in the volcano plot instead of the right-angled lines which corresponds to independent cutoffs for OR and chi-square statistic. The regularized-chi incorporates relatively more signals from variants with lower minor-allele-frequencies than chi-square test statistic. As rare variants tend to have stronger functional effects, regularized-chi is better suited to the task of prioritization of candidate genes. Copyright © 2013 Elsevier Ltd. All rights reserved.

The Prognostic Value of Epithelial Membrane Protein 1 (EMP-1) in Patients with Laryngeal Carcinoma

PubMed Central

Liu, Chang; Wei, Xiaojun; Li, Feng; Wang, Li; Ruan, Xinjian; Jia, Jia; Zhang, Xia

2017-01-01

Background In the present study, we aimed to investigate the prognostic value of epithelial membrane protein 1 (EMP-1) gene in patients diagnosed with laryngeal carcinoma (LC). Material/Methods Patients who were pathologically diagnosed with LC were enrolled in the present study. The expression levels of EMP-1 in tumor tissues and corresponding normal tissues collected from the LC patients were detected by semi-reverse transcriptase polymerase chain reaction (semi-RT-PCR). Chi-square analysis was used to evaluate the relationship between EMP-1 expression level and clinical characteristics. Survival analysis for the study population was analyzed by Kaplan-Meier method with log rank test. Additionally, Cox regression model was applied to evaluate the prognostic value of EMP-1 in LC patients. Results 106 LC patients, including 55 men and 51 women, were enrolled in the present study. Semi-RT-PCR demonstrated that the expression level of EMP-1 was decreased in tumor tissues, compared with adjacent normal tissues (p<0.001). Moreover, the level was significantly associated with lymph node metastasis, histological grade, and clinical stage (p<0.05 for all). In addition, low levels of EMP-1 was significantly correlated with poor survival rate (log rank test, p=0.020). Cox regression analysis indicated that EMP-1 was an independent marker for LC prognosis (HR=2.755, 95% CI=1.123–6.760, p=0.027). Conclusions The abnormal expression of EMP-1 may be associated with progression of LC and the gene may act as a prognostic marker for LC. PMID:28779068

The Prognostic Value of Epithelial Membrane Protein 1 (EMP-1) in Patients with Laryngeal Carcinoma.

PubMed

Liu, Chang; Wei, Xiaojun; Li, Feng; Wang, Li; Ruan, Xinjian; Jia, Jia; Zhang, Xia

2017-08-05

BACKGROUND In the present study, we aimed to investigate the prognostic value of epithelial membrane protein 1 (EMP-1) gene in patients diagnosed with laryngeal carcinoma (LC). MATERIAL AND METHODS Patients who were pathologically diagnosed with LC were enrolled in the present study. The expression levels of EMP-1 in tumor tissues and corresponding normal tissues collected from the LC patients were detected by semi-reverse transcriptase polymerase chain reaction (semi-RT-PCR). Chi-square analysis was used to evaluate the relationship between EMP-1 expression level and clinical characteristics. Survival analysis for the study population was analyzed by Kaplan-Meier method with log rank test. Additionally, Cox regression model was applied to evaluate the prognostic value of EMP-1 in LC patients. RESULTS 106 LC patients, including 55 men and 51 women, were enrolled in the present study. Semi-RT-PCR demonstrated that the expression level of EMP-1 was decreased in tumor tissues, compared with adjacent normal tissues (p<0.001). Moreover, the level was significantly associated with lymph node metastasis, histological grade, and clinical stage (p<0.05 for all). In addition, low levels of EMP-1 was significantly correlated with poor survival rate (log rank test, p=0.020). Cox regression analysis indicated that EMP-1 was an independent marker for LC prognosis (HR=2.755, 95% CI=1.123-6.760, p=0.027). CONCLUSIONS The abnormal expression of EMP-1 may be associated with progression of LC and the gene may act as a prognostic marker for LC.

A genetic polymorphism in TOX3 is associated with survival of gastric cancer in a Chinese population.

PubMed

Zhang, Xiaojing; Zhu, Haixia; Wu, Xiaomin; Wang, Meilin; Gu, Dongying; Gong, Weida; Xu, Zhi; Tan, Yongfei; Gong, Yongling; Zhou, Jianwei; Tang, Cuiju; Tong, Na; Chen, Jinfei; Zhang, Zhengdong

2013-01-01

Recently, genetic polymorphism (rs3803662C>T) in TOX3 was reported to induce the risk of breast cancer. In this study, we hypothesized that rs3803662 could influence gastric cancer survival outcomes. With multiplex SNaPshot method, we genotyped TOX3 rs3803662 in 880 gastric patients with surgical resection. The association between genotype and survival outcomes was performed by the Kaplan-Meier method, Cox regression analysis models and the log-rank test. There was no association in the analyses of rs3803662 and survival of gastric cancer. However, the stratified analysis by histology showed that rs3803662 CT/TT genotype was associated with a significantly better survival for diffuse-type gastric cancer (log-rank p = 0.030, hazard ratio [HR]  = 0.67, 95% confidence interval [CI]  = 0.46-0.96), than the CC genotype. In addition, this favorable effect was especially obvious among gastric cancer patients with tumor size >5 cm, T3 and T4 depth of invasion, lymph node metastasis, no drinking, no distant metastasis, no chemotherapy and gastric cardia cancer. TOX3 rs3803662 might play an important role in the prognostic outcome and treatment of gastric cancer, especially perhaps further help in explaining the reduced risk of death associated with diffuse-type gastric cancer.

A public hedonic analysis of environmental attributes in an open space preservation program

NASA Astrophysics Data System (ADS)

Nordman, Erik E.

The Town of Brookhaven, on Long Island, NY, has implemented an open space preservation program to protect natural areas, and the ecosystem services they provide, from suburban growth. I used a public hedonic model of Brookhaven's open space purchases to estimate implicit prices for various environmental attributes, locational variables and spatial metrics. I also measured the correlation between cost per acre and non-monetary environmental benefit scores and tested whether including cost data, as opposed to non-monetary environmental benefit score alone, would change the prioritization ranks of acquired properties. The mean acquisition cost per acre was 82,501. I identified the key on-site environmental and locational variables using stepwise regression for four functional forms. The log-log specification performed best ( R2adj= 0.727). I performed a second stepwise regression (log-log form) which included spatial metrics, calculated from a high-resolution land cover classification, in addition to the environmental and locational variables. This markedly improved the model's performance ( R2adj=0.866). Statistically significant variables included the property size, location in the Pine Barrens Compatible Growth Area, location in a FEMA flood zone, adjacency to public land, and several other environmental dummy variables. The single significant spatial metric, the fractal dimension of the tree cover class, had the largest elasticity of any variable. Of the dummy variables, location within the Compatible Growth Area had the largest implicit price (298,792 per acre). The priority rank for the two methods, non-monetary environmental benefit score alone and the ratio of non-monetary environmental benefit score to acquisition cost were significantly positively correlated. This suggests that, despite the lack of cost data in their ranking method, Brookhaven does not suffer from efficiency losses. The economics literature encourages using both environmental benefits and acquisition costs to ensure cost-effective conservation programs. I recommend that Brookhaven consider acquisition costs in addition to environmental benefits to avert potential efficiency losses in future open space purchases. This dissertation shows that the addition of spatial metrics can enhance the performance of hedonic models. It also provides a baseline valuation for the environmental attributes of Brookhaven' open spaces and shows that location is critical when dealing with open space preservation programs.

Prediction of survival with multi-scale radiomic analysis in glioblastoma patients.

PubMed

Chaddad, Ahmad; Sabri, Siham; Niazi, Tamim; Abdulkarim, Bassam

2018-06-19

We propose a multiscale texture features based on Laplacian-of Gaussian (LoG) filter to predict progression free (PFS) and overall survival (OS) in patients newly diagnosed with glioblastoma (GBM). Experiments use the extracted features derived from 40 patients of GBM with T1-weighted imaging (T1-WI) and Fluid-attenuated inversion recovery (FLAIR) images that were segmented manually into areas of active tumor, necrosis, and edema. Multiscale texture features were extracted locally from each of these areas of interest using a LoG filter and the relation between features to OS and PFS was investigated using univariate (i.e., Spearman's rank correlation coefficient, log-rank test and Kaplan-Meier estimator) and multivariate analyses (i.e., Random Forest classifier). Three and seven features were statistically correlated with PFS and OS, respectively, with absolute correlation values between 0.32 and 0.36 and p < 0.05. Three features derived from active tumor regions only were associated with OS (p < 0.05) with hazard ratios (HR) of 2.9, 3, and 3.24, respectively. Combined features showed an AUC value of 85.37 and 85.54% for predicting the PFS and OS of GBM patients, respectively, using the random forest (RF) classifier. We presented a multiscale texture features to characterize the GBM regions and predict he PFS and OS. The efficiency achievable suggests that this technique can be developed into a GBM MR analysis system suitable for clinical use after a thorough validation involving more patients. Graphical abstract Scheme of the proposed model for characterizing the heterogeneity of GBM regions and predicting the overall survival and progression free survival of GBM patients. (1) Acquisition of pretreatment MRI images; (2) Affine registration of T1-WI image with its corresponding FLAIR images, and GBM subtype (phenotypes) labelling; (3) Extraction of nine texture features from the three texture scales fine, medium, and coarse derived from each of GBM regions; (4) Comparing heterogeneity between GBM regions by ANOVA test; Survival analysis using Univariate (Spearman rank correlation between features and survival (i.e., PFS and OS) based on each of the GBM regions, Kaplan-Meier estimator and log-rank test to predict the PFS and OS of patient groups that grouped based on median of feature), and multivariate (random forest model) for predicting the PFS and OS of patients groups that grouped based on median of PFS and OS.

Upper-Room Ultraviolet Light and Negative Air Ionization to Prevent Tuberculosis Transmission

PubMed Central

Escombe, A. Roderick; Moore, David A. J; Gilman, Robert H; Navincopa, Marcos; Ticona, Eduardo; Mitchell, Bailey; Noakes, Catherine; Martínez, Carlos; Sheen, Patricia; Ramirez, Rocio; Quino, Willi; Gonzalez, Armando; Friedland, Jon S; Evans, Carlton A

2009-01-01

Background Institutional tuberculosis (TB) transmission is an important public health problem highlighted by the HIV/AIDS pandemic and the emergence of multidrug- and extensively drug-resistant TB. Effective TB infection control measures are urgently needed. We evaluated the efficacy of upper-room ultraviolet (UV) lights and negative air ionization for preventing airborne TB transmission using a guinea pig air-sampling model to measure the TB infectiousness of ward air. Methods and Findings For 535 consecutive days, exhaust air from an HIV-TB ward in Lima, Perú, was passed through three guinea pig air-sampling enclosures each housing approximately 150 guinea pigs, using a 2-d cycle. On UV-off days, ward air passed in parallel through a control animal enclosure and a similar enclosure containing negative ionizers. On UV-on days, UV lights and mixing fans were turned on in the ward, and a third animal enclosure alone received ward air. TB infection in guinea pigs was defined by monthly tuberculin skin tests. All guinea pigs underwent autopsy to test for TB disease, defined by characteristic autopsy changes or by the culture of Mycobacterium tuberculosis from organs. 35% (106/304) of guinea pigs in the control group developed TB infection, and this was reduced to 14% (43/303) by ionizers, and to 9.5% (29/307) by UV lights (both p < 0.0001 compared with the control group). TB disease was confirmed in 8.6% (26/304) of control group animals, and this was reduced to 4.3% (13/303) by ionizers, and to 3.6% (11/307) by UV lights (both p < 0.03 compared with the control group). Time-to-event analysis demonstrated that TB infection was prevented by ionizers (log-rank 27; p < 0.0001) and by UV lights (log-rank 46; p < 0.0001). Time-to-event analysis also demonstrated that TB disease was prevented by ionizers (log-rank 3.7; p = 0.055) and by UV lights (log-rank 5.4; p = 0.02). An alternative analysis using an airborne infection model demonstrated that ionizers prevented 60% of TB infection and 51% of TB disease, and that UV lights prevented 70% of TB infection and 54% of TB disease. In all analysis strategies, UV lights tended to be more protective than ionizers. Conclusions Upper-room UV lights and negative air ionization each prevented most airborne TB transmission detectable by guinea pig air sampling. Provided there is adequate mixing of room air, upper-room UV light is an effective, low-cost intervention for use in TB infection control in high-risk clinical settings. PMID:19296717

Robust Intratumor Partitioning to Identify High-Risk Subregions in Lung Cancer: A Pilot Study.

PubMed

Wu, Jia; Gensheimer, Michael F; Dong, Xinzhe; Rubin, Daniel L; Napel, Sandy; Diehn, Maximilian; Loo, Billy W; Li, Ruijiang

2016-08-01

To develop an intratumor partitioning framework for identifying high-risk subregions from (18)F-fluorodeoxyglucose positron emission tomography (FDG-PET) and computed tomography (CT) imaging and to test whether tumor burden associated with the high-risk subregions is prognostic of outcomes in lung cancer. In this institutional review board-approved retrospective study, we analyzed the pretreatment FDG-PET and CT scans of 44 lung cancer patients treated with radiation therapy. A novel, intratumor partitioning method was developed, based on a 2-stage clustering process: first at the patient level, each tumor was over-segmented into many superpixels by k-means clustering of integrated PET and CT images; next, tumor subregions were identified by merging previously defined superpixels via population-level hierarchical clustering. The volume associated with each of the subregions was evaluated using Kaplan-Meier analysis regarding its prognostic capability in predicting overall survival (OS) and out-of-field progression (OFP). Three spatially distinct subregions were identified within each tumor that were highly robust to uncertainty in PET/CT co-registration. Among these, the volume of the most metabolically active and metabolically heterogeneous solid component of the tumor was predictive of OS and OFP on the entire cohort, with a concordance index or CI of 0.66-0.67. When restricting the analysis to patients with stage III disease (n=32), the same subregion achieved an even higher CI of 0.75 (hazard ratio 3.93, log-rank P=.002) for predicting OS, and a CI of 0.76 (hazard ratio 4.84, log-rank P=.002) for predicting OFP. In comparison, conventional imaging markers, including tumor volume, maximum standardized uptake value, and metabolic tumor volume using threshold of 50% standardized uptake value maximum, were not predictive of OS or OFP, with CI mostly below 0.60 (log-rank P>.05). We propose a robust intratumor partitioning method to identify clinically relevant, high-risk subregions in lung cancer. We envision that this approach will be applicable to identifying useful imaging biomarkers in many cancer types. Copyright © 2016 Elsevier Inc. All rights reserved.

Interpreting wireline measurements in coal beds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnston, D.J.

1991-06-01

When logging coal seams with wireline tools, the interpretation method needed to evaluate the coals is different from that used for conventional oil and gas reservoirs. Wireline logs identify coals easily. For an evaluation, the contribution of each coal component on the raw measurements must be considered. This paper will discuss how each log measurement is affected by each component. The components of a coal will be identified as the mineral matter, macerals, moisture content, rank, gas content, and cleat porosity. The measurements illustrated are from the resistivity, litho-density, neutron, sonic, dielectric, and geochemical tools. Once the coal component effectsmore » have been determined, an interpretation of the logs can be made. This paper will illustrate how to use these corrected logs in a coal evaluation.« less

Impact of Different Aortic Entry Tear Sites on Early Outcomes and Long-Term Survival in Patients with Stanford A Acute Aortic Dissection.

PubMed

Merkle, Julia; Sabashnikov, Anton; Deppe, Antje Christin; Weber, Saskia; Mader, Navid; Choi, Yeong-Hoon; Liakopoulos, Oliver; Kuhn-Régnier, Ferdinand; Wahlers, Thorsten

2018-06-13

 Stanford A acute aortic dissection (AAD) is a life-threatening emergency. The aim of this study was to compare the impact of three different aortic entry tear sites on early outcomes and long-term survival of patients with Stanford A AAD.  From January 2006 to April 2015, a total of 240 consecutive patients with diagnosed Stanford A AAD underwent emergent, isolated surgical aortic repair in our center. Patients were divided into three groups comprising isolated ascending aorta, proximal aortic arch, and distal aortic arch entry tear site and were followed up for up to 9 years.  Thirty-day mortality as well as major cerebrovascular events were significantly different between the three groups ( p  = 0.007 and p  = 0.048, respectively). Overall cumulative short- and long-term survival of all patients revealed significant differences (Log-Rank p  = 0.002), whereas survival of all patients free from major cerebrovascular events was similar (Log-Rank p  = 0.780). Subgroup analysis of short- and long-term survival of patients showed significant differences in terms of men (Log-Rank p  = 0.043), women (Log-Rank p  = 0.004), patients over 65 years of age (Log-Rank p  = 0.007), and hypertensive patients (Log-Rank p  = 0.003). Kaplan-Meier survival estimation plots significantly showed poorest survival for distal aortic arch entry tear site group.  The location of the primary entry tear in patients with Stanford A AAD significantly influences early outcomes, short- and long-term survival of patients, whereas survival of patients free from major cerebrovascular events showed similar results among the three groups. Distal aortic entry tear site showed poorest outcomes and survival. Georg Thieme Verlag KG Stuttgart · New York.

Enhancing tumor apparent diffusion coefficient histogram skewness stratifies the postoperative survival in recurrent glioblastoma multiforme patients undergoing salvage surgery.

PubMed

Zolal, Amir; Juratli, Tareq A; Linn, Jennifer; Podlesek, Dino; Sitoci Ficici, Kerim Hakan; Kitzler, Hagen H; Schackert, Gabriele; Sobottka, Stephan B; Rieger, Bernhard; Krex, Dietmar

2016-05-01

Objective To determine the value of apparent diffusion coefficient (ADC) histogram parameters for the prediction of individual survival in patients undergoing surgery for recurrent glioblastoma (GBM) in a retrospective cohort study. Methods Thirty-one patients who underwent surgery for first recurrence of a known GBM between 2008 and 2012 were included. The following parameters were collected: age, sex, enhancing tumor size, mean ADC, median ADC, ADC skewness, ADC kurtosis and fifth percentile of the ADC histogram, initial progression free survival (PFS), extent of second resection and further adjuvant treatment. The association of these parameters with survival and PFS after second surgery was analyzed using log-rank test and Cox regression. Results Using log-rank test, ADC histogram skewness of the enhancing tumor was significantly associated with both survival (p = 0.001) and PFS after second surgery (p = 0.005). Further parameters associated with prolonged survival after second surgery were: gross total resection at second surgery (p = 0.026), tumor size (0.040) and third surgery (p = 0.003). In the multivariate Cox analysis, ADC histogram skewness was shown to be an independent prognostic factor for survival after second surgery. Conclusion ADC histogram skewness of the enhancing lesion, enhancing lesion size, third surgery, as well as gross total resection have been shown to be associated with survival following the second surgery. ADC histogram skewness was an independent prognostic factor for survival in the multivariate analysis.

Simple prognostic model for patients with advanced cancer based on performance status.

PubMed

Jang, Raymond W; Caraiscos, Valerie B; Swami, Nadia; Banerjee, Subrata; Mak, Ernie; Kaya, Ebru; Rodin, Gary; Bryson, John; Ridley, Julia Z; Le, Lisa W; Zimmermann, Camilla

2014-09-01

Providing survival estimates is important for decision making in oncology care. The purpose of this study was to provide survival estimates for outpatients with advanced cancer, using the Eastern Cooperative Oncology Group (ECOG), Palliative Performance Scale (PPS), and Karnofsky Performance Status (KPS) scales, and to compare their ability to predict survival. ECOG, PPS, and KPS were completed by physicians for each new patient attending the Princess Margaret Cancer Centre outpatient Oncology Palliative Care Clinic (OPCC) from April 2007 to February 2010. Survival analysis was performed using the Kaplan-Meier method. The log-rank test for trend was employed to test for differences in survival curves for each level of performance status (PS), and the concordance index (C-statistic) was used to test the predictive discriminatory ability of each PS measure. Measures were completed for 1,655 patients. PS delineated survival well for all three scales according to the log-rank test for trend (P < .001). Survival was approximately halved for each worsening performance level. Median survival times, in days, for each ECOG level were: EGOG 0, 293; ECOG 1, 197; ECOG 2, 104; ECOG 3, 55; and ECOG 4, 25.5. Median survival times, in days, for PPS (and KPS) were: PPS/KPS 80-100, 221 (215); PPS/KPS 60 to 70, 115 (119); PPS/KPS 40 to 50, 51 (49); PPS/KPS 10 to 30, 22 (29). The C-statistic was similar for all three scales and ranged from 0.63 to 0.64. We present a simple tool that uses PS alone to prognosticate in advanced cancer, and has similar discriminatory ability to more complex models. Copyright © 2014 by American Society of Clinical Oncology.

Treatment of Suicide Attempters With Bipolar Disorder: A Randomized Clinical Trial Comparing Lithium and Valproate in the Prevention of Suicidal Behavior

PubMed Central

Oquendo, Maria A.; Galfalvy, Hanga C.; Currier, Dianne; Grunebaum, Michael F.; Sher, Leo; Sullivan, Gregory M.; Burke, Ainsley K.; Harkavy-Friedman, Jill; Sublette, M. Elizabeth; Parsey, Ramin V.; Mann, J. John

2013-01-01

Objective Bipolar disorder is associated with high risk for suicidal acts. Observational studies suggest a protective effect of lithium against suicidal behavior. However, testing this effect in randomized clinical trials is logistically and ethically challenging. The authors tested the hypothesis that lithium offers bipolar patients with a history of suicide attempt greater protection against suicidal behavior compared to valproate. Method Patients with bipolar disorder and past suicide attempts (N=98) were randomly assigned to treatment with lithium or valproate, plus adjunctive medications as indicated, in a double-blind 2.5-year trial. An intent-to-treat analysis was performed using the log-rank test for survival data. Two models were fitted: time to suicide attempt and time to suicide event (attempt or hospitalization or change in medication in response to suicide plans). Results There were 45 suicide events in 35 participants, including 18 suicide attempts made by 14 participants, six from the lithium group and eight from the valproate group. There were no suicides. Intent-to-treat analysis using the log-rank test showed no differences between treatment groups in time to suicide attempt or to suicide event. Post hoc power calculations revealed that the modest sample size, reflective of challenges in recruitment, only permits detection of a relative risk of 5 or greater. Conclusions Despite the high frequency of suicide events during the study, this randomized controlled trial detected no difference between lithium and valproate in time to suicide attempt or suicide event in a sample of suicide attempters with bipolar disorder. However, smaller clinically significant differences between the two drugs were not ruled out. PMID:21768611

Single nucleotide polymorphisms in the mitochondrial displacement loop and outcome of esophageal squamous cell carcinoma.

PubMed

Zhang, Ruixing; Wang, Rui; Zhang, Fengbin; Wu, Chensi; Fan, Haiyan; Li, Yan; Wang, Cuiju; Guo, Zhanjun

2010-11-26

Accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been described for different types of cancers and might be associated with cancer risk and disease outcome. We used a population-based series of esophageal squamous cell carcinoma (ESCC) patients for investigating the prediction power of SNPs in mitochondrial D-loop. The D-loop region of mtDNA was sequenced for 60 ESCC patients recorded in the Fourth Hospital of Hebei Medical University between 2003 and 2004. The 5 year survival curve were calculated with the Kaplan-Meier method and compared by the log-rank test at each SNP site, a multivariate survival analysis was also performed with the Cox proportional hazards method. The SNP sites of nucleotides 16274G/A, 16278C/T and 16399A/G were identified for prediction of post-operational survival by the log-rank test. In an overall multivariate analysis, the 16278 and 16399 alleles were identified as independent predictors of ESCC outcome. The length of survival of patients with the minor allele 16278T genotype was significantly shorter than that of patients with 16278C at the 16278 site (relative risk, 3.001; 95% CI, 1.029 - 8.756; p = 0.044). The length of survival of patients with the minor allele 16399G genotype was significantly shorter than that of patients with the more frequent allele 16399A at the 16399 site in ESCC patients (relative risk, 3.483; 95% CI, 1.068 - 11.359; p = 0.039). Genetic polymorphisms in the D-loop are independent prognostic markers for patients with ESCC. Accordingly, the analysis of genetic polymorphisms in the mitochondrial D-loop can help identify patient subgroups at high risk of a poor disease outcome.

CHEK2*1100delC heterozygosity in women with breast cancer associated with early death, breast cancer-specific death, and increased risk of a second breast cancer.

PubMed

Weischer, Maren; Nordestgaard, Børge G; Pharoah, Paul; Bolla, Manjeet K; Nevanlinna, Heli; Van't Veer, Laura J; Garcia-Closas, Montserrat; Hopper, John L; Hall, Per; Andrulis, Irene L; Devilee, Peter; Fasching, Peter A; Anton-Culver, Hoda; Lambrechts, Diether; Hooning, Maartje; Cox, Angela; Giles, Graham G; Burwinkel, Barbara; Lindblom, Annika; Couch, Fergus J; Mannermaa, Arto; Grenaker Alnæs, Grethe; John, Esther M; Dörk, Thilo; Flyger, Henrik; Dunning, Alison M; Wang, Qin; Muranen, Taru A; van Hien, Richard; Figueroa, Jonine; Southey, Melissa C; Czene, Kamila; Knight, Julia A; Tollenaar, Rob A E M; Beckmann, Matthias W; Ziogas, Argyrios; Christiaens, Marie-Rose; Collée, Johanna Margriet; Reed, Malcolm W R; Severi, Gianluca; Marme, Frederik; Margolin, Sara; Olson, Janet E; Kosma, Veli-Matti; Kristensen, Vessela N; Miron, Alexander; Bogdanova, Natalia; Shah, Mitul; Blomqvist, Carl; Broeks, Annegien; Sherman, Mark; Phillips, Kelly-Anne; Li, Jingmei; Liu, Jianjun; Glendon, Gord; Seynaeve, Caroline; Ekici, Arif B; Leunen, Karin; Kriege, Mieke; Cross, Simon S; Baglietto, Laura; Sohn, Christof; Wang, Xianshu; Kataja, Vesa; Børresen-Dale, Anne-Lise; Meyer, Andreas; Easton, Douglas F; Schmidt, Marjanka K; Bojesen, Stig E

2012-12-10

We tested the hypotheses that CHEK2*1100delC heterozygosity is associated with increased risk of early death, breast cancer-specific death, and risk of a second breast cancer in women with a first breast cancer. From 22 studies participating in the Breast Cancer Association Consortium, 25,571 white women with invasive breast cancer were genotyped for CHEK2*1100delC and observed for up to 20 years (median, 6.6 years). We examined risk of early death and breast cancer-specific death by estrogen receptor status and risk of a second breast cancer after a first breast cancer in prospective studies. CHEK2*1100delC heterozygosity was found in 459 patients (1.8%). In women with estrogen receptor-positive breast cancer, multifactorially adjusted hazard ratios for heterozygotes versus noncarriers were 1.43 (95% CI, 1.12 to 1.82; log-rank P = .004) for early death and 1.63 (95% CI, 1.24 to 2.15; log-rank P < .001) for breast cancer-specific death. In all women, hazard ratio for a second breast cancer was 2.77 (95% CI, 2.00 to 3.83; log-rank P < .001) increasing to 3.52 (95% CI, 2.35 to 5.27; log-rank P < .001) in women with estrogen receptor-positive first breast cancer only. Among women with estrogen receptor-positive breast cancer, CHEK2*1100delC heterozygosity was associated with a 1.4-fold risk of early death, a 1.6-fold risk of breast cancer-specific death, and a 3.5-fold risk of a second breast cancer. This is one of the few examples of a genetic factor that influences long-term prognosis being documented in an extensive series of women with breast cancer.

Search by photo methodology for signature properties assessment by human observers

NASA Astrophysics Data System (ADS)

Selj, Gorm K.; Heinrich, Daniela H.

2015-05-01

Reliable, low-cost and simple methods for assessment of signature properties for military purposes are very important. In this paper we present such an approach that uses human observers in a search by photo assessment of signature properties of generic test targets. The method was carried out by logging a large number of detection times of targets recorded in relevant terrain backgrounds. The detection times were harvested by using human observers searching for targets in scene images shown by a high definition pc screen. All targets were identically located in each "search image", allowing relative comparisons (and not just rank by order) of targets. To avoid biased detections, each observer only searched for one target per scene. Statistical analyses were carried out for the detection times data. Analysis of variance was chosen if detection times distribution associated with all targets satisfied normality, and non-parametric tests, such as Wilcoxon's rank test, if otherwise. The new methodology allows assessment of signature properties in a reproducible, rapid and reliable setting. Such assessments are very complex as they must sort out what is of relevance in a signature test, but not loose information of value. We believe that choosing detection times as the primary variable for a comparison of signature properties, allows a careful and necessary inspection of observer data as the variable is continuous rather than discrete. Our method thus stands in opposition to approaches based on detections by subsequent, stepwise reductions in distance to target, or based on probability of detection.

Developing Surveillance Methodology for Agricultural and Logging Injury in New Hampshire Using Electronic Administrative Data Sets.

PubMed

Scott, Erika E; Hirabayashi, Liane; Krupa, Nicole L; Sorensen, Julie A; Jenkins, Paul L

2015-08-01

Agriculture and logging rank among industries with the highest rates of occupational fatality and injury. Establishing a nonfatal injury surveillance system is a top priority in the National Occupational Research Agenda. Sources of data such as patient care reports (PCRs) and hospitalization data have recently transitioned to electronic databases. Using narrative and location codes from PCRs, along with International Classification of Diseases, 9th Revision, external cause of injury codes (E-codes) in hospital data, researchers are designing a surveillance system to track farm and logging injury. A total of 357 true agricultural or logging cases were identified. These data indicate that it is possible to identify agricultural and logging injury events in PCR and hospital data. Multiple data sources increase catchment; nevertheless, limitations in methods of identification of agricultural and logging injury contribute to the likely undercount of injury events.

Biological maturity at birth, the course of the subsequent ontogenetic stages and age at menarche.

PubMed

Szwed, A; Kosińska, M

2012-08-01

The main aim of the study was to assess the influence of biological maturity at birth on growth processes in the subsequent years and during puberty in girls. The material of this study comes from the outpatient clinic cards and cross-sectional research on girls from the province of Wielkopolska in Poland. It includes data of 527 girls. The influence of perinatal maturity on body weight in the later stages of ontogeny was determined with the use of the Kruskal-Wallis test and the Mann-Whitney U test. In order to determine the relationship between perinatal maturity and age at menarche, the survival analysis module was used. The results show a diverse influence of perinatal maturity on the values of body weight achieved in later years of life. The indicated predictive factors included both birth weight and gestational age. In the examined girls menarche occurred between the 10th year and the 17th year of life (X¯=12.87, s=1.26; Me=13 years). The comparison showed a significant variation in age at menarche depending on the length of pregnancy (log-rank χ(2)(2)=27.068, p<0.0001) and birth weight (log-rank χ(2)(2)=23.241, p<0.0001). There was no variation in maturation of the examined girls conditioned by the occurrence of intra-uterine growth retardation (log-rank χ(2)(2)=2.046, p>0.05). Remote prognoses as to the postnatal development of preterm-born children and/or children with low birth weight indicate adverse influence of these variables on age at menarche. Perinatal biological maturity of a newborn conditions the course of postnatal development. Copyright © 2012 Elsevier GmbH. All rights reserved.

Linear and nonlinear methods in modeling the aqueous solubility of organic compounds.

PubMed

Catana, Cornel; Gao, Hua; Orrenius, Christian; Stouten, Pieter F W

2005-01-01

Solubility data for 930 diverse compounds have been analyzed using linear Partial Least Square (PLS) and nonlinear PLS methods, Continuum Regression (CR), and Neural Networks (NN). 1D and 2D descriptors from MOE package in combination with E-state or ISIS keys have been used. The best model was obtained using linear PLS for a combination between 22 MOE descriptors and 65 ISIS keys. It has a correlation coefficient (r2) of 0.935 and a root-mean-square error (RMSE) of 0.468 log molar solubility (log S(w)). The model validated on a test set of 177 compounds not included in the training set has r2 0.911 and RMSE 0.475 log S(w). The descriptors were ranked according to their importance, and at the top of the list have been found the 22 MOE descriptors. The CR model produced results as good as PLS, and because of the way in which cross-validation has been done it is expected to be a valuable tool in prediction besides PLS model. The statistics obtained using nonlinear methods did not surpass those got with linear ones. The good statistic obtained for linear PLS and CR recommends these models to be used in prediction when it is difficult or impossible to make experimental measurements, for virtual screening, combinatorial library design, and efficient leads optimization.

Prevalence of Cognitive Impairment and Association With Survival Among Older Patients With Hematologic Cancers.

PubMed

Hshieh, Tammy T; Jung, Wooram F; Grande, Laura J; Chen, Jiaying; Stone, Richard M; Soiffer, Robert J; Driver, Jane A; Abel, Gregory A

2018-05-01

As the population ages, cognitive impairment has promised to become increasingly common among patients with cancer. Little is known about how specific domains of cognitive impairment may be associated with survival among older patients with hematologic cancers. To determine the prevalence of domain-specific cognitive impairment and its association with overall survival among older patients with blood cancer. This prospective observational cohort study included all patients 75 years and older who presented for initial consultation in the leukemia, myeloma, or lymphoma clinics of a large tertiary hospital in Boston, Massachusetts, from February 1, 2015, to March 31, 2017. Patients underwent screening for frailty and cognitive dysfunction and were followed up for survival. The Clock-in-the-Box (CIB) test was used to screen for executive dysfunction. A 5-word delayed recall test was used to screen for impairment in working memory. The Fried frailty phenotype and Rockwood cumulative deficit model of frailty were also assessed to characterize participants as robust, prefrail, or frail. Among 420 consecutive patients approached, 360 (85.7%) agreed to undergo frailty assessment (232 men [64.4%] and 128 women [35.6%]; mean [SD] age, 79.8 [3.9] years), and 341 of those (94.7%) completed both cognitive screening tests. One hundred twenty-seven patients (35.3%) had probable executive dysfunction on the CIB, and 62 (17.2%) had probable impairment in working memory on the 5-word delayed recall. Impairment in either domain was modestly correlated with the Fried frailty phenotype (CIB, ρ = 0.177; delayed recall, ρ = 0.170; P = .01 for both), and many phenotypically robust patients also had probable cognitive impairment (24 of 104 [23.1%] on CIB and 9 of 104 [8.7%] on delayed recall). Patients with impaired working memory had worse median survival (10.9 [SD, 12.9] vs 12.2 [SD, 14.7] months; log-rank P < .001), including when stratified by indolent cancer (log-rank P = .01) and aggressive cancer (P < .001) and in multivariate analysis when adjusting for age, comorbidities, and disease aggressiveness (odds ratio, 0.26; 95% CI, 0.13-0.50). Impaired working memory was also associated with worse survival for those undergoing intensive treatment (log-rank P < .001). Executive dysfunction was associated with worse survival only among patients who underwent intensive treatment (log-rank P = .03). These data suggest that domains of cognitive dysfunction may be prevalent in older patients with blood cancer and may have differential predictive value for survival. Targeted interventions are needed for this vulnerable patient population.

Prognostic significance of biochemical markers in African Burkitt's lymphoma.

PubMed

Arthur, F K N; Owusu, L; Yeboah, F A; Rettig, T; Osei-Akoto, A

2011-10-01

BACKGROUND AND PURPOSE Endemic Burkitt's lymphoma (eBL) remains the prevalent form of paediatric cancer in tropical Africa with subtle pathological differences. This calls for intensified efforts to validate the global prognostic markers within local settings for improved cancer treatment and survival. This study proposes prognostic markers for enhanced eBL treatment and management. PATIENTS AND METHOD One hundred and eighty histologically and/or clinically diagnosed BL patients at Komfo Anokye Teaching Hospital, Kumasi, Ghana were eligible for this cross-sectional eight-year retrospective study. Biochemical, clinical and demographic data, before chemotherapy administration, were documented and examined for their progression-free (PFS) and overall survival (OS) significance. RESULTS A mean age of 6 (SD=2.7, range: 1-16) years was observed with general male dominance (M:F=1.69:1). Total serum lactate dehydrogenase (HR=2.04; 95% CI, 1.25-3.32; log rank=8.3; p=0.004), serum creatinine (HR=3.59; 95% CI, 1.62-7.98; log rank=15.4; p=0.002) and St. Jude stage (HR=1.74; 95% CI, 1.11-2.73; log rank=8.0; p=0.015) were important independent prognostic biochemical markers for both PFS and OS. Age, serum calcium, uric acid, potassium, sodium and phosphorus were non-prognostic. CONCLUSION The better monitoring of these prognostic indices coupled with risk-stratification treatment may improve patients' survival, especially in resource-limited settings.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cooper, Benjamin T.; Formenti-Ujlaki, George F.; Li, Xiaochun

Purpose: To report the results of a prospective randomized trial comparing a daily versus weekly boost to the tumor cavity during the course of accelerated radiation to the breast with patients in the prone position. Methods and Materials: From 2009 to 2012, 400 patients with stage 0 to II breast cancer who had undergone segmental mastectomy participated in an institutional review board–approved trial testing prone breast radiation therapy to 40.5 Gy in 15 fractions 5 d/wk to the whole breast, after randomization to a concomitant daily boost to the tumor bed of 0.5 Gy, or a weekly boost of 2 Gy, on Friday.more » The present noninferiority trial tested the primary hypothesis that a weekly boost produced no more acute toxicity than did a daily boost. The recurrence-free survival was estimated for both treatment arms using the Kaplan-Meier method; the relative risk of recurrence or death was estimated, and the 2 arms were compared using the log-rank test. Results: At a median follow-up period of 45 months, no deaths related to breast cancer had occurred. The weekly boost regimen produced no more grade ≥2 acute toxicity than did the daily boost regimen (8.1% vs 10.4%; noninferiority Z = −2.52; P=.006). No statistically significant difference was found in the cumulative incidence of long-term fibrosis or telangiectasia of grade ≥2 between the 2 arms (log-rank P=.923). Two local and two distant recurrences developed in the daily treatment arm and three local and one distant developed in the weekly arm. The 4-year recurrence-free survival rate was not different between the 2 treatment arms (98% for both arms). Conclusions: A tumor bed boost delivered either daily or weekly was tolerated similarly during accelerated prone breast radiation therapy, with excellent control of disease and comparable cosmetic results.« less

Variations in Duchenne muscular dystrophy course in a multi-ethnic UK population: potential influence of socio-economic factors.

PubMed

Hufton, Margaret; Roper, Helen

2017-08-01

To explore variation in clinical course and steroid treatment in Duchenne muscular dystrophy (DMD) by ethnic origin and socio-economic status. In this longitudinal cohort study, clinical outcome was defined as age at loss of ambulation (LOA). Ages are presented as months for accurate calculation. Steroid use was reviewed against national guidelines. Kaplan-Meier survival analysis was used to determine probabilities over time of LOA. Log-rank test was used to evaluate comparisons between ethnic and socio-economic groups. From 2005 to 2014, 71 children were newly diagnosed with DMD. Complete data were available on 69, including 33 of white British heritage and 23 of South Asian heritage. Mean age at diagnosis (without known family history) was 45.7 months; white British ethnicity 42.1 months (range 14-86mo), South Asian ethnicity 50.2 months (range 5-98mo). Twenty-four males lost ambulation. Those of South Asian heritage lost ambulation earlier (mean LOA 105.8mo [8y 10mo]) than those of white British heritage (mean LOA 117.8mo [9y 10mo]): log-rank test score 0.012 (p<0.05). Those most deprived did worse: mean age at LOA 130.0 months (10y 10mo) for the top 20 per cent and 102.5 months (8y 6mo) in the lower 20 per cent: log-rank test score 0.035 (p<0.05). The most socially deprived were diagnosed earlier and started steroids earlier. Of those of South Asian heritage, 18 per cent declined steroids, compared with 9 per cent of white British heritage. Also, 44 per cent of those of South Asian heritage stopped steroids compared with 17 per cent of those of white British heritage. Patients from South Asian and deprived backgrounds had earlier LOA. Genetic disease modifiers are likely to be implicated, but social and cultural factors influence access to treatment. © 2017 Mac Keith Press.

Association of day 4 cumulative fluid balance with mortality in critically ill patients with influenza: A multicenter retrospective cohort study in Taiwan.

PubMed

Chao, Wen-Cheng; Tseng, Chien-Hua; Chien, Ying-Chun; Sheu, Chau-Chyun; Tsai, Ming-Ju; Fang, Wen-Feng; Chen, Yu-Mu; Kao, Kuo-Chin; Hu, Han-Chung; Perng, Wann-Cherng; Yang, Kuang-Yao; Chen, Wei-Chih; Liang, Shinn-Jye; Wu, Chieh-Liang; Wang, Hao-Chien; Chan, Ming-Cheng

2018-01-01

Fluid balance is a fundamental management of patients with sepsis, and this study aimed to investigate the impact of cumulative fluid balance on critically ill patients with influenza admitted to an intensive care unit (ICU). This multicenter retrospective cohort study was conducted by the Taiwan Severe Influenza Research Consortium (TSIRC) which includes eight medical centers. Patients with virology-proven influenza infection admitted to ICUs between October 2015 and March 2016 were included for analysis. A total of 296 patients were enrolled (mean age: 61.4±15.6 years; 62.8% men), and 92.2% (273/296) of them required mechanical ventilation. In the survivors, the daily fluid balance was positive from day 1 to day 3, and then gradually became negative from day 4 to day 7, whereas daily fluid balance was continuously positive in the non-survivors. Using the cumulative fluid balance from day 1-4 as a cut-off point, we found that a negative cumulative day 1-4 fluid balance was associated with a lower 30-day mortality rate (log-rank test, P = 0.003). To evaluate the impact of shock on this association, we divided the patients into shock and non-shock groups. The positive correlation between negative day 1-4 fluid balance and mortality was significant in the non-shock group (log-rank test, P = 0.008), but not in the shock group (log-rank test, P = 0.396). In a multivariate Cox proportional hazard regression model adjusted for age, sex, cerebrovascular disease, and PaO2/FiO2, day 1-4 fluid balance was independently associated with a higher 30-day mortality rate (aHR 1.088, 95% CI: 1.007-1.174). A negative day 1-4 cumulative fluid balance was associated with a lower mortality rate in critically ill patients with influenza. Our findings indicate the critical role of conservative fluid strategy in the management of patients with complicated influenza.

Gastro-oesophageal reflux disease increases the risk of intensive care unit admittance and mechanical ventilation use among patients with chronic obstructive pulmonary disease: a nationwide population-based cohort study.

PubMed

Tsai, Chen-Liang; Lin, Yu-Huei; Wang, Meng-Ting; Chien, Li-Nien; Jeng, Chii; Chian, Chih-Feng; Perng, Wann-Cherng; Chiang, Chi-Huei; Chiou, Hung-Yi

2015-03-24

Gastro-oesophageal reflux disease (GORD) is common among chronic obstructive pulmonary disease (COPD) patients and may have a deleterious effect on COPD prognosis. However, few studies have investigated whether GORD increases the risk of severe outcomes such as intensive care unit (ICU) admittance or mechanical ventilator use among COPD patients. Propensity score matching by age, sex, comorbidities and COPD severity was used to match the 1,210 COPD patients with GORD sourced in this study to 2,420 COPD patients without GORD. The Kaplan-Meier method was used to explore the incidence of ICU admittance and machine ventilation with the log rank test being used to test for differences. Cox regression analysis was used to explore the risk of ICU admittance and mechanical ventilation use for patients with and without GORD. During the 12-month follow-up, GORD patients and non-GORD patients had 5.22 and 3.01 ICU admittances per 1000 person-months, and 4.34 and 2.41 mechanical ventilation uses per 1000 person-month, respectively. The log rank test revealed a difference in the incidence of ICU admittance and machine ventilation between the two cohorts. GORD was found to be an independent predicator of ICU admittance (adjusted hazard ratio (HRadj) 1.75, 95% confidence interval (CI) 1.28-2.38) and mechanical ventilation (HRadj 1.92, 95% CI 1.35-2.72). This is the first investigation to detect a significantly higher incidence rate and independently increased risk of admission to an ICU and mechanical ventilation use among COPD patients who subsequently developed GORD during the first year following their GORD diagnosis than COPD patients who did not develop GORD.

Long non-coding RNA FEZF1-AS1 is up-regulated and associated with poor prognosis in patients with cervical cancer.

PubMed

Zhang, H-H; Li, A-H

2018-06-01

Long noncoding RNA FEZF1-AS1 (FEZF1-AS1) has been showed to involve in a variety of cancers. However, its function and clinical significance in cervical cancer (CC) have not been investigated. The aim of this study was to explore the prognostic value of FEZF1-AS1 in CC patients. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used to determine the expression level of FEZF1-AS1 in CC specimens and adjacent normal cervical tissues. Association between FEZF1-AS1 expression and clinicopathological characteristics was analyzed x2-test. The Kaplan-Meier method was used to estimate survival curves, and the log-rank statistic was used to test the role of FEZF1-AS1 expression. The possibility of FEZF1-AS1 as a prognostic biomarker for CC was examined by Cox proportional hazard regression model. We found that FEZF1-AS1 expression levels were significantly higher in CC tissues compared with adjacent non-cancerous tissues (p < 0.01). High expressions of FEZF1-AS1 were significantly association with poorer histological grade (p = 0.004), positive distant metastasis (p = 0.002) and advanced FIGO stage (p = 0.001). Furthermore, patients with low FEZF1-AS1 expression lived shorter than those with high FEZF1-AS1 expression (Log-rank test, p < 0.0034). Cox regression analysis demonstrated that FEZF1-AS1 expression level was an independent prognostic factor for CC overall survival rates (p = 0.008). We firstly provided clinical evidence that FEZF1-AS1 may be a possible biomarker of poor prognosis in CC.

Impact of hypertension on early outcomes and long-term survival of patients undergoing aortic repair with Stanford A dissection.

PubMed

Merkle, Julia; Sabashnikov, Anton; Deppe, Antje-Christin; Zeriouh, Mohamed; Eghbalzadeh, Kaveh; Weber, Carolyn; Rahmanian, Parwis; Kuhn, Elmar; Madershahian, Navid; Kroener, Axel; Choi, Yeong-Hoon; Kuhn-Régnier, Ferdinand; Liakopoulos, Oliver; Wahlers, Thorsten

2018-04-01

Stanford A acute aortic dissection (AAD) is a life-threatening emergency, typically occurring in hypertensive patients, requiring immediate surgical repair. The aim of this study was to evaluate early outcomes and long-term survival of hypertensive patients in comparison to normotensive patients suffering from Stanford A AAD. In our center, 240 patients with Stanford A AAD underwent aortic surgical repair from January 2006 to April 2015. After statistical and logistic regression analysis, Kaplan-Meier survival estimation was performed, with up to 9-year follow-up. The proportion of hypertensive patients suffering from Stanford A AAD was 75.4% (n=181). There were only few statistically significant differences in terms of basic demographics, comorbidities, preoperative baseline and clinical characteristics of hypertensive patients in comparison to normotensive patients. Hypertensive patients were significantly older (p=0.008), more frequently received hemi-arch repair (p=0.028) and selective brain perfusion (p=0.001). Our study showed similar statistical results in terms of 30-day mortality (p=0.196), long-term overall cumulative survival of patients (Log-Rank p=0.506) and survival of patients free from cerebrovascular events (Log-Rank p=0.186). Furthermore, subgroup analysis for long-term survival in terms of men (Log-Rank p=0.853), women (Log-Rank p=0.227), patients under and above 65 years of age (Log-Rank p=0.188 and Log-Rank p=0.602, respectively) and patients undergoing one of the three types of aortic repair surgery showed similar results for normotensive and hypertensive patient groups. Subgroup analysis for long-term survival of patients free from cerebrovascular events for women, patients under 65 years of age and patients undergoing aortic arch repair showed significant differences between the two groups in favor of hypertensive patients. Hypertensive patients suffering from Stanford A AAD were older, more frequently received hemi-arch replacement and were not associated with increased risk of 30-day mortality and poorer long-term survival compared to normotensive patients.

Survival analysis for a large scale forest health issue: Missouri oak decline

Treesearch

C.W. Woodall; P.L. Grambsch; W. Thomas; W.K. Moser

2005-01-01

Survival analysis methodologies provide novel approaches for forest mortality analysis that may aid in detecting, monitoring, and mitigating of large-scale forest health issues. This study examined survivor analysis for evaluating a regional forest health issue - Missouri oak decline. With a statewide Missouri forest inventory, log-rank tests of the effects of...

A minimum version of log-rank test for testing the existence of cancer cure using relative survival data.

PubMed

Yu, Binbing

2012-01-01

Cancer survival is one of the most important measures to evaluate the effectiveness of treatment and early diagnosis. The ultimate goal of cancer research and patient care is the cure of cancer. As cancer treatments progress, cure becomes a reality for many cancers if patients are diagnosed early and get effective treatment. If a cure does exist for a certain type of cancer, it is useful to estimate the time of cure. For cancers that impose excess risk of mortality, it is informative to understand the difference in survival between cancer patients and the general cancer-free population. In population-based cancer survival studies, relative survival is the standard measure of excess mortality due to cancer. Cure is achieved when the survival of cancer patients is equivalent to that of the general population. This definition of cure is usually called the statistical cure, which is an important measure of burden due to cancer. In this paper, a minimum version of the log-rank test is proposed to test the equivalence of cancer patients' survival using the relative survival data. Performance of the proposed test is evaluated by simulation. Relative survival data from population-based cancer registries in SEER Program are used to examine patients' survival after diagnosis for various major cancer sites. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of Surgical Resection of the Primary Tumor on Overall Survival in Patients With Metastatic Pheochromocytoma or Sympathetic Paraganglioma.

PubMed

Roman-Gonzalez, Alejandro; Zhou, Shouhao; Ayala-Ramirez, Montserrat; Shen, Chan; Waguespack, Steven G; Habra, Mouhammed A; Karam, Jose A; Perrier, Nancy; Wood, Christopher G; Jimenez, Camilo

2018-07-01

To determine whether primary tumor resection in patients with metastatic pheochromocytoma or paraganglioma (PPG) is associated with longer overall survival (OS). Patients with metastatic PPG have poor survival outcomes. The impact of surgical resection of the primary tumor on OS is not known. We retrospectively studied patients with metastatic PPG treated at the University of Texas, MD Anderson Cancer Center from January 2000 through January 2015. Kaplan-Meier analysis with log-rank tests was used to compare OS among patients undergoing primary tumor resection and patients not treated surgically. Propensity score method was applied to adjust for selection bias using demographic, clinical, biochemical, genetic, imaging, and pathologic information. A total of 113 patients with metastatic PPG were identified. Eighty-nine (79%) patients had surgery and 24 (21%) patients did not. Median OS was longer in patients who had surgery than in patients who did not [148 months, 95% confidence interval (CI) 112.8-183.2 months vs 36 months, 95% CI 27.2-44.8 months; P < 0.001].Fifty-three (46%) patients had synchronous metastases; of these patients, those who had surgery had longer OS than those who did not (85 months, 95% CI 64.5-105.4 months vs 36 months, 95% CI 29.7-42.3 months; P < 0.001). Patients who had surgery had a similar ECOG performance status to the ones who did not (P = 0.1798, two sample t test; P = 0.2449, Wilcoxon rank sum test). Univariate and propensity score analysis confirmed that patients treated with surgery had longer OS than those not treated surgically irrespective of age, race, primary tumor size and location, number of metastatic sites, and genetic background (log-rank P < 0.001).In patients with hormonally active tumors (70.8%), the symptoms of catecholamine excess improved after surgery. However, the tumor burden was a more important determinant of OS than hormonal secretion. Primary tumor resection in patients with metastatic PPG appeared to be associated with improved OS. In patients with hormonally active tumors, surgical resection led to better blood pressure control.

The exponentiated Hencky-logarithmic strain energy. Part II: Coercivity, planar polyconvexity and existence of minimizers

NASA Astrophysics Data System (ADS)

Neff, Patrizio; Lankeit, Johannes; Ghiba, Ionel-Dumitrel; Martin, Robert; Steigmann, David

2015-08-01

We consider a family of isotropic volumetric-isochoric decoupled strain energies based on the Hencky-logarithmic (true, natural) strain tensor log U, where μ > 0 is the infinitesimal shear modulus, is the infinitesimal bulk modulus with the first Lamé constant, are dimensionless parameters, is the gradient of deformation, is the right stretch tensor and is the deviatoric part (the projection onto the traceless tensors) of the strain tensor log U. For small elastic strains, the energies reduce to first order to the classical quadratic Hencky energy which is known to be not rank-one convex. The main result in this paper is that in plane elastostatics the energies of the family are polyconvex for , extending a previous finding on its rank-one convexity. Our method uses a judicious application of Steigmann's polyconvexity criteria based on the representation of the energy in terms of the principal invariants of the stretch tensor U. These energies also satisfy suitable growth and coercivity conditions. We formulate the equilibrium equations, and we prove the existence of minimizers by the direct methods of the calculus of variations.

Exploring Empirical Rank-Frequency Distributions Longitudinally through a Simple Stochastic Process

PubMed Central

Finley, Benjamin J.; Kilkki, Kalevi

2014-01-01

The frequent appearance of empirical rank-frequency laws, such as Zipf’s law, in a wide range of domains reinforces the importance of understanding and modeling these laws and rank-frequency distributions in general. In this spirit, we utilize a simple stochastic cascade process to simulate several empirical rank-frequency distributions longitudinally. We focus especially on limiting the process’s complexity to increase accessibility for non-experts in mathematics. The process provides a good fit for many empirical distributions because the stochastic multiplicative nature of the process leads to an often observed concave rank-frequency distribution (on a log-log scale) and the finiteness of the cascade replicates real-world finite size effects. Furthermore, we show that repeated trials of the process can roughly simulate the longitudinal variation of empirical ranks. However, we find that the empirical variation is often less that the average simulated process variation, likely due to longitudinal dependencies in the empirical datasets. Finally, we discuss the process limitations and practical applications. PMID:24755621

Exploring empirical rank-frequency distributions longitudinally through a simple stochastic process.

PubMed

Finley, Benjamin J; Kilkki, Kalevi

2014-01-01

The frequent appearance of empirical rank-frequency laws, such as Zipf's law, in a wide range of domains reinforces the importance of understanding and modeling these laws and rank-frequency distributions in general. In this spirit, we utilize a simple stochastic cascade process to simulate several empirical rank-frequency distributions longitudinally. We focus especially on limiting the process's complexity to increase accessibility for non-experts in mathematics. The process provides a good fit for many empirical distributions because the stochastic multiplicative nature of the process leads to an often observed concave rank-frequency distribution (on a log-log scale) and the finiteness of the cascade replicates real-world finite size effects. Furthermore, we show that repeated trials of the process can roughly simulate the longitudinal variation of empirical ranks. However, we find that the empirical variation is often less that the average simulated process variation, likely due to longitudinal dependencies in the empirical datasets. Finally, we discuss the process limitations and practical applications.

Structure-preserving model reduction of large-scale logistics networks. Applications for supply chains

NASA Astrophysics Data System (ADS)

Scholz-Reiter, B.; Wirth, F.; Dashkovskiy, S.; Makuschewitz, T.; Schönlein, M.; Kosmykov, M.

2011-12-01

We investigate the problem of model reduction with a view to large-scale logistics networks, specifically supply chains. Such networks are modeled by means of graphs, which describe the structure of material flow. An aim of the proposed model reduction procedure is to preserve important features within the network. As a new methodology we introduce the LogRank as a measure for the importance of locations, which is based on the structure of the flows within the network. We argue that these properties reflect relative importance of locations. Based on the LogRank we identify subgraphs of the network that can be neglected or aggregated. The effect of this is discussed for a few motifs. Using this approach we present a meta algorithm for structure-preserving model reduction that can be adapted to different mathematical modeling frameworks. The capabilities of the approach are demonstrated with a test case, where a logistics network is modeled as a Jackson network, i.e., a particular type of queueing network.

Use of Internet Audience Measurement Data to Gauge Market Share for Online Health Information Services

PubMed Central

Benson, Dennis; LaCroix, Eve-Marie; Siegel, Elliot R; Fariss, Susan

2005-01-01

Background The transition to a largely Internet and Web-based environment for dissemination of health information has changed the health information landscape and the framework for evaluation of such activities. A multidimensional evaluative approach is needed. Objective This paper discusses one important dimension of Web evaluation—usage data. In particular, we discuss the collection and analysis of external data on website usage in order to develop a better understanding of the health information (and related US government information) market space, and to estimate the market share or relative levels of usage for National Library of Medicine (NLM) and National Institutes of Health (NIH) websites compared to other health information providers. Methods The primary method presented is Internet audience measurement based on Web usage by external panels of users and assembled by private vendors—in this case, comScore. A secondary method discussed is Web usage based on Web log software data. The principle metrics for both methods are unique visitors and total pages downloaded per month. Results NLM websites (primarily MedlinePlus and PubMed) account for 55% to 80% of total NIH website usage depending on the metric used. In turn, NIH.gov top-level domain usage (inclusive of NLM) ranks second only behind WebMD in the US domestic home health information market and ranks first on a global basis. NIH.gov consistently ranks among the top three or four US government top-level domains based on global Web usage. On a site-specific basis, the top health information websites in terms of global usage appear to be WebMD, MSN Health, PubMed, Yahoo! Health, AOL Health, and MedlinePlus. Based on MedlinePlus Web log data and external Internet audience measurement data, the three most heavily used cancer-centric websites appear to be www.cancer.gov (National Cancer Institute), www.cancer.org (American Cancer Society), and www.breastcancer.org (non-profit organization). Conclusions Internet audience measurement has proven useful to NLM, with significant advantages compared to sole reliance on usage data from Web log software. Internet audience data has helped NLM better understand the relative usage of NLM and NIH websites in the intersection of the health information and US government information market sectors, which is the primary market intersector for NLM and NIH. However important, Web usage is only one dimension of a complete Web evaluation framework, and other primary research methods, such as online user surveys, usability tests, and focus groups, are also important for comprehensive evaluation that includes qualitative elements, such as user satisfaction and user friendliness, as well as quantitative indicators of website usage. PMID:15998622

Effect of amiodarone therapy on mortality in patients with left ventricular dysfunction and asymptomatic complex ventricular arrhythmias: Argentine Pilot Study of Sudden Death and Amiodarone (EPAMSA).

PubMed

Garguichevich, J J; Ramos, J L; Gambarte, A; Gentile, A; Hauad, S; Scapin, O; Sirena, J; Tibaldi, M; Toplikar, J

1995-09-01

The efficiency of prophylactic antiarrhythmic treatment with amiodarone in reducing 1-year mortality in patients with reduced left ventricular ejection fraction ( < 35%) and asymptomatic ventricular arrhythmias (Lown classes 2 and 4) was investigated in a prospective, multicenter, randomized, controlled study. Among 127 patients who entered the study, 61 were assigned to no antiarrhythmic therapy (control group [CG] and 66 to amiodarone treatment (amiodarone group [AG]). Amiodarone was administered at a dosage of 800 mg/day for 2 weeks followed by 400 mg/day thereafter. A 12-month follow-up was completed for 106 patients (57 in the AG and 49 in the CG). Amiodarone reduced the overall mortality rate, which was 10.5% in the AG versus 28.6% in the CG (odds ratio [OR] 0.29; 95% confidence interval [CI] 0.10 to 0.84; log-rank test 0.02) and sudden death rate, which was 7.0% in the AG versus 20.4% in the CG (OR 0.29; 95% CI 0.08 to 1.00; log-rank test 0.04). Side effects were rare, and in only three patients did amiodarone treatment have to be discontinued.

TENSOR DECOMPOSITIONS AND SPARSE LOG-LINEAR MODELS

PubMed Central

Johndrow, James E.; Bhattacharya, Anirban; Dunson, David B.

2017-01-01

Contingency table analysis routinely relies on log-linear models, with latent structure analysis providing a common alternative. Latent structure models lead to a reduced rank tensor factorization of the probability mass function for multivariate categorical data, while log-linear models achieve dimensionality reduction through sparsity. Little is known about the relationship between these notions of dimensionality reduction in the two paradigms. We derive several results relating the support of a log-linear model to nonnegative ranks of the associated probability tensor. Motivated by these findings, we propose a new collapsed Tucker class of tensor decompositions, which bridge existing PARAFAC and Tucker decompositions, providing a more flexible framework for parsimoniously characterizing multivariate categorical data. Taking a Bayesian approach to inference, we illustrate empirical advantages of the new decompositions. PMID:29332971

Optimizing Earth Data Search Ranking using Deep Learning and Real-time User Behaviour

NASA Astrophysics Data System (ADS)

Jiang, Y.; Yang, C. P.; Armstrong, E. M.; Huang, T.; Moroni, D. F.; McGibbney, L. J.; Greguska, F. R., III

2017-12-01

Finding Earth science data has been a challenging problem given both the quantity of data available and the heterogeneity of the data across a wide variety of domains. Current search engines in most geospatial data portals tend to induce end users to focus on one single data characteristic dimension (e.g., term frequency-inverse document frequency (TF-IDF) score, popularity, release date, etc.). This approach largely fails to take account of users' multidimensional preferences for geospatial data, and hence may likely result in a less than optimal user experience in discovering the most applicable dataset out of a vast range of available datasets. With users interacting with search engines, sufficient information is already hidden in the log files. Compared with explicit feedback data, information that can be derived/extracted from log files is virtually free and substantially more timely. In this dissertation, I propose an online deep learning framework that can quickly update the learning function based on real-time user clickstream data. The contributions of this framework include 1) a log processor that can ingest, process and create training data from web logs in a real-time manner; 2) a query understanding module to better interpret users' search intent using web log processing results and metadata; 3) a feature extractor that identifies ranking features representing users' multidimensional interests of geospatial data; and 4) a deep learning based ranking algorithm that can be trained incrementally using user behavior data. The search ranking results will be evaluated using precision at K and normalized discounted cumulative gain (NDCG).

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

PubMed

Edgar, Robert C

2004-01-01

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

Investigating a Judgemental Rank-Ordering Method for Maintaining Standards in UK Examinations

ERIC Educational Resources Information Center

Black, Beth; Bramley, Tom

2008-01-01

A new judgemental method of equating raw scores on two tests, based on rank-ordering scripts from both tests, has been developed by Bramley. The rank-ordering method has potential application as a judgemental standard-maintaining mechanism, because given a mark on one test (e.g. the A grade boundary mark), the equivalent mark (i.e. at the same…

Abnormal sleep duration associated with hastened depressive recurrence in bipolar disorder.

PubMed

Gershon, Anda; Do, Dennis; Satyanarayana, Satyanand; Shah, Saloni; Yuen, Laura D; Hooshmand, Farnaz; Miller, Shefali; Wang, Po W; Ketter, Terence A

2017-08-15

Abnormal sleep duration (ASD, <6 or ≥9h) is common in bipolar disorder (BD), and often persists beyond acute mood episodes. Few longitudinal studies have examined the ASD's impact upon BD illness course. The current study examined the longitudinal impact of ASD upon bipolar depressive recurrence/recovery. Outpatients referred to the Stanford BD Clinic during 2000-2011 were assessed with the Systematic Treatment Enhancement Program for BD (STEP-BD) Affective Disorders Evaluation at baseline, and with the Clinical Monitoring Form at monthly follow-ups for up to two years of naturalistic treatment. Prevalence and clinical correlates of ASD in 93 recovered (euthymic ≥8 weeks) and 153 depressed BD patients were assessed. Kaplan-Meier analyses (Log-Rank tests) assessed relationships between baseline ASD and longitudinal depressive severity, with Cox Proportional Hazard analyses assessing potential mediators. ASD was only half as common among recovered versus depressed BD outpatients, but was significantly associated with hastened depressive recurrence (Log-Rank p=0.007), mediated by lifetime anxiety disorder and attenuated by lifetime history of psychosis, and had only a non-significant tendency towards association with delayed depressive recovery (Log-Rank p=0.07). In both recovered and depressed BD outpatients, baseline ASD did not have significant association with any baseline BD illness characteristic. Self-reported sleep duration. Limited generalizability beyond our predominately white, female, educated, insured American BD specialty clinic sample. Baseline ASD among recovered BD patients may be a risk marker for hastened depressive recurrence, suggesting it could be an important therapeutic target between mood episodes. Copyright © 2017 Elsevier B.V. All rights reserved.

Frailty Index Developed From a Cancer-Specific Geriatric Assessment and the Association With Mortality Among Older Adults With Cancer.

PubMed

Guerard, Emily J; Deal, Allison M; Chang, YunKyung; Williams, Grant R; Nyrop, Kirsten A; Pergolotti, Mackenzi; Muss, Hyman B; Sanoff, Hanna K; Lund, Jennifer L

2017-07-01

Background: An objective measure is needed to identify frail older adults with cancer who are at increased risk for poor health outcomes. The primary objective of this study was to develop a frailty index from a cancer-specific geriatric assessment (GA) and evaluate its ability to predict all-cause mortality among older adults with cancer. Patients and Methods: Using a unique and novel data set that brings together GA data with cancer-specific and long-term mortality data, we developed the Carolina Frailty Index (CFI) from a cancer-specific GA based on the principles of deficit accumulation. CFI scores (range, 0-1) were categorized as robust (0-0.2), pre-frail (0.2-0.35), and frail (>0.35). The primary outcome for evaluating predictive validity was all-cause mortality. The Kaplan-Meier method and log-rank tests were used to compare survival between frailty groups, and Cox proportional hazards regression models were used to evaluate associations. Results: In our sample of 546 older adults with cancer, the median age was 72 years, 72% were women, 85% were white, and 47% had a breast cancer diagnosis. Overall, 58% of patients were robust, 24% were pre-frail, and 18% were frail. The estimated 5-year survival rate was 72% in robust patients, 58% in pre-frail patients, and 34% in frail patients (log-rank test, P <.0001). Frail patients had more than a 2-fold increased risk of all-cause mortality compared with robust patients (adjusted hazard ratio, 2.36; 95% CI, 1.51-3.68). Conclusions: The CFI was predictive of all-cause mortality in older adults with cancer, a finding that was independent of age, sex, cancer type and stage, and number of medical comorbidities. The CFI has the potential to become a tool that oncologists can use to objectively identify frailty in older adults with cancer. Copyright © 2017 by the National Comprehensive Cancer Network.

Positive surgical margins in robot-assisted partial nephrectomy: a multi-institutional analysis of oncologic outcomes (leave no tumor behind).

PubMed

Khalifeh, Ali; Kaouk, Jihad H; Bhayani, Sam; Rogers, Craig; Stifelman, Michael; Tanagho, Youssef S; Kumar, Ramesh; Gorin, Michael A; Sivarajan, Ganesh; Samarasekera, Dinesh; Allaf, Mohamad E

2013-11-01

Expanding indications for robot-assisted partial nephrectomy raise major oncologic concerns for positive surgical margins. Previous reports showed no correlation between positive surgical margins and oncologic outcomes. We report a multi-institutional experience with the oncologic outcomes of positive surgical margins on robot-assisted partial nephrectomy. Pathological and clinical followup data were reviewed from an institutional review board approved, prospectively maintained joint database from 5 institutions. Tumors with malignant pathology were isolated and statistically analyzed for demographics and oncologic followup. The log rank test was used to compare recurrence-free and metastasis-free survival between patients with positive and negative surgical margins. The proportional hazards method was used to assess the influence of multiple factors, including positive surgical margins, on recurrence and metastasis. A total of 943 robot-assisted partial nephrectomies for malignant tumors were successfully completed. Of the patients 21 (2.2%) had positive surgical margins on final pathological assessment, resulting in 2 groups, including the 21 with positive surgical margins and 922 with negative surgical margins. Positive surgical margin cases had higher recurrence and metastasis rates (p<0.001). As projected by the Kaplan-Meier method in the population as a whole at followup out to 63.6 months, 5-year recurrence-free and metastasis-free survival was 94.8% and 97.5%, respectively. There was a statistically significant difference in recurrence-free and metastasis-free survival between patients with positive and negative surgical margins (log rank test<0.001), which favored negative surgical margins. Positive surgical margins showed an 18.4-fold higher HR for recurrence when adjusted for multiple tumors, tumor size, tumor growth pattern and pathological stage. Positive surgical margins on final pathological evaluation increase the HR of recurrence and metastasis. In addition to pathological and molecular tumor characteristics, this should be considered to plan appropriate management. Copyright © 2013 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

HIV-1 RNA May Decline More Slowly in Semen than in Blood following Initiation of Efavirenz-Based Antiretroviral Therapy

PubMed Central

Graham, Susan M.; Holte, Sarah E.; Dragavon, Joan A.; Ramko, Kelly M.; Mandaliya, Kishor N.; McClelland, R. Scott; Peshu, Norbert M.; Sanders, Eduard J.; Krieger, John N.; Coombs, Robert W.

2012-01-01

Objectives Antiretroviral therapy (ART) decreases HIV-1 RNA levels in semen and reduces sexual transmission from HIV-1-infected men. Our objective was to study the time course and magnitude of seminal HIV-1 RNA decay after initiation of efavirenz-based ART among 13 antiretroviral-naïve Kenyan men. Methods HIV-1 RNA was quantified (lower limit of detection, 120 copies/mL) in blood and semen at baseline and over the first month of ART. Median log10 HIV-1 RNA was compared at each time-point using Wilcoxon Signed Rank tests. Perelson’s two-phase viral decay model and nonlinear random effects were used to compare decay rates in blood and semen. Results Median baseline HIV-1 RNA was 4.40 log10 copies/mL in blood (range, 3.20–5.08 log10 copies/mL) and 3.69 log10 copies/mL in semen (range, <2.08–4.90 log10 copies/mL). The median reduction in HIV-1 RNA by day 28 was 1.90 log10 copies/mL in blood (range, 0.56–2.68 log10 copies/mL) and 1.36 log10 copies/mL in semen (range, 0–2.66 log10 copies/mL). ART led to a decrease from baseline by day 7 in blood and day 14 in semen (p = 0.005 and p = 0.006, respectively). The initial modeled decay rate was slower in semen than in blood (p = 0.06). There was no difference in second-phase decay rates between blood and semen. Conclusions Efavirenz-based ART reduced HIV-1 RNA levels more slowly in semen than in blood. Although this difference was of borderline significance in this small study, our observations suggest that there is suboptimal suppression of seminal HIV-1 RNA for some men in the early weeks of treatment. PMID:22912795

Inhibition of plasmin-mediated TAFI activation may affect development but not progression of abdominal aortic aneurysms

PubMed Central

Bridge, Katherine; Revill, Charlotte; Macrae, Fraser; Bailey, Marc; Yuldasheva, Nadira; Wheatcroft, Stephen; Butlin, Roger; Foster, Richard; Scott, D. Julian; Gils, Ann; Ariёns, Robert

2017-01-01

Objective Thrombin-activatable fibrinolysis inhibitor (TAFI) reduces the breakdown of fibrin clots through its action as an indirect inhibitor of plasmin. Studies in TAFI-deficient mice have implicated a potential role for TAFI in Abdominal Aortic Aneurysm (AAA) disease. The role of TAFI inhibition on AAA formation in adult ApoE-/- mice is unknown. The aim of this paper was to investigate the effects of TAFI inhibition on AAA development and progression. Methods Using the Angiotensin II model of AAA, male ApoE-/- mice were infused with Angiotensin II 750ng/kg/min with or without a monoclonal antibody inhibitor of plasmin-mediated activation of TAFI, MA-TCK26D6, or a competitive small molecule inhibitor of TAFI, UK-396082. Results Inhibition of TAFI in the Angiotensin II model resulted in a decrease in the mortality associated with AAA rupture (from 40.0% to 16.6% with MA-TCK26D6 (log-rank Mantel Cox test p = 0.16), and 8.3% with UK-396082 (log-rank Mantel Cox test p = 0.05)). Inhibition of plasmin-mediated TAFI activation reduced the incidence of AAA from 52.4% to 30.0%. However, late treatment with MA-TCK26D6 once AAA were already established had no effect on the progression of AAA in this model. Conclusions The formation of intra-mural thrombus is responsible for the dissection and early rupture in the angiotensin II model of AAA, and this process can be prevented through inhibition of TAFI. Late treatment with a TAFI inhibitor does not prevent AAA progression. These data may indicate a role for inhibition of plasmin-mediated TAFI activation in the early stages of AAA development, but not in its progression. PMID:28472123

Estimating sales and sales market share from sales rank data for consumer appliances

NASA Astrophysics Data System (ADS)

Touzani, Samir; Van Buskirk, Robert

2016-06-01

Our motivation in this work is to find an adequate probability distribution to fit sales volumes of different appliances. This distribution allows for the translation of sales rank into sales volume. This paper shows that the log-normal distribution and specifically the truncated version are well suited for this purpose. We demonstrate that using sales proxies derived from a calibrated truncated log-normal distribution function can be used to produce realistic estimates of market average product prices, and product attributes. We show that the market averages calculated with the sales proxies derived from the calibrated, truncated log-normal distribution provide better market average estimates than sales proxies estimated with simpler distribution functions.

Use of Internet audience measurement data to gauge market share for online health information services.

PubMed

Wood, Fred B; Benson, Dennis; LaCroix, Eve-Marie; Siegel, Elliot R; Fariss, Susan

2005-07-01

The transition to a largely Internet and Web-based environment for dissemination of health information has changed the health information landscape and the framework for evaluation of such activities. A multidimensional evaluative approach is needed. This paper discusses one important dimension of Web evaluation-usage data. In particular, we discuss the collection and analysis of external data on website usage in order to develop a better understanding of the health information (and related US government information) market space, and to estimate the market share or relative levels of usage for National Library of Medicine (NLM) and National Institutes of Health (NIH) websites compared to other health information providers. The primary method presented is Internet audience measurement based on Web usage by external panels of users and assembled by private vendors-in this case, comScore. A secondary method discussed is Web usage based on Web log software data. The principle metrics for both methods are unique visitors and total pages downloaded per month. NLM websites (primarily MedlinePlus and PubMed) account for 55% to 80% of total NIH website usage depending on the metric used. In turn, NIH.gov top-level domain usage (inclusive of NLM) ranks second only behind WebMD in the US domestic home health information market and ranks first on a global basis. NIH.gov consistently ranks among the top three or four US government top-level domains based on global Web usage. On a site-specific basis, the top health information websites in terms of global usage appear to be WebMD, MSN Health, PubMed, Yahoo! Health, AOL Health, and MedlinePlus. Based on MedlinePlus Web log data and external Internet audience measurement data, the three most heavily used cancer-centric websites appear to be www.cancer.gov (National Cancer Institute), www.cancer.org (American Cancer Society), and www.breastcancer.org (non-profit organization). Internet audience measurement has proven useful to NLM, with significant advantages compared to sole reliance on usage data from Web log software. Internet audience data has helped NLM better understand the relative usage of NLM and NIH websites in the intersection of the health information and US government information market sectors, which is the primary market intersector for NLM and NIH. However important, Web usage is only one dimension of a complete Web evaluation framework, and other primary research methods, such as online user surveys, usability tests, and focus groups, are also important for comprehensive evaluation that includes qualitative elements, such as user satisfaction and user friendliness, as well as quantitative indicators of website usage.

Fast iterative solution of the Bethe-Salpeter eigenvalue problem using low-rank and QTT tensor approximation

NASA Astrophysics Data System (ADS)

Benner, Peter; Dolgov, Sergey; Khoromskaia, Venera; Khoromskij, Boris N.

2017-04-01

In this paper, we propose and study two approaches to approximate the solution of the Bethe-Salpeter equation (BSE) by using structured iterative eigenvalue solvers. Both approaches are based on the reduced basis method and low-rank factorizations of the generating matrices. We also propose to represent the static screen interaction part in the BSE matrix by a small active sub-block, with a size balancing the storage for rank-structured representations of other matrix blocks. We demonstrate by various numerical tests that the combination of the diagonal plus low-rank plus reduced-block approximation exhibits higher precision with low numerical cost, providing as well a distinct two-sided error estimate for the smallest eigenvalues of the Bethe-Salpeter operator. The complexity is reduced to O (Nb2) in the size of the atomic orbitals basis set, Nb, instead of the practically intractable O (Nb6) scaling for the direct diagonalization. In the second approach, we apply the quantized-TT (QTT) tensor representation to both, the long eigenvectors and the column vectors in the rank-structured BSE matrix blocks, and combine this with the ALS-type iteration in block QTT format. The QTT-rank of the matrix entities possesses almost the same magnitude as the number of occupied orbitals in the molecular systems, No

The 5-year incidence of bleb-related infection and its risk factors after filtering surgeries with adjunctive mitomycin C: collaborative bleb-related infection incidence and treatment study 2.

PubMed

Yamamoto, Tetsuya; Sawada, Akira; Mayama, Chihiro; Araie, Makoto; Ohkubo, Shinji; Sugiyama, Kazuhisa; Kuwayama, Yasuaki

2014-05-01

To report the 5-year incidence of bleb-related infection after mitomycin C-augmented glaucoma filtering surgery and to investigate the risk factors for infections. Prospective, observational cohort study. A total of 1098 eyes of 1098 glaucoma patients who had undergone mitomycin C-augmented trabeculectomy or trabeculectomy combined with phacoemulsification and intraocular lens implantation performed at 34 clinical centers. Patients were followed up at 6-month intervals for 5 years, with special attention given to bleb-related infections. The follow-up data were analyzed via Kaplan-Meier survival analysis and the Cox proportional hazards model. Incidence of bleb-related infection over 5 years and risk factors for infections. Of the 1098 eyes, a bleb-related infection developed in 21 eyes. Kaplan-Meier survival analysis revealed that the incidence of bleb-related infection was 2.2±0.5% (cumulative incidence ± standard error) at the 5-year follow-up for all cases, whereas it was 7.9±3.1% and 1.7±0.4% for cases with and without a history of bleb leakage, respectively (P = 0.000, log-rank test). When only eyes with a well-functioning bleb were counted, it was 3.9±1.0%. No differences were found between the trabeculectomy cases and the combined surgery cases (P = 0.398, log-rank test) or between cases with a fornix-based flap and those with a limbal-based flap (P = 0.651, log-rank test). The Cox model revealed that a history of bleb leakage and younger age were risk factors for infections. The 5-year cumulative incidence of bleb-related infection was 2.2±0.5% in eyes treated with mitomycin C-augmented trabeculectomy or trabeculectomy combined with phacoemulsification and intraocular lens implantation in our prospective, multicenter study. Bleb leakage and younger age were the main risk factors for infections. Copyright © 2014 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

A double-blind placebo-controlled, randomised study comparing gemcitabine and marimastat with gemcitabine and placebo as first line therapy in patients with advanced pancreatic cancer

PubMed Central

Bramhall, S R; Schulz, J; Nemunaitis, J; Brown, P D; Baillet, M; Buckels, J A C

2002-01-01

Pancreatic cancer is the fifth most common cause of cancer death in the western world and the prognosis for unresectable disease remains poor. Recent advances in conventional chemotherapy and the development of novel ‘molecular’ treatment strategies with different toxicity profiles warrant investigation as combination treatment strategies. This randomised study in pancreatic cancer compares marimastat (orally administered matrix metalloproteinase inhibitor) in combination with gemcitabine to gemcitabine alone. Two hundred and thirty-nine patients with unresectable pancreatic cancer were randomised to receive gemcitabine (1000 mg m−2) in combination with either marimastat or placebo. The primary end-point was survival. Objective tumour response and duration of response, time to treatment failure and disease progression, quality of life and safety were also assessed. There was no significant difference in survival between gemcitabine and marimastat and gemcitabine and placebo (P=0.95 log-rank test). Median survival times were 165.5 and 164 days and 1-year survival was 18% and 17% respectively. There were no significant differences in overall response rates (11 and 16% respectively), progression-free survival (P=0.68 log-rank test) or time to treatment failure (P=0.70 log-rank test) between the treatment arms. The gemcitabine and marimastat combination was well tolerated with only 2.5% of patients withdrawn due to presumed marimastat toxicity. Grade 3 or 4 musculoskeletal toxicities were reported in only 4% of the marimastat treated patients, although 59% of marimastat treated patients reported some musculoskeletal events. The results of this study provide no evidence to support a combination of marimastat with gemcitabine in patients with advanced pancreatic cancer. The combination of marimastat with gemcitabine was well tolerated. Further studies of marimastat as a maintenance treatment following a response or stable disease on gemcitabine may be justified. British Journal of Cancer (2002) 87, 161–167. doi:10.1038/sj.bjc.6600446 www.bjcancer.com © 2002 Cancer Research UK PMID:12107836

Analysis of Duplicated Multiple-Samples Rank Data Using the Mack-Skillings Test.

PubMed

Carabante, Kennet Mariano; Alonso-Marenco, Jose Ramon; Chokumnoyporn, Napapan; Sriwattana, Sujinda; Prinyawiwatkul, Witoon

2016-07-01

Appropriate analysis for duplicated multiple-samples rank data is needed. This study compared analysis of duplicated rank preference data using the Friedman versus Mack-Skillings tests. Panelists (n = 125) ranked twice 2 orange juice sets: different-samples set (100%, 70%, vs. 40% juice) and similar-samples set (100%, 95%, vs. 90%). These 2 sample sets were designed to get contrasting differences in preference. For each sample set, rank sum data were obtained from (1) averaged rank data of each panelist from the 2 replications (n = 125), (2) rank data of all panelists from each of the 2 separate replications (n = 125 each), (3) jointed rank data of all panelists from the 2 replications (n = 125), and (4) rank data of all panelists pooled from the 2 replications (n = 250); rank data (1), (2), and (4) were separately analyzed by the Friedman test, although those from (3) by the Mack-Skillings test. The effect of sample sizes (n = 10 to 125) was evaluated. For the similar-samples set, higher variations in rank data from the 2 replications were observed; therefore, results of the main effects were more inconsistent among methods and sample sizes. Regardless of analysis methods, the larger the sample size, the higher the χ(2) value, the lower the P-value (testing H0 : all samples are not different). Analyzing rank data (2) separately by replication yielded inconsistent conclusions across sample sizes, hence this method is not recommended. The Mack-Skillings test was more sensitive than the Friedman test. Furthermore, it takes into account within-panelist variations and is more appropriate for analyzing duplicated rank data. © 2016 Institute of Food Technologists®

Survival analysis in telemetry studies: The staggered entry design

USGS Publications Warehouse

Pollock, K.H.; Winterstein, S.R.; Bunck, C.M.; Curtis, P.D.

1989-01-01

A simple description of the Kaplan-Meier procedure is presented with an example using northern bobwhite quail survival data. The Kaplan- Meier procedure was then generalized to allow gradual (or staggered) entry of animals into the study, allowing animals being lost (or censored) due to radio failure, radio loss, or emigration of the animal from the study area. Additionally, the applicability and generalization of the log rank test, a test to compare two survival distributions, was demonstrated. Computer program was developed and is available from authors.

Identification of significant features by the Global Mean Rank test.

PubMed

Klammer, Martin; Dybowski, J Nikolaj; Hoffmann, Daniel; Schaab, Christoph

2014-01-01

With the introduction of omics-technologies such as transcriptomics and proteomics, numerous methods for the reliable identification of significantly regulated features (genes, proteins, etc.) have been developed. Experimental practice requires these tests to successfully deal with conditions such as small numbers of replicates, missing values, non-normally distributed expression levels, and non-identical distributions of features. With the MeanRank test we aimed at developing a test that performs robustly under these conditions, while favorably scaling with the number of replicates. The test proposed here is a global one-sample location test, which is based on the mean ranks across replicates, and internally estimates and controls the false discovery rate. Furthermore, missing data is accounted for without the need of imputation. In extensive simulations comparing MeanRank to other frequently used methods, we found that it performs well with small and large numbers of replicates, feature dependent variance between replicates, and variable regulation across features on simulation data and a recent two-color microarray spike-in dataset. The tests were then used to identify significant changes in the phosphoproteomes of cancer cells induced by the kinase inhibitors erlotinib and 3-MB-PP1 in two independently published mass spectrometry-based studies. MeanRank outperformed the other global rank-based methods applied in this study. Compared to the popular Significance Analysis of Microarrays and Linear Models for Microarray methods, MeanRank performed similar or better. Furthermore, MeanRank exhibits more consistent behavior regarding the degree of regulation and is robust against the choice of preprocessing methods. MeanRank does not require any imputation of missing values, is easy to understand, and yields results that are easy to interpret. The software implementing the algorithm is freely available for academic and commercial use.

Preventive dental management of osteonecrosis of the jaws related to zoledronic acid treatment.

PubMed

Coello-Suanzes, J A; Rollon-Ugalde, V; Castaño-Seiquer, A; Lledo-Villar, E; Herce-Lopez, J; Infante-Cossio, P; Rollon-Mayordomo, A

2018-02-07

To evaluate the effect of preventive dental management on reducing the incidence and delaying the onset of bisphosphonate-related osteonecrosis of the jaw (BRONJ) in patients treated with intravenous zoledronic acid (ZA). This single-center clinical study included 255 cancer patients monitored over a 6-year period. Patients received dental treatment prior (Group A) or after (Group B) the initiation of ZA therapy. Dental treatments performed, incidence proportion (IP) and incidence rate (IR) in both groups were analyzed using significance tests. BRONJ onset were estimated using the Kaplan-Meier estimator and log-rank test. Independent risk factors to develop BRONJ were evaluated using Cox regression analysis models. 37 patients suffered from BRONJ (IP=14.5%), 7.3% in group A and 36.5% in group B (p=0.000). The IR was 0.007 patients/month in group B and 0.004 in group A. BRONJ free survival at 3 years were 97% in group A and 66% in group B. Survival curves were significant (p=0.056) according to log-rank test. Multivariate Cox models showed that dental extractions (p=0.000) were significant. BRONJ occurred significantly in patients who underwent dental extractions after the initiation of ZA and did not accomplish a preventive dental program. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A combined QSAR and partial order ranking approach to risk assessment.

PubMed

Carlsen, L

2006-04-01

QSAR generated data appear as an attractive alternative to experimental data as foreseen in the proposed new chemicals legislation REACH. A preliminary risk assessment for the aquatic environment can be based on few factors, i.e. the octanol-water partition coefficient (Kow), the vapour pressure (VP) and the potential biodegradability of the compound in combination with the predicted no-effect concentration (PNEC) and the actual tonnage in which the substance is produced. Application of partial order ranking, allowing simultaneous inclusion of several parameters leads to a mutual prioritisation of the investigated substances, the prioritisation possibly being further analysed through the concept of linear extensions and average ranks. The ranking uses endpoint values (log Kow and log VP) derived from strictly linear 'noise-deficient' QSAR models as input parameters. Biodegradation estimates were adopted from the BioWin module of the EPI Suite. The population growth impairment of Tetrahymena pyriformis was used as a surrogate for fish lethality.

Unbiased split variable selection for random survival forests using maximally selected rank statistics.

PubMed

Wright, Marvin N; Dankowski, Theresa; Ziegler, Andreas

2017-04-15

The most popular approach for analyzing survival data is the Cox regression model. The Cox model may, however, be misspecified, and its proportionality assumption may not always be fulfilled. An alternative approach for survival prediction is random forests for survival outcomes. The standard split criterion for random survival forests is the log-rank test statistic, which favors splitting variables with many possible split points. Conditional inference forests avoid this split variable selection bias. However, linear rank statistics are utilized by default in conditional inference forests to select the optimal splitting variable, which cannot detect non-linear effects in the independent variables. An alternative is to use maximally selected rank statistics for the split point selection. As in conditional inference forests, splitting variables are compared on the p-value scale. However, instead of the conditional Monte-Carlo approach used in conditional inference forests, p-value approximations are employed. We describe several p-value approximations and the implementation of the proposed random forest approach. A simulation study demonstrates that unbiased split variable selection is possible. However, there is a trade-off between unbiased split variable selection and runtime. In benchmark studies of prediction performance on simulated and real datasets, the new method performs better than random survival forests if informative dichotomous variables are combined with uninformative variables with more categories and better than conditional inference forests if non-linear covariate effects are included. In a runtime comparison, the method proves to be computationally faster than both alternatives, if a simple p-value approximation is used. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

A hybrid framework for reservoir characterization using fuzzy ranking and an artificial neural network

NASA Astrophysics Data System (ADS)

Wang, Baijie; Wang, Xin; Chen, Zhangxin

2013-08-01

Reservoir characterization refers to the process of quantitatively assigning reservoir properties using all available field data. Artificial neural networks (ANN) have recently been introduced to solve reservoir characterization problems dealing with the complex underlying relationships inherent in well log data. Despite the utility of ANNs, the current limitation is that most existing applications simply focus on directly implementing existing ANN models instead of improving/customizing them to fit the specific reservoir characterization tasks at hand. In this paper, we propose a novel intelligent framework that integrates fuzzy ranking (FR) and multilayer perceptron (MLP) neural networks for reservoir characterization. FR can automatically identify a minimum subset of well log data as neural inputs, and the MLP is trained to learn the complex correlations from the selected well log data to a target reservoir property. FR guarantees the selection of the optimal subset of representative data from the overall well log data set for the characterization of a specific reservoir property; and, this implicitly improves the modeling and predication accuracy of the MLP. In addition, a growing number of industrial agencies are implementing geographic information systems (GIS) in field data management; and, we have designed the GFAR solution (GIS-based FR ANN Reservoir characterization solution) system, which integrates the proposed framework into a GIS system that provides an efficient characterization solution. Three separate petroleum wells from southwestern Alberta, Canada, were used in the presented case study of reservoir porosity characterization. Our experiments demonstrate that our method can generate reliable results.

Genetic Polymorphisms in RNA Binding Proteins Contribute to Breast Cancer Survival

PubMed Central

Upadhyay, Rohit; Sanduja, Sandhya; Kaza, Vimala; Dixon, Dan A.

2012-01-01

The RNA-binding proteins TTP and HuR control expression of numerous genes associated with breast cancer pathogenesis by regulating mRNA stability. However, the role of genetic variation in TTP (ZFP36) and HuR (ELAVL1) genes is unknown in breast cancer prognosis. A total of 251 breast cancer patients (170 Caucasians and 81 African-Americans) were enrolled and followed-up from 2001 to 2011 (or until death). Genotyping was performed for 10 SNPs in ZFP36 and 7 in ELAVL1 genes. On comparing both races with one another, significant differences were found for clinical and genetic variables. The influence of genetic polymorphisms on survival was analyzed by using Cox-regression, Kaplan-Meier analysis, and the log-rank test. Univariate (Kaplan-Meier/Cox-regression) and multivariate (Cox-regression) analysis showed that the TTP gene polymorphism ZFP36*2 A>G was significantly associated with poor prognosis of Caucasian patients (HR = 2.03; 95% CI = 1.09–3.76; P = 0.025; log-rank P = 0.022). None of the haplotypes, but presence of more than six risk genotypes in Caucasian patients, was significantly associated with poor prognosis (HR=2.42; 95% CI=1.17–4.99; P = 0.017; log-rank P = 0.007). The effect of ZFP36*2 A>G on gene expression was evaluated from patients' tissue samples. Both TTP mRNA and protein expression was significantly decreased in ZFP36*2 G allele carriers compared to A allele homozygotes. Conversely, upregulation of the TTP-target gene COX-2 was observed ZFP36*2 G allele carriers. Through its ability to attenuate TTP gene expression, the ZFP36*2 A>G gene polymorphism has appeared as a novel prognostic breast cancer marker in Caucasian patients. PMID:22907529

Functional Role of CLIC1 Ion Channel in Glioblastoma-Derived Stem/Progenitor Cells

PubMed Central

2013-01-01

Background Chloride channels are physiologically involved in cell division and motility. Chloride intracellular channel 1 (CLIC1) is overexpressed in a variety of human solid tumors compared with normal tissues, suggesting a potential involvement of CLIC1 in the regulation of tumorigenesis. This led us to investigate the role of CLIC1 in gliomagenesis. Methods We used the neurosphere system to isolate stem/progenitor cells from human glioblastomas (GBMs). CLIC1 targeting in GBM neurospheres was achieved by both lentiviral-mediated short-hairpin RNA transduction and CLIC1 antibody treatment, and its effect on stem-like properties was analyzed in vitro by proliferation and clonogenic assays and in vivo by orthotopic injection in immunocompromised mice. Channel activity was studied by perforated patch clamp technique. Differences in expression were analyzed by analysis of variance with Tamhane’s multiple comparison test. Kaplan–Meier analyses and log-rank test were used to assess survival. All statistical tests were two-sided. Results CLIC1 was statistically significantly overexpressed in GBMs compared with normal brain tissues (P < .001) with a better survival of patients with CLIC1 low-expressing tumors (CLIC1low vs CLIC1high survival: χ2 = 74.35; degrees of freedom = 1; log-rank P < .001). CLIC1 was variably expressed in patient-derived GBM neurospheres and was found enriched in the stem/progenitor compartment. CLIC1 silencing reduced proliferative (P < .01), clonogenic (P < .01), and tumorigenic capacity (P < .05) of stem/progenitor cells. The reduction of CLIC1 chloride currents with a specific CLIC1 antibody mirrored the biological effects of CLIC1 silencing in GBM patient–derived neurospheres. Conclusions Reduced gliomagenesis after CLIC1 targeting in tumoral stem/progenitor cells and the finding that CLIC1 expression is inversely associated with patient survival suggest CLIC1 as a potential target and prognostic biomarker. PMID:24115360

Characteristics of Chinese herbal medicine usage and its effect on survival of lung cancer patients in Taiwan.

PubMed

Li, Te-Mao; Yu, Yang-Hao; Tsai, Fuu-Jen; Cheng, Chi-Fung; Wu, Yang-Chang; Ho, Tsung-Jung; Liu, Xiang; Tsang, Hsinyi; Lin, Ting-Hsu; Liao, Chiu-Chu; Huang, Shao-Mei; Li, Ju-Pi; Lin, Jung-Chun; Lin, Chih-Chien; Liang, Wen-Miin; Lin, Ying-Ju

2018-03-01

In Taiwan, lung cancer remains one of the deadliest cancers. Survival of lung cancer patients remains low, ranging from 6% to 18%. Studies have shown that Chinese herbal medicine (CHM) can be used to induce cell apoptosis and exhibit anti-inflammatoryanti-inflammatory activities in cancer cells. This study aimed to investigate the frequencies and patterns of CHM treatment for lung cancer patients and the effect of CHM on their survival probability in Taiwan. We identified 6939 lung cancer patients (ICD-9-CM: 162). We allocated 264 CHM users and 528 CHM-non users, matched for age, gender, duration, and regular treatment. Chi-square test, conditional multivariable logistic regression, Kaplan-Meier method, and the log-rank test were used in this study. The CHM group was characterized by a longer follow up time and more cases of hyperlipidemia and liver cirrhosis. This group exhibited a lower mortality hazard ratio (0.48, 95% confidence interval [0.39-0.61], p < 0.001), after adjusting for comorbidities. The trend was also observed that the cumulative survival probability was higher in CHM than in non-CHM users (p < 0.0001, log rank test). Analysis of their CHM prescription pattern revealed that Bu-Zhong-Yi-Qi-Tang (BZYQT), Xiang-Sha-Liu-Jun-Zi-Tang (XSLJZT), and Bai-He-Gu-Jin-Tang (BHGJT); and Bei-Mu (BM), Xing-Ren (XR) and Ge-Gen (GG) were found to be the top three formulas and herbs, respectively. Among them, BM was the core CHM of the major cluster, and Jie-Geng (JG) and Mai-Men-Dong-Tang (MMDT) were important CHMs by CHM network analysis. The use of CHM as an adjunctive therapy may reduce the mortality hazard ratio of lung cancer patients. The investigation of their comprehensive CHM prescription patterns might be useful in future large-scale, randomized clinical investigations of agent effectiveness, safety, and potential interactions with conventional treatments for lung cancer patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of Chinese herbal medicine on stroke patients with type 2 diabetes.

PubMed

Tsai, Fuu-Jen; Ho, Tsung-Jung; Cheng, Chi-Fung; Liu, Xiang; Tsang, Hsinyi; Lin, Ting-Hsu; Liao, Chiu-Chu; Huang, Shao-Mei; Li, Ju-Pi; Lin, Cheng-Wen; Lin, Jaung-Geng; Lin, Jung-Chun; Lin, Chih-Chien; Liang, Wen-Miin; Lin, Ying-Ju

2017-03-22

Complications of type 2 diabetes (T2D) include stroke, which is a cerebrovascular disturbance characterized by reduced blood flow in the brain, leading to death or physical disability. Chinese herbal medicine (CHM) has been widely used in ancient China for the treatment of diabetes and stroke by supplementing Qi and activating blood circulation. This study aimed to investigate the frequencies and patterns of CHM treatment for stroke patients with T2D and the outcomes of long-term use in Taiwan. We identified 3079 stroke patients (ICD-9-CM: 430-438) with T2D. We allocated 618 stroke patients, matched for age, gender, and T2D-to-stroke duration, to both CHM and non-CHM groups. Chi-square test, conditional multivariable logistic regression, Kaplan-Meier method, and the log-rank test were used in this study. The CHM group was characterized by more cases of chronic obstructive pulmonary disease, ulcer disease, hyperlipidemia, tobacco use, and higher income. The cumulative survival probability was higher in the CHM group (P<0.001, log rank test); after adjusting for comorbidities, income, and urbanization level, this group also exhibited a lower mortality hazard ratio (0.37, 95% confidence interval [0.25-0.55]). Shu-Jing-Huo-Xue-Tang, Xue-Fu-Zhu-Yu-Tang, and Du-Huo-Ji-Sheng-Tang; and Dan-Shen, Niu-Xi, and Yan-Hu-Suo represented the top three formulas and herbs, respectively. The use of CHM as adjunctive therapy may improve the overall survival (OS) of stroke patients with T2D. The list of the comprehensive herbal medicines that they used might be useful in future large-scale, randomized clinical investigations of agent effectiveness, safety, and potential interactions with conventional treatments in stroke patients with T2D. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Bundle in the Bronx: Impact of a Transition-of-Care Outpatient Parenteral Antibiotic Therapy Bundle on All-Cause 30-Day Hospital Readmissions

PubMed Central

Nori, Priya; Mowrey, Wenzhu; Zukowski, Elisabeth; Gohil, Shruti; Sarwar, Uzma; Weston, Gregory; Urrely, Riganni; Palombelli, Matthew; Pierino, Vinnie Frank; Parsons, Vanessa; Ehrlich, Amy; Ostrowsky, Belinda; Corpuz, Marilou; Pirofski, Liise-anne

2017-01-01

Abstract Background. A streamlined transition from inpatient to outpatient care can decrease 30-day readmissions. Outpatient parenteral antibiotic therapy (OPAT) programs have not reduced readmissions; an OPAT bundle has been suggested to improve outcomes. We implemented a transition-of-care (TOC) OPAT bundle and assessed the effects on all-cause, 30-day hospital readmission. Methods. Retrospectively, patients receiving postdischarge intravenous antibiotics were evaluated before and after implementation of a TOC-OPAT program in Bronx, New York, between July, 2015 and February, 2016. Pearson’s χ2 test was used to compare 30-day readmissions between groups, and logistic regression was used to adjust for covariates. Time from discharge to readmission was analyzed to assess readmission risk, using log-rank test to compare survival curves and Cox proportional hazards model to adjust for covariates. Secondary outcomes, 30-day emergency department (ED) visits, and mortality were analyzed similarly. Results. Compared with previous standard care (n = 184), the TOC-OPAT group (n = 146) had significantly lower 30-day readmissions before (13.0% vs 26.1%, P < .01) and after adjustment for covariates (odds ratio [OR] = 0.51; 95% confidence interval [CI], 0.27–0.94; P = .03). In time-dependent analyses, TOC-OPAT patients were at significantly lower risk for readmission (log-rank test, P < .01; hazard ratio = 0.56; 95% CI, 0.32–0.97; P = .04). Propensity-matched sensitivity analysis showed lower readmissions in the TOC-OPAT group (13.6% vs 24.6%, P = .04), which was attenuated after adjustment (OR = 0.51; 95% CI, 0.25–1.05; P = .07). Mortality and ED visits were similar in both groups. Conclusions. Our TOC-OPAT patients had reduced 30-day readmissions compared with the previous standard of care. An effective TOC-OPAT bundle can successfully improve patient outcomes in an economically disadvantaged area. PMID:28852672

Primary care and survival among American Indian patients with diabetes in the Southwest United States: Evaluation of a cohort study at Gallup Indian Medical Center, 2009-2016.

PubMed

King, Caroline; Atwood, Sidney; Brown, Chris; Nelson, Adrianne Katrina; Lozada, Mia; Wei, Jennie; Merino, Maricruz; Curley, Cameron; Muskett, Olivia; Sabo, Samantha; Gampa, Vikas; Orav, John; Shin, Sonya

2018-06-01

To evaluate the role of primary care healthcare delivery on survival for American Indian patients with diabetes in the southwest United States. Data from patients with diabetes admitted to Gallup Indian Medical Center between 2009 and 2016 were analyzed using a log-rank test and Cox Proportional Hazards analyses. Of the 2661 patients included in analysis, 286 patients died during the study period. Having visited a primary care provider in the year prior to first admission of the study period was protective against all-cause mortality in unadjusted analysis (HR (95% CI)=0.47 (0.31, 0.73)), and after adjustment. The log-rank test indicated there is a significant difference in overall survival by primary care engagement history prior to admission (p<0.001). The median survival time for patients who had seen a primary care provider was 2322days versus 2158days for those who had not seen a primary care provider. Compared with those who did not see a primary care provider in the year prior to admission, having seen a primary care provider was associated with improved survival after admission. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Cross-Validation of Survival Bump Hunting by Recursive Peeling Methods.

PubMed

Dazard, Jean-Eudes; Choe, Michael; LeBlanc, Michael; Rao, J Sunil

2014-08-01

We introduce a survival/risk bump hunting framework to build a bump hunting model with a possibly censored time-to-event type of response and to validate model estimates. First, we describe the use of adequate survival peeling criteria to build a survival/risk bump hunting model based on recursive peeling methods. Our method called "Patient Recursive Survival Peeling" is a rule-induction method that makes use of specific peeling criteria such as hazard ratio or log-rank statistics. Second, to validate our model estimates and improve survival prediction accuracy, we describe a resampling-based validation technique specifically designed for the joint task of decision rule making by recursive peeling (i.e. decision-box) and survival estimation. This alternative technique, called "combined" cross-validation is done by combining test samples over the cross-validation loops, a design allowing for bump hunting by recursive peeling in a survival setting. We provide empirical results showing the importance of cross-validation and replication.

Cross-Validation of Survival Bump Hunting by Recursive Peeling Methods

PubMed Central

Dazard, Jean-Eudes; Choe, Michael; LeBlanc, Michael; Rao, J. Sunil

2015-01-01

We introduce a survival/risk bump hunting framework to build a bump hunting model with a possibly censored time-to-event type of response and to validate model estimates. First, we describe the use of adequate survival peeling criteria to build a survival/risk bump hunting model based on recursive peeling methods. Our method called “Patient Recursive Survival Peeling” is a rule-induction method that makes use of specific peeling criteria such as hazard ratio or log-rank statistics. Second, to validate our model estimates and improve survival prediction accuracy, we describe a resampling-based validation technique specifically designed for the joint task of decision rule making by recursive peeling (i.e. decision-box) and survival estimation. This alternative technique, called “combined” cross-validation is done by combining test samples over the cross-validation loops, a design allowing for bump hunting by recursive peeling in a survival setting. We provide empirical results showing the importance of cross-validation and replication. PMID:26997922

Importance of postprocedural Wound, Ischemia, and foot Infection (WIfI) restaging in predicting limb salvage.

PubMed

Leithead, Charles; Novak, Zdenek; Spangler, Emily; Passman, Marc A; Witcher, Adam; Patterson, Mark A; Beck, Adam W; Pearce, Benjamin J

2018-02-01

The Wound, Ischemia, and foot Infection (WIfI) classification system was created to encompass demographic changes and expanding techniques of revascularization to perform meaningful analyses of outcomes in the treatment of the threatened limb. The WIfI index is intended to be analogous to the TNM staging system for cancer, with restaging to be done after control of infection and after revascularization. Our goal was to evaluate the effectiveness of WIfI restaging after therapy in the prediction of limb outcomes. Preoperative WIfI scoring was performed prospectively for all critical limb ischemia patients who underwent revascularization from January 2014 to June 2015. WIfI restaging and assessment of outcomes were performed retrospectively through August 2016. WIfI classification was determined at the following intervals: preoperatively, immediately postoperatively, and 1 month and 6 months after intervention. Amputation-free survival (AFS) was the primary end point. Kaplan-Meier plot analysis and comparisons of preoperative grades with respective postoperative grades were performed using paired t-test, χ 2 test, and correlation analyses. A total of 180 limbs and 172 critical limb ischemia patients underwent revascularization, of which 29 limbs had major amputations (16%). Wound grades generally improved after surgery across the entire cohort. Major amputation was associated with preoperative wound grade and remained associated with wound grade at postoperative restaging at 1 month and beyond on the basis of amputation frequency analysis (preoperatively, 1 month, and 6 months, P = .03, < .001, and < .001, respectively). Wound grade was significantly associated with AFS at 1 month and 6 months after intervention (log-rank, P < .001 for restaging intervals). Ischemia grades improved initially with a slight decline across the cohort at 6 months. Ischemia grade at 1 month postoperatively was associated with AFS (log-rank, P = .03). Foot infection grades also improved at each time interval. Foot infection grade was associated with AFS at 1 month postoperatively (log-rank, P < .001) and at 6 months (log-rank, P = .017). WIfI restaging is an important tool for predicting limb loss and assessing adequacy of intervention, more so than baseline WIfI alone. The 1- and 6-month postoperative ischemia grade correlated with AFS, whereas preoperative grade did not. The 1- and 6-month postoperative wound and foot infection grades additionally correlated with AFS. WIfI restaging at 1 month and 6 months postoperatively may help identify a cohort that remains at higher risk for limb loss and may merit more expeditious reintervention. Copyright © 2017 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Performance of combined fragmentation and retention prediction for the identification of organic micropollutants by LC-HRMS.

PubMed

Hu, Meng; Müller, Erik; Schymanski, Emma L; Ruttkies, Christoph; Schulze, Tobias; Brack, Werner; Krauss, Martin

2018-03-01

In nontarget screening, structure elucidation of small molecules from high resolution mass spectrometry (HRMS) data is challenging, particularly the selection of the most likely candidate structure among the many retrieved from compound databases. Several fragmentation and retention prediction methods have been developed to improve this candidate selection. In order to evaluate their performance, we compared two in silico fragmenters (MetFrag and CFM-ID) and two retention time prediction models (based on the chromatographic hydrophobicity index (CHI) and on log D). A set of 78 known organic micropollutants was analyzed by liquid chromatography coupled to a LTQ Orbitrap HRMS with electrospray ionization (ESI) in positive and negative mode using two fragmentation techniques with different collision energies. Both fragmenters (MetFrag and CFM-ID) performed well for most compounds, with average ranking the correct candidate structure within the top 25% and 22 to 37% for ESI+ and ESI- mode, respectively. The rank of the correct candidate structure slightly improved when MetFrag and CFM-ID were combined. For unknown compounds detected in both ESI+ and ESI-, generally positive mode mass spectra were better for further structure elucidation. Both retention prediction models performed reasonably well for more hydrophobic compounds but not for early eluting hydrophilic substances. The log D prediction showed a better accuracy than the CHI model. Although the two fragmentation prediction methods are more diagnostic and sensitive for candidate selection, the inclusion of retention prediction by calculating a consensus score with optimized weighting can improve the ranking of correct candidates as compared to the individual methods. Graphical abstract Consensus workflow for combining fragmentation and retention prediction in LC-HRMS-based micropollutant identification.

Clinical Impact of the Number of Treatment Cycles in First-Line Docetaxel for Patients With Metastatic Castration-Resistant Prostate Cancer.

PubMed

Kongsted, Per; Svane, Inge Marie; Lindberg, Henriette; Sengeløv, Lisa

2017-04-01

We investigated the impact of the number of docetaxel cycles administered in patients with metastatic castration-resistant prostate cancer (mCRPC) treated with first-line chemotherapy. Charts from 421 consecutive patients who initiated standard treatment with docetaxel-based chemotherapy (75 mg/m 2 every 3 weeks) between 2007 and 2013 were reviewed. Patients who received < 6 cycles of docetaxel were excluded from the analysis. Remaining patients were divided into 2 groups on the basis of whether or not ≥ 9 cycles of docetaxel were administered (n = 108 and 184, respectively). Reasons for treatment discontinuation and postdocetaxel treatments were registered. Prostate-specific antigen (PSA) responses were defined as a confirmed ≥ 50% decrease in baseline PSA levels. Overall survival (OS) was calculated from start of therapy using the Kaplan-Meier method. Cox proportional hazards were calculated to estimate the effect of clinical variables on OS. OS was longer in patients treated with ≥ 9 cycles of docetaxel (21.9 months vs. 17.2 months; P < .0001, log rank). Survival also favored patients treated with ≥ 9 cycles of docetaxel when only patients ending docetaxel because of toxicity or treatment conclusion (22.3 vs. 19.4 months; P = .048, log rank) or patients who achieved a PSA response (22.3 vs. 18.7 months; P = .012, log rank) were evaluated. mCRPC-related prognostic factors and patients who received ≥ 1 subsequent line of therapy post-docetaxel were well balanced. On the basis of our retrospective findings, a superior OS was found in patients treated with ≥ 9 cycles of docetaxel when adjusting for known prognostic factors. Dose reductions might increase the number of docetaxel cycles administered. Copyright © 2016 Elsevier Inc. All rights reserved.

Prognostic Impact of the Combination of Recurrence Score and Quantitative Estrogen Receptor Expression (ESR1) on Predicting Late Distant Recurrence Risk in Estrogen Receptor–Positive Breast Cancer After 5 Years of Tamoxifen: Results From NRG Oncology/National Surgical Adjuvant Breast and Bowel Project B-28 and B-14

PubMed Central

Wolmark, Norman; Baehner, Frederick L.; Butler, Steven M.; Tang, Gong; Jamshidian, Farid; Sing, Amy P.; Shak, Steven; Paik, Soonmyung

2016-01-01

Purpose We determined the utility of the 21-Gene Recurrence Score (RS) in predicting late (> 5 years) distant recurrence (LDR) in stage I and II breast cancer within high and low-ESR1–expressing groups. Patients and Methods RS was assessed in chemotherapy/tamoxifen-treated, estrogen receptor (ER) –positive, node-positive National Surgical Adjuvant Breast and Bowel Project B-28 patients and tamoxifen-treated, ER-positive, node-negative B-14 patients. The association of the RS with risk of distant recurrence (DR) 0 to 5 years and those at risk > 5 years was assessed. An ESR1 expression cut point was optimized in B-28 and tested in B-14. Results Median follow-up was 11.2 years for B-28 and 13.9 years for B-14. Of 1,065 B-28 patients, 36% had low (< 18), 34% intermediate (18 to 30), and 30% high (≥ 31) RS. Of 668 B-14 patients, 51% had low, 22% intermediate, and 27% high RS. Median ESR1 expression by reverse transcriptase polymerase chain reaction was: B-28, 9.7 normalized expression cycle threshold units (CT) and B-14, 10.7 CT. In B-28, RS was associated with DR 0 to 5 years (log-rank P < .001) and > 5 to 10 years (log-rank P = .02) regardless of ESR1 expression. An ESR1 expression cut point of 9.1 CT was identified in B-28. It was validated in B-14 patients for whom the RS was associated with DR in years 5 to 15: 6.8% (95% CI, 4.4% to 10.6%) versus 11.2% (95% CI, 6.2% to 19.9%) versus 16.4% (95% CI, 10.2% to 25.7%) for RS < 18, RS 18 to 30, and RS ≥ 31, respectively (log-rank P = .01). Conclusion For LDR, RS is strongly prognostic in patients with higher quantitative ESR1. Risk of LDR is relatively low for patients with low RS. These results suggest the value of extended tamoxifen therapy merits evaluation in patients with intermediate and high RS with higher ESR1 expression at initial diagnosis. PMID:27217450

Generalized Higher Order Orthogonal Iteration for Tensor Learning and Decomposition.

PubMed

Liu, Yuanyuan; Shang, Fanhua; Fan, Wei; Cheng, James; Cheng, Hong

2016-12-01

Low-rank tensor completion (LRTC) has successfully been applied to a wide range of real-world problems. Despite the broad, successful applications, existing LRTC methods may become very slow or even not applicable for large-scale problems. To address this issue, a novel core tensor trace-norm minimization (CTNM) method is proposed for simultaneous tensor learning and decomposition, and has a much lower computational complexity. In our solution, first, the equivalence relation of trace norm of a low-rank tensor and its core tensor is induced. Second, the trace norm of the core tensor is used to replace that of the whole tensor, which leads to two much smaller scale matrix TNM problems. Finally, an efficient alternating direction augmented Lagrangian method is developed to solve our problems. Our CTNM formulation needs only O((R N +NRI)log(√{I N })) observations to reliably recover an N th-order I×I×…×I tensor of n -rank (r,r,…,r) , compared with O(rI N-1 ) observations required by those tensor TNM methods ( I > R ≥ r ). Extensive experimental results show that CTNM is usually more accurate than them, and is orders of magnitude faster.

Determination of the distribution coefficient (log Kd) of oxytetracycline, tylosin A, olaquindox and metronidazole in manure.

PubMed

Loke, Marie-Louise; Tjørnelund, Jette; Halling-Sørensen, Bent

2002-07-01

Olaquindox (log Kow = -2.3) and metronidazole (log Kow = -0.1) both have low tendencies to sorp to particles in manure. This corresponds with the negative log Kow values of these antibiotics. Tylosin (log Kow = 1.63) and oxytetracycline (log Kow = -1.12) sorp relatively strongly to the manure particles and have log Kd values between 1.5 and 2.0. The tendency to bind to manure was ranked after increasing binding as follows: metronidazole < olaquindox < tylosin A and oxytetracycline. This order of ranking is consistent with results of sorption in soil. Our experiments illustrate that for some antibacterial agents estimation of the partitioning coefficients, Kd, cannot be made from Kow and f(oc) alone. Sorption of oxytetracycline to manure is much higher than expected from the negative log Kow value of the compound. It is believed that sorption of oxytetracycline to manure is influenced by ionic binding to divalent metal ions as such Mg2+ and Ca2+ as well as other charged compounds in the matrix. Binding of oxytetracycline to soil is stronger than the binding to manure. This is most likely due to the strong mineral related metal complexes formed between soil, metal ion and oxytetracycline. These complexes are not known to exist in manure. The relatively strong sorption of tylosin A to manure corresponds with data found for soil sorption of tylosin. Tylosin has a log Kow value of 2.5, thus it is not surprising that this drug binds strongly to manure.

Randomized clinical study comparing metallic and glass fiber post in restoration of endodontically treated teeth.

PubMed

Gbadebo, Olaide S; Ajayi, Deborah M; Oyekunle, Oyekunle O Dosumu; Shaba, Peter O

2014-01-01

Post-retained crowns are indicated for endodontically treated teeth (ETT) with severely damaged coronal tissue. Metallic custom and prefabricated posts have been used over the years, however, due to unacceptable color, extreme rigidity and corrosion, fiber posts, which are flexible, aesthetically pleasing and have modulus of elasticity comparable with dentin were introduced. To compare clinical performance of metallic and glass fiber posts in restoration of ETT. 40 ETT requiring post retained restorations were included. These teeth were randomly allocated into 2 groups. Twenty teeth were restored using a glass fiber-reinforced post (FRP) and 20 others received stainless steel parapost (PP), each in combination with composite core buildups. Patients were observed at 1 and 6 months after post placement and cementation of porcelain fused to metal (PFM) crown. Marginal gap consideration, post retention, post fracture, root fracture, crown fracture, crown decementation and loss of restoration were part of the data recorded. All teeth were assessed clinically and radiographically. Fisher's exact test was used for categorical values while log-rank test was used for descriptive statistical analysis. One tooth in the PP group failed, secondary to decementation of the PFM crown giving a 2.5% overall failure while none in the FRP group failed. The survival rate of FRP was thus 100% while it was 97.5% in the PP group. This however was not statistically significant (log-rank test, P = 0.32). Glass FRPs performed better than the metallic post based on short-term clinical performance.

Association Between Statin Use and Endometrial Cancer Survival.

PubMed

Nevadunsky, Nicole S; Van Arsdale, Anne; Strickler, Howard D; Spoozak, Lori A; Moadel, Alyson; Kaur, Gurpreet; Girda, Eugenia; Goldberg, Gary L; Einstein, Mark H

2015-07-01

To evaluate the association of 3 hydroxy-3-methyl-glutaryl-coenzyme A reductase inhibitor (statin) use and concordant polypharmacy with disease-specific survival from endometrial cancer. A retrospective cohort study was conducted of 985 endometrial cancer cases treated from January 1999 through December 2009 at a single institution. Disease-specific survival was estimated by Kaplan-Meier analyses. A Cox proportional hazards model was used to study factors associated with survival. All statistical tests were two-sided and performed using Stata. At the time of analysis, 230 patients (22% of evaluable patients) died of disease and median follow-up was 3.28 years. Disease-specific survival was greater (179/220 [81%]) for women with endometrial cancer taking statin therapy at the time of diagnosis and staging compared with women not using statins (423/570 [74%]) (log rank test, P=.03). This association persisted for the subgroup of patients with nonendometrioid endometrial tumors who were statin users (59/87 [68%]) compared with nonusers (93/193 [43%]) (log rank test, P=.02). The relationship remained significant (hazard ratio 0.63, 95% confidence interval [CI] 0.40-0.99) after adjusting for age, clinical stage, radiation, and other factors. Further evaluation of polypharmacy showed an association between concurrent statin and aspirin use with an especially low disease-specific mortality (hazard ratio 0.25, 95% CI 0.09-0.70) relative to those who used neither. Statin and aspirin use was associated with improved survival from nonendometrioid endometrial cancer.

Completion Dissection or Observation for Sentinel-Node Metastasis in Melanoma.

PubMed

Faries, Mark B; Thompson, John F; Cochran, Alistair J; Andtbacka, Robert H; Mozzillo, Nicola; Zager, Jonathan S; Jahkola, Tiina; Bowles, Tawnya L; Testori, Alessandro; Beitsch, Peter D; Hoekstra, Harald J; Moncrieff, Marc; Ingvar, Christian; Wouters, Michel W J M; Sabel, Michael S; Levine, Edward A; Agnese, Doreen; Henderson, Michael; Dummer, Reinhard; Rossi, Carlo R; Neves, Rogerio I; Trocha, Steven D; Wright, Frances; Byrd, David R; Matter, Maurice; Hsueh, Eddy; MacKenzie-Ross, Alastair; Johnson, Douglas B; Terheyden, Patrick; Berger, Adam C; Huston, Tara L; Wayne, Jeffrey D; Smithers, B Mark; Neuman, Heather B; Schneebaum, Schlomo; Gershenwald, Jeffrey E; Ariyan, Charlotte E; Desai, Darius C; Jacobs, Lisa; McMasters, Kelly M; Gesierich, Anja; Hersey, Peter; Bines, Steven D; Kane, John M; Barth, Richard J; McKinnon, Gregory; Farma, Jeffrey M; Schultz, Erwin; Vidal-Sicart, Sergi; Hoefer, Richard A; Lewis, James M; Scheri, Randall; Kelley, Mark C; Nieweg, Omgo E; Noyes, R Dirk; Hoon, Dave S B; Wang, He-Jing; Elashoff, David A; Elashoff, Robert M

2017-06-08

Sentinel-lymph-node biopsy is associated with increased melanoma-specific survival (i.e., survival until death from melanoma) among patients with node-positive intermediate-thickness melanomas (1.2 to 3.5 mm). The value of completion lymph-node dissection for patients with sentinel-node metastases is not clear. In an international trial, we randomly assigned patients with sentinel-node metastases detected by means of standard pathological assessment or a multimarker molecular assay to immediate completion lymph-node dissection (dissection group) or nodal observation with ultrasonography (observation group). The primary end point was melanoma-specific survival. Secondary end points included disease-free survival and the cumulative rate of nonsentinel-node metastasis. Immediate completion lymph-node dissection was not associated with increased melanoma-specific survival among 1934 patients with data that could be evaluated in an intention-to-treat analysis or among 1755 patients in the per-protocol analysis. In the per-protocol analysis, the mean (±SE) 3-year rate of melanoma-specific survival was similar in the dissection group and the observation group (86±1.3% and 86±1.2%, respectively; P=0.42 by the log-rank test) at a median follow-up of 43 months. The rate of disease-free survival was slightly higher in the dissection group than in the observation group (68±1.7% and 63±1.7%, respectively; P=0.05 by the log-rank test) at 3 years, based on an increased rate of disease control in the regional nodes at 3 years (92±1.0% vs. 77±1.5%; P<0.001 by the log-rank test); these results must be interpreted with caution. Nonsentinel-node metastases, identified in 11.5% of the patients in the dissection group, were a strong, independent prognostic factor for recurrence (hazard ratio, 1.78; P=0.005). Lymphedema was observed in 24.1% of the patients in the dissection group and in 6.3% of those in the observation group. Immediate completion lymph-node dissection increased the rate of regional disease control and provided prognostic information but did not increase melanoma-specific survival among patients with melanoma and sentinel-node metastases. (Funded by the National Cancer Institute and others; MSLT-II ClinicalTrials.gov number, NCT00297895 .).

ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer.

PubMed

Choueiri, Michel B; Shen, John Paul; Gross, Andrew M; Huang, Justin K; Ideker, Trey; Fanta, Paul

2015-01-01

In patients with metastatic colon cancer, response to first line chemotherapy is a strong predictor of overall survival (OS). Currently, oncologists lack diagnostic tests to determine which chemotherapy regimen offers the greatest chance for response in an individual patient. Here we present the results of gene expression analysis for two genes, ERCC1 and TS, measured with the commercially available ResponseDX: Colon assay (Response Genetics, Los Angeles, CA) in 41 patients with de novo metastatic colon cancer diagnosed between July 2008 and August 2013 at the University of California, San Diego. In addition ERCC1 and TS expression levels as determined by RNAseq and survival data for patients in TCGA were downloaded from the TCGA data portal. We found that patients with low expression of ERCC1 (n = 33) had significantly longer median OS (36.0 vs. 10.1 mo, HR 0.29, 95% CI .095 to .84, log-rank p = 9.0x10-6) and median time to treatment to failure (TTF) following first line chemotherapy (14.1 vs. 2.4 mo, HR 0.17, 95% CI 0.048 to 0.58, log-rank p = 5.3x10-4) relative to those with high expression (n = 4). After accounting for the covariates age, sex, tumor grade and ECOG performance status in a Cox proportional hazard model the association of low ERCC1 with longer OS (HR 0.18, 95% CI 0.14 to 0.26, p = 0.0448) and TTF (HR 0.16, 95% CI 0.14 to 0.21, p = 0.0053) remained significant. Patients with low TS expression (n = 29) had significantly longer median OS (36.0 vs. 14.8 mo, HR 0.25, 95% CI 0.074 to 0.82, log-rank p = 0.022) relative to those with high expression (n = 12). The combined low expression of ERCC1/TS was predictive of response in patients treated with FOLFOX (40% vs. 91%, RR 2.3, Fisher's exact test p = 0.03, n = 27), but not with FOLFIRI (71% vs. 71%, RR 1.0, Fisher's exact test p = 1, n = 14). Overall, these findings suggest that measurement of ERCC1 and TS expression has potential clinical utility in managing patients with metastatic colorectal cancer.

Clinical outcome and predictors of survival in patients with pneumocystis jirovecii pneumonia--results of a tertiary referral centre.

PubMed

Roembke, Felicitas; Heinzow, Hauke Sebastian; Gosseling, Thomas; Heinecke, Achim; Domagk, Dirk; Domschke, Wolfram; Meister, Tobias

2014-01-01

Pneumocystis jirovecii pneumonia also known as pneumocystis pneumonia (PCP) is an opportunistic respiratory infection in human immunodeficiency virus (HIV) patients that may also develop in non-HIV immunocompromised persons. The aim of our study was to evaluate mortality predictors of PCP patients in a tertiary referral centre. Fifty-one patients with symptomatic PCP were enrolled in the study. The patients had either HIV infection (n = 21) or other immunosuppressive conditions (n = 30). Baseline characteristics (e.g. age, sex and underlying disease) were retrieved. Kaplan-Meier analysis was employed to calculate survival. Comparisons were made by log-rank test. A multivariate analysis of factors influencing survival was carried out using the Cox regression model. Chi-squared test and Wilcoxon-Mann-Whitney test was applied as appropriate. The median survival time for the HIV group was >120 months compared with 3 months for the non-HIV group (P = 0.009). Three-month survival probability was also significantly greater in the HIV group compared with the non-HIV group (90% vs 41%, P = 0.002). In univariate log-rank test, intensive care unit (ICU) necessity, HIV negativity, age >50 years, haemoglobin <10g/dl, C-reactive protein >5 mg/dL and multiple comorbidities were significant negative predictors of survival. In the Cox regression model, ICU and HIV statuses turned out to be independent prognostic factors of survival. PCP is a serious problem in non-HIV immunocompromised patients in whom survival outcomes are worse than those in HIV patients. © 2013 John Wiley & Sons Ltd.

Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers.

PubMed

Eisinga, Rob; Heskes, Tom; Pelzer, Ben; Te Grotenhuis, Manfred

2017-01-25

The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is typically of interest to conduct pairwise comparison tests. Current approaches to such tests rely on large-sample approximations, due to the numerical complexity of computing the exact distribution. These approximate methods lead to inaccurate estimates in the tail of the distribution, which is most relevant for p-value calculation. We propose an efficient, combinatorial exact approach for calculating the probability mass distribution of the rank sum difference statistic for pairwise comparison of Friedman rank sums, and compare exact results with recommended asymptotic approximations. Whereas the chi-squared approximation performs inferiorly to exact computation overall, others, particularly the normal, perform well, except for the extreme tail. Hence exact calculation offers an improvement when small p-values occur following multiple testing correction. Exact inference also enhances the identification of significant differences whenever the observed values are close to the approximate critical value. We illustrate the proposed method in the context of biological machine learning, were Friedman rank sum difference tests are commonly used for the comparison of classifiers over multiple datasets. We provide a computationally fast method to determine the exact p-value of the absolute rank sum difference of a pair of Friedman rank sums, making asymptotic tests obsolete. Calculation of exact p-values is easy to implement in statistical software and the implementation in R is provided in one of the Additional files and is also available at http://www.ru.nl/publish/pages/726696/friedmanrsd.zip .

The effect of uncertainties in distance-based ranking methods for multi-criteria decision making

NASA Astrophysics Data System (ADS)

Jaini, Nor I.; Utyuzhnikov, Sergei V.

2017-08-01

Data in the multi-criteria decision making are often imprecise and changeable. Therefore, it is important to carry out sensitivity analysis test for the multi-criteria decision making problem. The paper aims to present a sensitivity analysis for some ranking techniques based on the distance measures in multi-criteria decision making. Two types of uncertainties are considered for the sensitivity analysis test. The first uncertainty is related to the input data, while the second uncertainty is towards the Decision Maker preferences (weights). The ranking techniques considered in this study are TOPSIS, the relative distance and trade-off ranking methods. TOPSIS and the relative distance method measure a distance from an alternative to the ideal and antiideal solutions. In turn, the trade-off ranking calculates a distance of an alternative to the extreme solutions and other alternatives. Several test cases are considered to study the performance of each ranking technique in both types of uncertainties.

Therapy reduction in patients with Down syndrome and myeloid leukemia: the international ML-DS 2006 trial.

PubMed

Uffmann, Madita; Rasche, Mareike; Zimmermann, Martin; von Neuhoff, Christine; Creutzig, Ursula; Dworzak, Michael; Scheffers, Lenie; Hasle, Henrik; Zwaan, C Michel; Reinhardt, Dirk; Klusmann, Jan-Henning

2017-06-22

Children with myeloid leukemia associated with Down syndrome (ML-DS) have superior outcome compared with non-DS patients, but suffer from higher constitutional cytotoxic drug susceptibility. We analyzed the outcome of 170 pediatric patients with ML-DS enrolled in the prospective, multicenter, open-label, nonrandomized ML-DS 2006 trial by Nordic Society for Pediatric Hematology and Oncology (NOPHO), Dutch Childhood Oncology Group (DCOG), and Acute Myeloid Leukemia-Berlin-Frankfurt-Münster (AML-BFM) study group. Compared with the historical control arm (reduced-intensity protocol for ML-DS patients from the AML-BFM 98 trial), treatment intensity was reduced by lowering the cumulative dose of etoposide (950 to 450 mg/m 2 ) and intrathecal central nervous system prophylaxis while omitting maintenance therapy. Still, 5-year overall survival (89% ± 3% vs 90% ± 4%; P log-rank = .64), event-free survival (EFS; 87% ± 3% vs 89% ± 4%; P log-rank = .71), and cumulative incidence of relapse/nonresponse (CIR/NR; 6% ± 3% vs 6% ± 2%; P Gray = .03) did not significantly differ between the ML-DS 2006 trial and the historical control arm. Poor early treatment response (5-year EFS, 58% ± 16% vs 88% ± 3%; P log rank = .0008) and gain of chromosome 8 (CIR/NR, 16% ± 7% vs 3% ± 2%, P Gray = .02; 5-year EFS, 73% ± 8% vs 91% ± 4%, P log rank = .018) were identified as independent prognostic factors predicting a worse EFS. Five of 7 relapsed patients (71%) with cytogenetic data had trisomy 8. Our study reveals prognostic markers for children with ML-DS and illustrates that reducing therapy did not impair excellent outcome. The trial was registered at EudraCT as #2007-006219-2. © 2017 by The American Society of Hematology.

A cross-site comparison of methods used for hydrogeologic characterization of the Galena-Platteville aquifer in Illinois and Wisconsin, with examples from selected Superfund sites

USGS Publications Warehouse

Kay, Robert T.; Mills, Patrick C.; Dunning, Charles P.; Yeskis, Douglas J.; Ursic, James R.; Vendl, Mark

2004-01-01

The effectiveness of 28 methods used to characterize the fractured Galena-Platteville aquifer at eight sites in northern Illinois and Wisconsin is evaluated. Analysis of government databases, previous investigations, topographic maps, aerial photographs, and outcrops was essential to understanding the hydrogeology in the area to be investigated. The effectiveness of surface-geophysical methods depended on site geology. Lithologic logging provided essential information for site characterization. Cores were used for stratigraphy and geotechnical analysis. Natural-gamma logging helped identify the effect of lithology on the location of secondary- permeability features. Caliper logging identified large secondary-permeability features. Neutron logs identified trends in matrix porosity. Acoustic-televiewer logs identified numerous secondary-permeability features and their orientation. Borehole-camera logs also identified a number of secondary-permeability features. Borehole ground-penetrating radar identified lithologic and secondary-permeability features. However, the accuracy and completeness of this method is uncertain. Single-point-resistance, density, and normal resistivity logs were of limited use. Water-level and water-quality data identified flow directions and indicated the horizontal and vertical distribution of aquifer permeability and the depth of the permeable features. Temperature, spontaneous potential, and fluid-resistivity logging identified few secondary-permeability features at some sites and several features at others. Flowmeter logging was the most effective geophysical method for characterizing secondary-permeability features. Aquifer tests provided insight into the permeability distribution, identified hydraulically interconnected features, the presence of heterogeneity and anisotropy, and determined effective porosity. Aquifer heterogeneity prevented calculation of accurate hydraulic properties from some tests. Different methods, such as flowmeter logging and slug testing, occasionally produced different interpretations. Aquifer characterization improved with an increase in the number of data points, the period of data collection, and the number of methods used.

A Contemporary Analysis of Heart Transplantation and Bridge-to-Transplant Mechanical Circulatory Support Outcomes in Cardiac Sarcoidosis.

PubMed

Crawford, Todd C; Okada, David R; Magruder, J Trent; Fraser, Charles; Patel, Nishant; Houston, Brian A; Whitman, Glenn J; Mandal, Kaushik; Zehr, Kenton J; Higgins, Robert S; Chen, Edward S; Tandri, Hari; Kasper, Edward K; Tedford, Ryan J; Russell, Stuart D; Gilotra, Nisha A

2018-06-01

Patients with end-stage cardiomyopathy due to cardiac sarcoidosis (CS) may be referred for mechanical circulatory support (MCS) and heart transplantation (HT). We describe outcomes of patients with CS undergoing HT, focusing on the use of MCS as a bridge to transplant (BTT). Using the United Network for Organ Sharing Scientific Registry of Transplant Recipients, we identified all adult waitlisted patients and isolated HT recipients from 2006 to 2015. These were divided into those with and without CS and further divided into those who did or did not receive MCS as BTT. Outcomes included 1- and 5-year post-transplantation freedom from mortality and 5-year freedom from primary graft failure. Over the study period, 31,528 patients were listed for HT, 148 (0.4%) of whom had CS. Among the CS patients, 34 (23%) received MCS as BTT. 18,348 patients (58%) eventually underwent HT, including 67 (0.4%) with CS, 20 (30%) of whom had received BTT MCS. Compared with non-CS diagnoses, CS patients had similar 1-year (91% vs 90%; log rank P = .88) and 5-year (83% vs 77%; log rank P = .46) freedom from mortality. Survival was also similar between CS BTT and non-CS BTT groups at 1 year (89% vs 89%; log-rank P = .92) and 5 years (72% vs 75%; log-rank P = .77). Survivals after HT were similar between CS and non-CS patients out to 5 years, and were also similar between CS and non-CS BTT cohorts. Both HT and BTT MCS should be considered in patients with CS. Copyright © 2018 Elsevier Inc. All rights reserved.

Influence of the antagonist material on the wear of different composites using two different wear simulation methods.

PubMed

Heintze, S D; Zellweger, G; Cavalleri, A; Ferracane, J

2006-02-01

The aim of the study was to evaluate two ceramic materials as possible substitutes for enamel using two wear simulation methods, and to compare both methods with regard to the wear results for different materials. Flat specimens (OHSU n=6, Ivoclar n=8) of one compomer and three composite materials (Dyract AP, Tetric Ceram, Z250, experimental composite) were fabricated and subjected to wear using two different wear testing methods and two pressable ceramic materials as stylus (Empress, experimental ceramic). For the OHSU method, enamel styli of the same dimensions as the ceramic stylus were fabricated additionally. Both wear testing methods differ with regard to loading force, lateral movement of stylus, stylus dimension, number of cycles, thermocycling and abrasive medium. In the OHSU method, the wear facets (mean vertical loss) were measured using a contact profilometer, while in the Ivoclar method (maximal vertical loss) a laser scanner was used for this purpose. Additionally, the vertical loss of the ceramic stylus was quantified for the Ivoclar method. The results obtained from each method were compared by ANOVA and Tukey's test (p<0.05). To compare both wear methods, the log-transformed data were used to establish relative ranks between material/stylus combinations and assessed by applying the Pearson correlation coefficient. The experimental ceramic material generated significantly less wear in Tetric Ceram and Z250 specimens compared to the Empress stylus in the Ivoclar method, whereas with the OHSU method, no difference between the two ceramic antagonists was found with regard to abrasion or attrition. The wear generated by the enamel stylus was not statistically different from that generated by the other two ceramic materials in the OHSU method. With the Ivoclar method, wear of the ceramic stylus was only statistically different when in contact with Tetric Ceram. There was a close correlation between the attrition wear of the OHSU and the wear of the Ivoclar method (Pearson coefficient 0.83, p=0.01). Pressable ceramic materials can be used as a substitute for enamel in wear testing machines. However, material ranking may be affected by the type of ceramic material chosen. The attrition wear of the OHSU method was comparable with the wear generated with the Ivoclar method.

Influence of clinical baseline findings on the survival of 2 post systems: a randomized clinical trial.

PubMed

Schmitter, Marc; Rammelsberg, Peter; Gabbert, Olaf; Ohlmann, Brigitte

2007-01-01

The aim of this prospective randomized controlled trial was to evaluate the influence of clinical baseline characteristics on the survival of 2 post systems. One hundred patients needing a post were included. Half the patients received a glass fiber-reinforced post (FRP), and the other half received metal screw posts (MSP). The posts were assigned randomly. In addition to demographic data, the following parameters were recorded: type of tooth (incisor/canine versus molar/premolar), length of the post in relation to root length (percentage), extent of coronal tooth destruction (percentage), ferrule height (in millimeters), type of restoration (fixed or removable partial denture), and presence of antagonistic contacts (yes/no). After at least 1 year (mean: 13.84 months), the patients were recalled. Statistical analysis was performed using the log-rank test and Cox regression analysis. The survival rate of FRPs was 93.5%. In the MSP group, the survival rate was significantly lower (75.6%; log-rank test, P = .049). Additionally, the metal posts were associated with more unfavorable complications, for example, root fracture. The type of the tooth and the degree of coronal tooth destruction influenced the survival of MSPs, whereas no influence of these variables could be seen for FRPs. FRPs are superior to MSPs with respect to short-term clinical performance. Especially for MSPs, clinical survival depends on several variables.

Comparison of multianalyte proficiency test results by sum of ranking differences, principal component analysis, and hierarchical cluster analysis.

PubMed

Škrbić, Biljana; Héberger, Károly; Durišić-Mladenović, Nataša

2013-10-01

Sum of ranking differences (SRD) was applied for comparing multianalyte results obtained by several analytical methods used in one or in different laboratories, i.e., for ranking the overall performances of the methods (or laboratories) in simultaneous determination of the same set of analytes. The data sets for testing of the SRD applicability contained the results reported during one of the proficiency tests (PTs) organized by EU Reference Laboratory for Polycyclic Aromatic Hydrocarbons (EU-RL-PAH). In this way, the SRD was also tested as a discriminant method alternative to existing average performance scores used to compare mutlianalyte PT results. SRD should be used along with the z scores--the most commonly used PT performance statistics. SRD was further developed to handle the same rankings (ties) among laboratories. Two benchmark concentration series were selected as reference: (a) the assigned PAH concentrations (determined precisely beforehand by the EU-RL-PAH) and (b) the averages of all individual PAH concentrations determined by each laboratory. Ranking relative to the assigned values and also to the average (or median) values pointed to the laboratories with the most extreme results, as well as revealed groups of laboratories with similar overall performances. SRD reveals differences between methods or laboratories even if classical test(s) cannot. The ranking was validated using comparison of ranks by random numbers (a randomization test) and using seven folds cross-validation, which highlighted the similarities among the (methods used in) laboratories. Principal component analysis and hierarchical cluster analysis justified the findings based on SRD ranking/grouping. If the PAH-concentrations are row-scaled, (i.e., z scores are analyzed as input for ranking) SRD can still be used for checking the normality of errors. Moreover, cross-validation of SRD on z scores groups the laboratories similarly. The SRD technique is general in nature, i.e., it can be applied to any experimental problem in which multianalyte results obtained either by several analytical procedures, analysts, instruments, or laboratories need to be compared.

Proton Beam Therapy and Concurrent Chemotherapy for Esophageal Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Steven H., E-mail: shlin@mdanderson.org; Komaki, Ritsuko; Liao Zhongxing

2012-07-01

Purpose: Proton beam therapy (PBT) is a promising modality for the management of thoracic malignancies. We report our preliminary experience of treating esophageal cancer patients with concurrent chemotherapy (CChT) and PBT (CChT/PBT) at MD Anderson Cancer Center. Methods and Materials: This is an analysis of 62 esophageal cancer patients enrolled on a prospective study evaluating normal tissue toxicity from CChT/PBT from 2006 to 2010. Patients were treated with passive scattering PBT with two- or three-field beam arrangement using 180 to 250 MV protons. We used the Kaplan-Meier method to assess time-to-event outcomes and compared the distributions between groups using themore » log-rank test. Results: The median follow-up time was 20.1 months for survivors. The median age was 68 years (range, 38-86). Most patients were males (82%) who had adenocarcinomas (76%) and Stage II-III disease (84%). The median radiation dose was 50.4 Gy (RBE [relative biologic equivalence]) (range, 36-57.6). The most common grade 2 to 3 acute toxicities from CChT/PBT were esophagitis (46.8%), fatigue (43.6%), nausea (33.9%), anorexia (30.1%), and radiation dermatitis (16.1%). There were two cases of grade 2 and 3 radiation pneumonitis and two cases of grade 5 toxicities. A total of 29 patients (46.8%) received preoperative CChT/PBT, with one postoperative death. The pathologic complete response (pCR) rate for the surgical cohort was 28%, and the pCR and near CR rates (0%-1% residual cells) were 50%. While there were significantly fewer local-regional recurrences in the preoperative group (3/29) than in the definitive CChT/PBT group (16/33) (log-rank test, p = 0.005), there were no differences in distant metastatic (DM)-free interval or overall survival (OS) between the two groups. Conclusions: This is the first report of patients treated with PBT/CChT for esophageal cancer. Our data suggest that this modality is associated with a few severe toxicities, but the pathologic response and clinical outcomes are encouraging. Prospective comparison with more traditional approach is warranted.« less

Proton Beam Therapy and concurrent chemotherapy for esophageal cancer

PubMed Central

Lin, Steven H.; Komaki, Ritsuko; Liao, Zhongxing; Wei, Caimiao; Myles, Bevan; Guo, Xiaomao; Palmer, Matthew; Mohan, Radhe; Swisher, Stephen G.; Hofstetter, Wayne L.; Ajani, Jaffer A.; Cox, James D.

2014-01-01

Purpose/Objective Proton beam therapy (PBT) is a promising modality for the management of thoracic malignancies. We report our preliminary experience of treating esophageal cancer patients with concurrent chemotherapy (CChT) and PBT at MD Anderson Cancer Center. Materials/Methods This is an analysis of 62 esophageal cancer patients enrolled on a prospective study evaluating normal tissue toxicity from CChT/PBT from 2006 to 2010. Patients were treated with Passive Scattering PBT with 2 or 3 field beam arrangement using 180–250 MV protons. We used the method of Kaplan and Meier to assess time to event outcomes and compared the distributions between groups using the log-rank test. Results The median follow-up time was 20.1 months for survivors. The median age was 68 years (range 38–86). Most were males (82%), had adenocarcinomas (76%) and had stage II-III disease (84%). The median radiation dose was 50.4 Gray-Equivalence (Gy(RBE)) (range 36–57.6). The most common grade 2–3 acute toxicities from CChT/PBT were esophagitis (46.8%), fatigue (43.6%), nausea (33.9%), anorexia (30.1%), and radiation dermatitis (16.1%). There were two cases of grade 2 and 3 radiation pneumonitis and two grade 5 toxicities. A total of 29 patients (46.8%) received preoperative CChT/PBT with one postoperative death. The pathologic complete response (pCR) rate for the surgical cohort was 28%, and the pCR and near CR rate (0–1% residual cells) was 50%. While there were significantly fewer local-regional recurrences in the preoperative group (3/29) as compared to the definitive CChT/PBT group (16/33) (log-rank test p=0.005), there were no differences in DM free interval or OS between the two groups. Conclusions This is the first report of patients treated with PBT/CChT for esophageal cancer. Our data suggest that this modality is associated with a few severe toxicities but the pathologic response and clinical outcomes are encouraging. Prospective comparison with more traditional approach is warranted. PMID:22417808

Evaluation of a device for standardized measurements of reading performance in a prepresbyopic population.

PubMed

Arad, Tschingis; Baumeister, Martin; Bühren, Jens; Kohnen, Thomas

2017-04-20

Automated measurements of reading performance are required for clinical trials involving presbyopia-correcting surgery options. Repeatability of a testing device for reading (Salzburg Reading Desk) was evaluated in a prepresbyopic population. Subjective reading performance of 50 subjects divided into 2 age groups (23-30 years and 38-49 years) with distance-corrected eyes was investigated with different log-scaled reading charts. At study entry, refractive parameters were measured and distance visual acuity assessed. Two standardized binocular measurements were performed for each subject (32.24 ± 9.87 days apart [mean ± SD]). The repeatability of the tests was estimated using correlation coefficients, Wilcoxon signed-rank test, and Bland-Altman method. The test parameters at both maximum reading rate (MRR) measurements demonstrate a strong relationship of age group 2 subjects (correlation coefficient [r] = 0.74 p = 10-4) and of younger subjects (age group 1: r = 0.69, p = 10-4). Prepresbyopic subjects of age group 2 showed moderate results for near reading distance (r = 0.67, p = 10-4); by contrast, younger subjects had poorer results (r = 0.55, p = 10-3). The Wilcoxon signed-rank test revealed agreement between measurements and Bland-Altman plots showed a wide data spread for MRR and near reading distance in both groups. The device measures repeatedly selected reading performance parameters of near real world conditions, such as MRR, in prepresbyopic populations if several factors are taken into account. The option to choose preferred distance leads to more variance in measuring repeated reading performance. German Clinical Trials Register (DRKS) registration reference number: DRKS00000784.

The sensitivity of relative toxicity rankings by the USF/NASA test method to some test variables

NASA Technical Reports Server (NTRS)

Hilado, C. J.; Labossiere, L. A.; Leon, H. A.; Kourtides, D. A.; Parker, J. A.; Hsu, M.-T. S.

1976-01-01

Pyrolysis temperature and the distance between the source and sensor of effluents are two important variables in tests for relative toxicity. Modifications of the USF/NASA toxicity screening test method to increase the upper temperature limit of pyrolysis, reduce the distance between the sample and the test animals, and increase the chamber volume available for animal occupancy, did not significantly alter rankings of relative toxicity of four representative materials. The changes rendered some differences no longer significant, but did not reverse any rankings. The materials studied were cotton, wool, aromatic polyamide, and polybenzimidazole.

Impact of INTERMACS Profile on Clinical Outcomes for Patients Supported With the Total Artificial Heart.

PubMed

Shah, Keyur B; Thanavaro, Kristin L; Tang, Daniel G; Quader, Mohammed A; Mankad, Anit K; Tchoukina, Inna; Thacker, Leroy R; Smallfield, Melissa C; Katlaps, Gundars; Hess, Michael L; Cooke, Richard H; Kasirajan, Vigneshwar

2016-11-01

Insufficient data delineate outcomes for Interagency Registry for Mechanically Assisted Circulatory Support (INTERMACS) profile 1 patients with the total artificial heart (TAH). We studied 66 consecutive patients implanted with the TAH at our institution from 2006 through 2012 and compared outcome by INTERMACS profile. INTERMACS profiles were adjudicated retrospectively by a reviewer blinded to clinical outcomes. Survival after TAH implantation at 6 and 12 months was 76% and 71%, respectively. INTERMACS profile 1 patients had decreased 6-month survival on the device compared with those in profiles 2-4 (74% vs 95%, log rank: P = .015). For the 50 patients surviving to heart transplantation, the 1-year posttransplant survival was 82%. There was no difference in 1-year survival when comparing patients in the INTERMACS 1 profile with less severe profiles (79% vs 84%; log rank test P = .7; hazard ratio [confidence interval] 1.3 [0.3-4.8]). Patients implanted with the TAH as INTERMACS profile 1 had reduced survival to transplantation compared with less sick profiles. INTERMACS profile at the time of TAH implantation did not affect 1-year survival after heart transplantation. Copyright © 2016 Elsevier Inc. All rights reserved.

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model.

PubMed

Diaz-Rodriguez, Sebastian; Bozada, Samantha M; Phifer, Jeremy R; Paluch, Andrew S

2016-11-01

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of [Formula: see text] log units (ranking 15 out of 62 entries), the correlation coefficient (R) was [Formula: see text] (ranking 35), and [Formula: see text] of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

Improving the AOAC use-dilution method by establishing a minimum log density value for test microbes on inoculated carriers.

PubMed

Tomasino, Stephen F; Pines, Rebecca M; Hamilton, Martin A

2009-01-01

The AOAC Use-Dilution methods, 955.14 (Salmonella enterica), 955.15 (Staphylococcus aureus), and 964.02 (Pseudomonas aeruginosa), are used to measure the efficacy of disinfectants on hard inanimate surfaces. The methods do not provide procedures to assess log density of the test microbe on inoculated penicylinders (carrier counts). Without a method to measure and monitor carrier counts, the associated efficacy data may not be reliable and repeatable. This report provides a standardized procedure to address this method deficiency. Based on carrier count data collected by four laboratories over an 8 year period, a minimum log density value is proposed to qualify the test results. Carrier count data were collected concurrently with 242 Use-Dilution tests. The tests were conducted on products bearing claims against P. aeruginosa and S. aureus with and without an organic soil load (OSL) added to the inoculum (as specified on the product label claim). Six carriers were assayed per test for a total of 1452 carriers. All 242 mean log densities were at least 6.0 (geometric mean of 1.0 x 10(6) CFU/carrier). The mean log densities did not exceed 7.5 (geometric mean of 3.2 x 10(7) CFU/carrier). For all microbes and OSL treatments, the mean log density (+/- SEM) was 6.7 (+/- 0.07) per carrier (a geometric mean of 5.39 x 10(6) CFU/carrier). The mean log density for six carriers per test showed good repeatability (0.29) and reproducibility (0.32). A minimum mean log density of 6.0 is proposed as a validity requirement for S. aureus and P. aeruginosa. The minimum level provides for the potential inherent variability that may be experienced by a wide range of laboratories and the slight effect due to the addition of an OSL. A follow-up report is planned to present data to support the carrier count procedure and carrier counts for S. enterica.

Association between vascular calcification assessed by simple radiography and non-fatal cardiovascular events in hemodialysis patients.

PubMed

Petrauskiene, Vaida; Vaiciuniene, Ruta; Bumblyte, Inga Arune; Kuzminskis, Vytautas; Ziginskiene, Edita; Grazulis, Saulius; Jonaitiene, Egle

2016-12-01

Vascular calcification (VC) is one of the factors associated with cardiovascular mortality in hemodialysis (HD) patients. Recommendations concerning screening for VC differ. Possible ability to prevent and reversibility of VC are major subjects on debate whether screening for VC could improve outcomes of renal patients. The objective of the study was to evaluate the significance of simple vascular calcification score (SVCS) based on plane radiographic films and to test its association with non-fatal cardiovascular events in patients on chronic HD. A study population consisted of 95 prevalent HD patients in the HD unit of Hospital of Lithuanian University of Health sciences Kaunas Clinics. Clinical data and laboratory tests information were collected from medical records. SVCS was evaluated as it is described by Adragao et al. After measurement of VC, HD patients were observed for novel non-fatal cardiovascular events. Patients were divided into two groups: SVCS≥3 (57 patients [60%]) and <3 (38 patients [40%]). The Kaplan-Meier survival curves show a significant difference in non-fatal cardiovascular events in the group with SVCS≥3 vs. <3 group (26.3% vs. 7.8%; log rank 5,49; P=0.018). Multivariate Cox regression analysis confirmed a negative impact of VC, hyperphosphatemia, and lower ejection fraction on cardiovascular events. No statistically significant differences were observed comparing parameters of Ca-P metabolism disorders between groups with different SVCS. On separate analysis, the presence of VC in hands was also associated with higher rate of novel cardiovascular events (score 0 goup-5 events [10.6%] vs. score≥1 group-13 events [27%], log rank P=0.035). VC assessed by simple and inexpensive radiological method was an independent predictor of novel non-fatal cardiovascular events in HD patients. Copyright © 2016 Association Société de néphrologie. Published by Elsevier SAS. All rights reserved.

Stent patency in patients with distal malignant biliary obstruction receiving chemo(radio)therapy

PubMed Central

Haal, Sylke; van Hooft, Jeanin E.; Rauws, Erik A. J.; Fockens, Paul; Voermans, Rogier P.

2017-01-01

Background and study aims  Recent literature suggests that chemo(radio)therapy might reduce the patency of plastic stents in patients with malignant biliary obstruction. Whether this might also be valid for other types of stents is unknown. The aim of this study was to determine the influence of chemo(radio)therapy on the patency of fully-covered self-expandable metal stents (FCSEMSs) and plastic stents. Patients and methods  We retrospectively reviewed the electronic medical records of patients with distal malignant biliary obstruction who underwent biliary stent placement between April 2001 and July 2015. Primary outcome was duration of stent patency. Secondary outcome was stent patency at 3 and 6 months. We used Kaplan–Meier survival analyses to compare stent patency rates between patients who received chemo(radio)therapy and patients who did not. Results  A total of 291 biliary stents (151 metal and 140 plastic) were identified. The median cumulative stent patency of FCSEMSs did not differ between patients receiving chemo(radio)therapy (n = 51) and those (n = 100) who did not ( P  = 0.70, log-rank test). The estimated cumulative stent patency of plastic stents was also comparable in 99 patients without and 41 patients with chemo(radio)therapy ( P  = 0.73, log-rank test). At 3 and 6 months, FCSEMS patency rates were 87 % and 83 % in patients without chemo(radio)therapy and 96 % and 83 % in patients with therapy, respectively. Plastic patency rates were 69 % and 55 % in patients without and 85 % and 39 % in patients with therapy, respectively. After 1 year, 78 % of the FCSEMSs were still patent in patients without chemo(radio)therapy and 69 % of the FCSEMSs were still patent in patients with therapy. Conclusion  Our data indicate that chemo(radio)therapy does not reduce the patency of biliary fully-covered metal and plastic stents. PMID:29090242

Anthracycline-based triplets do not improve the efficacy of platinum-fluoropyrimidine doublets in first-line treatment of advanced gastric cancer: real-world data from the AGAMEMON National Cancer Registry.

PubMed

Carmona-Bayonas, A; Jiménez-Fonseca, P; Custodio, A; Sánchez Cánovas, M; Hernández, R; Pericay, C; Echavarria, I; Lacalle, A; Visa, L; Rodríguez Palomo, A; Mangas, M; Cano, J M; Buxo, E; Álvarez-Manceñido, F; García, T; Lorenzo, J E; Ferrer-Cardona, M; Viudez, A; Azkarate, A; Ramchandani, A; Arias, D; Longo, F; López, C; Sánchez Bayona, R; Limón, M L; Díaz-Serrano, A; Fernández Montes, A; Sala, P; Cerdá, P; Rivera, F; Gallego, J

2018-01-01

Although anthracycline-based triplets are one of the most widely used schedules to treat advanced gastric cancer (AGC), the benefit of including epirubicin in these therapeutic combinations remains unknown. This study aims to evaluate both the efficacy and tolerance of triplets with epirubicin vs. doublets with platinum-fluoropyrimidine in a national AGC registry. Patients with AGC treated with polychemotherapy without trastuzumab at 28 hospitals in Spain between 2008 and 2016 were included. The effect of anthracycline-based triplets against doublets was evaluated by propensity score matching (PSM) and Cox proportional hazards (PH) regression. A total of 1002 patients were included (doublets, n = 653; anthracycline-based triplets, n = 349). The multivariable Cox PH regression failed to detect significantly increased OS in favor of triplets with anthracyclines: HR 0.90 (95% CI, 0.78-1.05), p = 0.20035. After PSM, the sample contained 325 pairs with similar baseline characteristics. This method was also unable to reveal an increase in OS: 10.5 (95% CI, 9.7-12.3) vs. 9.9 (95% CI, 9.2-11.4) months, HR 0.91 (CI 95%, 0.76-1.083), and (log-rank test, p = 0.226). Response rates (42.1 vs. 33.1%, p = 0.12) and PFS (HR 0.95, CI 95%, 0.80-1.13, log-rank test, p = 0.873) were not significantly higher with epirubicin-based regimens. The triplets were associated with greater grade 3-4 hematological toxicity, and increased hospitalization due to toxicity by 68%. The addition of epirubicin is viable, but 23.7% discontinued treatment because of adverse effects or patient decision. Anthracyclines added to platinum-fluoropyrimidine doublets did not improve the response rate or survival outcomes in patients with AGC but entailed greater toxicity.

DNA methyltransferase3a expression is an independent poor prognostic indicator in gastric cancer

PubMed Central

Cao, Xue-Yuan; Ma, Hong-Xi; Shang, Yan-Hong; Jin, Mei-Shan; Kong, Fei; Jia, Zhi-Fang; Cao, Dong-Hui; Wang, Yin-Ping; Suo, Jian; Jiang, Jing

2014-01-01

AIM: To explore the alteration of DNA methyltransferase expression in gastric cancer and to assess its prognostic value. METHODS: From April 2000 to December 2010, 227 men and 73 women with gastric cancer were enrolled in the study. The expression of DNA methyltransferases (DNMTs), including DNMT1, DNMT3a and DNMT3b, in the 300 cases of gastric carcinoma, of which 85 had paired adjacent normal gastric mucus samples, was evaluated by immunohistochemistry using a tissue microarray. Serum anti-Helicobacter pylori (H. pylori) IgG was detected by enzyme-linked immunosorbent assay (ELISA). The relationships between the above results and the clinicopathological characteristics were analyzed. Their prognostic value was evaluated using the Cox proportional hazards model. RESULTS: In gastric cancer, expression of DNMTs was mainly seen in the nucleus. Weak staining was also observed in the cytoplasm. Expression of DNMT1, DNMT3a and DNMT3b in gastric cancer was significantly higher compared to that in the paired control samples (60.0% vs 37.6%, 61.2% vs 4.7%, and 94.1% vs 71.8%, P < 0.01). The overall survival rate was significantly higher in the DNMT3a negative group than in the DNMT3a positive group in gastric cancer patients (Log-rank test, P = 0.032). No significant correlation was observed between DNMT1 and DNMT3b expression and the overall survival time (Log-rank test, P = 0.289, P = 0.347). Multivariate regression analysis indicated that DNMT3a expression (P = 0.025) and TNM stage (P < 0.001), but not DNMT1 (P = 0.54) or DNMT3b (P = 0.62), were independent prognostic factors in gastric cancer. H. pylori infection did not induce protein expression of DNMTs. CONCLUSION: The results suggest that expression of DNMT3a is an independent poor prognostic indicator in gastric cancer. DNMT3a might play an important role in gastric carcinogenesis. PMID:25009393

Prognostic Significance of Diffuse Large B-Cell Lymphoma Cell of Origin Determined by Digital Gene Expression in Formalin-Fixed Paraffin-Embedded Tissue Biopsies

PubMed Central

Scott, David W.; Mottok, Anja; Ennishi, Daisuke; Wright, George W.; Farinha, Pedro; Ben-Neriah, Susana; Kridel, Robert; Barry, Garrett S.; Hother, Christoffer; Abrisqueta, Pau; Boyle, Merrill; Meissner, Barbara; Telenius, Adele; Savage, Kerry J.; Sehn, Laurie H.; Slack, Graham W.; Steidl, Christian; Staudt, Louis M.; Connors, Joseph M.; Rimsza, Lisa M.; Gascoyne, Randy D.

2015-01-01

Purpose To evaluate the prognostic impact of cell-of-origin (COO) subgroups, assigned using the recently described gene expression–based Lymph2Cx assay in comparison with International Prognostic Index (IPI) score and MYC/BCL2 coexpression status (dual expressers). Patients and Methods Reproducibility of COO assignment using the Lymph2Cx assay was tested employing repeated sampling within tumor biopsies and changes in reagent lots. The assay was then applied to pretreatment formalin-fixed paraffin-embedded tissue (FFPET) biopsies from 344 patients with de novo diffuse large B-cell lymphoma (DLBCL) uniformly treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) at the British Columbia Cancer Agency. MYC and BCL2 protein expression was assessed using immunohistochemistry on tissue microarrays. Results The Lymph2Cx assay provided concordant COO calls in 96% of 49 repeatedly sampled tumor biopsies and in 100% of 83 FFPET biopsies tested across reagent lots. Critically, no frank misclassification (activated B-cell–like DLBCL to germinal center B-cell–like DLBCL or vice versa) was observed. Patients with activated B-cell–like DLBCL had significantly inferior outcomes compared with patients with germinal center B-cell–like DLBCL (log-rank P < .001 for time to progression, progression-free survival, disease-specific survival, and overall survival). In pairwise multivariable analyses, COO was associated with outcomes independent of IPI score and MYC/BCL2 immunohistochemistry. The prognostic significance of COO was particularly evident in patients with intermediate IPI scores and the non–MYC-positive/BCL2-positive subgroup (log-rank P < .001 for time to progression). Conclusion Assignment of DLBCL COO by the Lymph2Cx assay using FFPET biopsies identifies patient groups with significantly different outcomes after R-CHOP, independent of IPI score and MYC/BCL2 dual expression. PMID:26240231

Effect of the lung allocation score on lung transplantation in the United States.

PubMed

Egan, Thomas M; Edwards, Leah B

2016-04-01

On May 4, 2005, the system for allocation of deceased donor lungs for transplant in the United States changed from allocation based on waiting time to allocation based on the lung allocation score (LAS). We sought to determine the effect of the LAS on lung transplantation in the United States. Organ Procurement and Transplantation Network data on listed and transplanted patients were analyzed for 5 calendar years before implementation of the LAS (2000-2004), and compared with data from 6 calendar years after implementation (2006-2011). Counts were compared between eras using the Wilcoxon rank sum test. The rates of transplant increase within each era were compared using an F-test. Survival rates computed using the Kaplan-Meier method were compared using the log-rank test. After introduction of the LAS, waitlist deaths decreased significantly, from 500/year to 300/year; the number of lung transplants increased, with double the annual increase in rate of lung transplants, despite no increase in donors; the distribution of recipient diagnoses changed dramatically, with significantly more patients with fibrotic lung disease receiving transplants; age of recipients increased significantly; and 1-year survival had a small but significant increase. Allocating lungs for transplant based on urgency and benefit instead of waiting time was associated with fewer waitlist deaths, more transplants performed, and a change in distribution of recipient diagnoses to patients more likely to die on the waiting list. Copyright © 2016 International Society for Heart and Lung Transplantation. All rights reserved.

Does autologous blood transfusion during liver transplantation for hepatocellular carcinoma increase risk of recurrence?

PubMed Central

Araujo, Raphael LC; Pantanali, Carlos Andrés; Haddad, Luciana; Rocha Filho, Joel Avancini; D’Albuquerque, Luiz Augusto Carneiro; Andraus, Wellington

2016-01-01

AIM: To analyze outcomes in patients who underwent liver transplantation (LT) for hepatocellular carcinoma (HCC) and received autologous intraoperative blood salvage (IBS). METHODS: Consecutive HCC patients who underwent LT were studied retrospectively and analyzed according to the use of IBS or not. Demographic and surgical data were collected from a departmental prospective maintained database. Statistical analyses were performed using the Fisher’s exact test and the Wilcoxon rank sum test to examine covariate differences between patients who underwent IBS and those who did not. Univariate and multivariate Cox regression models were developed to evaluate recurrence and death, and survival probabilities were estimated using the Kaplan-Meier method and compared by the log-rank test. RESULTS: Between 2002 and 2012, 158 consecutive patients who underwent LT in the same medical center and by the same surgical team were identified. Among these patients, 122 (77.2%) were in the IBS group and 36 (22.8%) in the non-IBS group. The overall survival (OS) and recurrence free survival (RFS) at 5 years were 59.7% and 83.3%, respectively. No differences in OS (P = 0.51) or RFS (P = 0.953) were detected between the IBS and non-IBS groups. On multivariate analysis for OS, degree of tumor differentiation remained as the only independent predictor. Regarding patients who received IBS, no differences were detected in OS or RFS (P = 0.055 and P = 0.512, respectively) according to the volume infused, even when outcomes at 90 d or longer were analyzed separately (P = 0.518 for both outcomes). CONCLUSION: No differences in RFS or OS were detected according to IBS use. Trials addressing this question are justified and should be designed to detect small differences in long-term outcomes. PMID:26981190

Finding differentially expressed genes in high dimensional data: Rank based test statistic via a distance measure.

PubMed

Mathur, Sunil; Sadana, Ajit

2015-12-01

We present a rank-based test statistic for the identification of differentially expressed genes using a distance measure. The proposed test statistic is highly robust against extreme values and does not assume the distribution of parent population. Simulation studies show that the proposed test is more powerful than some of the commonly used methods, such as paired t-test, Wilcoxon signed rank test, and significance analysis of microarray (SAM) under certain non-normal distributions. The asymptotic distribution of the test statistic, and the p-value function are discussed. The application of proposed method is shown using a real-life data set. © The Author(s) 2011.

Germline Variation in HSD3B1 as a Novel Biomarker in Prostate Cancer

DTIC Science & Technology

2017-10-01

metastasis. Taken together, these results indicate that HSD3B1 genotype is a powerful genetic biomarker of resistance to ADT, and can be used to...salvage ADT. We analyzed differences in these endpoints according to genotype using an additive genetic model with the log-rank trend test...indicate that HSD3B1 genotype is a powerful genetic biomarker of resistance to ADT, and can be used to identify men who might benefit from escalated

E2F transcription factor 2 variants as predictive biomarkers for recurrence risk in patients with squamous cell carcinoma of the oropharynx.

PubMed

Li, Yuncheng; Sturgis, Erich M; Zhu, Lijun; Cao, Xiaoli; Wei, Qingyi; Zhang, Hua; Li, Guojun

2017-04-01

Because E2F transcription factor 2 (E2F2) promoter polymorphisms have been implicated in carcinogenesis and prognosis, we investigated associations between genetic variants in five E2F2 promoter polymorphisms and recurrence risk of squamous cell carcinoma of the oropharynx (SCCOP) in 1 008 patients. A log-rank test and multivariable Cox models were used to assess the associations. Compared with patients with variant genotypes of E2F2-rs2742976 and E2F2-rs3218123, patients with common homozygous genotypes had better disease-free survival (both log-rank, P < 0.001) and lower SCCOP recurrence risk (HR, 0.4, 95% CI, 0.3-0.6 and HR, 0.3, 95% CI, 0.2-0.5, respectively) after multivariable adjustment. Furthermore, among patients with HPV16-positive tumors, those with common homozygous genotypes of E2F2-rs2742976 and E2F2-rs3218123 had better disease-free survival rates (both log-rank, P < 0.001) and lower recurrence risk (HR, 0.1, 95% CI, 0.1-0.4 and HR, 0.1, 95% CI, 0.0-0.2, respectively) than patients with variant genotypes. However, no significant differences were found for the other three polymorphisms. After combining the risk genotypes of the five polymorphisms and using the high-risk group (2-5 risk genotypes) as the reference group, we found that the low-risk groups (0 or 1 risk genotype) had significantly lower recurrence risk among all patients (HR, 0.4, 95% CI, 0.3-0.6) and among HPV16-positive patients (HR, 0.2, 95% CI, 0.1-0.5). Our findings suggest that E2F2 polymorphisms may individually or jointly modify SCCOP recurrence risk, particularly for SCCOP patients with HPV16-positive tumors. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Ligand- and cell-dependent determinants of internalization and cAMP modulation by delta opioid receptor (DOR) agonists

PubMed Central

Charfi, Iness; Nagi, Karim; Mnie-Filali, Ouissame; Thibault, Dominic; Balboni, Gianfranco; Schiller, Peter W.; Trudeau, Louis-Eric

2014-01-01

Signaling bias refers to G protein-coupled receptor ligand ability to preferentially activate one type of signal over another. Bias to evoke signaling as opposed to sequestration has been proposed as a predictor of opioid ligand potential for generating tolerance. Here we measured whether delta opioid receptor agonists preferentially inhibited cyclase activity over internalization in HEK cells. Efficacy (τ) and affinity (KA) values were estimated from functional data and bias was calculated from efficiency coefficients (log τ/KA). This approach better represented the data as compared to alternative methods that estimate bias exclusively from τ values. Log (τ/KA) coefficients indicated that SNC-80 and UFP-512 promoted cyclase inhibition more efficiently than DOR internalization as compared to DPDPE (bias factor for SNC-80: 50 and for UFP-512: 132). Molecular determinants of internalization were different in HEK293 cells and neurons with βarrs contributing to internalization in both cell types, while PKC and GRK2 activities were only involved in neurons. Rank orders of ligand ability to engage different internalization mechanisms in neurons were compared to rank order of Emax values for cyclase assays in HEK cells. Comparison revealed a significant reversal in rank order for cyclase Emax values and βarr-dependent internalization in neurons, indicating that these responses were ligand-specific. Despite this evidence, and because kinases involved in internalization were not the same across cellular backgrounds, it is not possible to assert if the magnitude and nature of bias revealed by rank orders of maximal responses is the same as the one measured in HEK cells. PMID:24022593

Factors for Predicting Outcomes among Non-HIV Patients with Pulmonary Tuberculosis

PubMed Central

Tsukahara, Toshinori; Horita, Nobuyuki; Tashiro, Ken; Nagai, Kenjiro; Shinkai, Masaharu; Yamamoto, Masaki; Sato, Takashi; Hara, Yu; Nagakura, Hideyuki; Shibata, Yuji; Watanabe, Hiroki; Nakashima, Kentaro; Ushio, Ryota; Nagashima, Akimichi; Ikeda, Misako; Narita, Atsuya; Sasaki, Katsuhito; Kobayashi, Nobuaki; Kudo, Makoto; Kaneko, Takeshi

2017-01-01

Objective Onodera's Prognostic Nutritional Index (PNI), determined as “10× albumin (g/dL) + 0.005× lymphocyte count (/μL),” was originally designed to determine the risk of complications following gastrointestinal surgery. This single-center, retrospective observational study was designed to investigate whether or not the PNI can predict the treatment outcome. Methods We consecutively reviewed HIV-negative pulmonary tuberculosis adults in an isolation ward. Most patients were being treated with standard three- or four-drug regimens. Patients were discharged after consecutive negative smears/cultures were confirmed. The risk of all-cause death was assessed using a multivariable Cox proportional hazard model and a log-rank trend test. Results During the observation period, we observed 371 consecutive patients with a median age of 72 (interquartile range [IQR]: 54-82) years. In our cohort, 295 (79.5%) patients were discharged alive, and 76 (20.5%) died in-hospital. Patients who died in-hospital had a lower PNI [median 21.2 (IQR: 18.5-25.9)] than those who were discharged alive [median 35.1 (IQR: 28.0-43.3); p<0.001]. The area under the receiver operating characteristic curve was 0.87. After dividing the patients based on the baseline PNI quartile, those patients with a lower PNI showed a poorer survival than those with a higher PNI (log-rank trend p<0.001). After adjusting for other baseline variables, the baseline PNI was still associated with in-hospital death with a hazard ratio of 0.86 (95% confidence interval: 0.82-0.91, p<0.001). Conclusion Our results showed that a low PNI was clearly related to a poor survival prognosis in smear-positive HIV-negative pulmonary tuberculosis inpatients. PMID:29021438

Factors for Predicting Outcomes among Non-HIV Patients with Pulmonary Tuberculosis.

PubMed

Tsukahara, Toshinori; Horita, Nobuyuki; Tashiro, Ken; Nagai, Kenjiro; Shinkai, Masaharu; Yamamoto, Masaki; Sato, Takashi; Hara, Yu; Nagakura, Hideyuki; Shibata, Yuji; Watanabe, Hiroki; Nakashima, Kentaro; Ushio, Ryota; Nagashima, Akimichi; Ikeda, Misako; Narita, Atsuya; Sasaki, Katsuhito; Kobayashi, Nobuaki; Kudo, Makoto; Kaneko, Takeshi

2017-12-15

Objective Onodera's Prognostic Nutritional Index (PNI), determined as "10× albumin (g/dL) + 0.005× lymphocyte count (/μL)," was originally designed to determine the risk of complications following gastrointestinal surgery. This single-center, retrospective observational study was designed to investigate whether or not the PNI can predict the treatment outcome. Methods We consecutively reviewed HIV-negative pulmonary tuberculosis adults in an isolation ward. Most patients were being treated with standard three- or four-drug regimens. Patients were discharged after consecutive negative smears/cultures were confirmed. The risk of all-cause death was assessed using a multivariable Cox proportional hazard model and a log-rank trend test. Results During the observation period, we observed 371 consecutive patients with a median age of 72 (interquartile range [IQR]: 54-82) years. In our cohort, 295 (79.5%) patients were discharged alive, and 76 (20.5%) died in-hospital. Patients who died in-hospital had a lower PNI [median 21.2 (IQR: 18.5-25.9)] than those who were discharged alive [median 35.1 (IQR: 28.0-43.3); p<0.001]. The area under the receiver operating characteristic curve was 0.87. After dividing the patients based on the baseline PNI quartile, those patients with a lower PNI showed a poorer survival than those with a higher PNI (log-rank trend p<0.001). After adjusting for other baseline variables, the baseline PNI was still associated with in-hospital death with a hazard ratio of 0.86 (95% confidence interval: 0.82-0.91, p<0.001). Conclusion Our results showed that a low PNI was clearly related to a poor survival prognosis in smear-positive HIV-negative pulmonary tuberculosis inpatients.

Lack of Thy1 (CD90) expression in neuroblastomas is correlated with impaired survival.

PubMed

Fiegel, Henning C; Kaifi, Jussuf T; Quaas, Alexander; Varol, Emine; Krickhahn, Annika; Metzger, Roman; Sauter, Guido; Till, Holger; Izbicki, Jakob R; Erttmann, Rudolf; Kluth, Dietrich

2008-01-01

Neuroblastoma (NBL) is the most common solid tumor in children. Tumors in advanced stage or with positive risk factors still have a poor prognosis. Thy1 (CD90) is a membrane glycoprotein expressed in thymus, retinal ganglionic cells, and several types of stem cells. The aim of this study was to assess Thy1 expression in NBL and analyze the correlation with clinical outcome. Sixty-three specimens of NBL were stained for Thy1 on a tissue microarray by immunohistochemistry. Fresh frozen tumor tissues were used for RNA isolation, and RT-PCR analysis for Thy1-mRNA expression was performed. Patients' survival data were correlated with Thy1 status using a log rank test and a Cox regression multivariate analysis. Thy1 was expressed on 51 (81%) of the tumors. Kaplan-Meier survival analysis showed a significantly impaired survival in patients with NBL missing Thy1 (P < 0.005 by log-rank test). A multivariate Cox regression showed an independent prognostic value of Thy1 status for overall survival (P < 0.05). In addition, the frequency of events and deaths was significantly higher in the group of patients with Thy1 negative tumors, as assessed by ANOVA analysis (P < 0.05 by F-test). The data showed that Thy1-negative NBL patients have a significantly impaired overall survival compared with Thy1-positive NBL patients. Thus, Thy1 seemed to be a marker with a specific prognostic value in NBL patients. Future studies are aiming at the biological role of this marker in the tumor cell differentiation.

The choice of statistical methods for comparisons of dosimetric data in radiotherapy.

PubMed

Chaikh, Abdulhamid; Giraud, Jean-Yves; Perrin, Emmanuel; Bresciani, Jean-Pierre; Balosso, Jacques

2014-09-18

Novel irradiation techniques are continuously introduced in radiotherapy to optimize the accuracy, the security and the clinical outcome of treatments. These changes could raise the question of discontinuity in dosimetric presentation and the subsequent need for practice adjustments in case of significant modifications. This study proposes a comprehensive approach to compare different techniques and tests whether their respective dose calculation algorithms give rise to statistically significant differences in the treatment doses for the patient. Statistical investigation principles are presented in the framework of a clinical example based on 62 fields of radiotherapy for lung cancer. The delivered doses in monitor units were calculated using three different dose calculation methods: the reference method accounts the dose without tissues density corrections using Pencil Beam Convolution (PBC) algorithm, whereas new methods calculate the dose with tissues density correction for 1D and 3D using Modified Batho (MB) method and Equivalent Tissue air ratio (ETAR) method, respectively. The normality of the data and the homogeneity of variance between groups were tested using Shapiro-Wilks and Levene test, respectively, then non-parametric statistical tests were performed. Specifically, the dose means estimated by the different calculation methods were compared using Friedman's test and Wilcoxon signed-rank test. In addition, the correlation between the doses calculated by the three methods was assessed using Spearman's rank and Kendall's rank tests. The Friedman's test showed a significant effect on the calculation method for the delivered dose of lung cancer patients (p <0.001). The density correction methods yielded to lower doses as compared to PBC by on average (-5 ± 4.4 SD) for MB and (-4.7 ± 5 SD) for ETAR. Post-hoc Wilcoxon signed-rank test of paired comparisons indicated that the delivered dose was significantly reduced using density-corrected methods as compared to the reference method. Spearman's and Kendall's rank tests indicated a positive correlation between the doses calculated with the different methods. This paper illustrates and justifies the use of statistical tests and graphical representations for dosimetric comparisons in radiotherapy. The statistical analysis shows the significance of dose differences resulting from two or more techniques in radiotherapy.

Cirrhosis Diagnosis and Liver Fibrosis Staging: Transient Elastometry Versus Cirrhosis Blood Test.

PubMed

Calès, Paul; Boursier, Jérôme; Oberti, Frédéric; Bardou, Derek; Zarski, Jean-Pierre; de Lédinghen, Victor

2015-07-01

Elastometry is more accurate than blood tests for cirrhosis diagnosis. However, blood tests were developed for significant fibrosis, with the exception of CirrhoMeter developed for cirrhosis. We compared the performance of Fibroscan and CirrhoMeter, and classic binary cirrhosis diagnosis versus new fibrosis staging for cirrhosis diagnosis. The diagnostic population included 679 patients with hepatitis C and liver biopsy (Metavir staging and morphometry), Fibroscan, and CirrhoMeter. The prognostic population included 1110 patients with chronic liver disease and both tests. Binary diagnosis: AUROCs for cirrhosis were: Fibroscan: 0.905; CirrhoMeter: 0.857; and P=0.041. Accuracy (Youden cutoff) was: Fibroscan: 85.4%; CirrhoMeter: 79.2%; and P<0.001. Fibrosis classification provided 6 classes (F0/1, F1/2, F2±1, F3±1, F3/4, and F4). Accuracy was: Fibroscan: 88.2%; CirrhoMeter: 88.8%; and P=0.77. A simplified fibrosis classification comprised 3 categories: discrete (F1±1), moderate (F2±1), and severe (F3/4) fibrosis. Using this simplified classification, CirrhoMeter predicted survival better than Fibroscan (respectively, χ=37.9 and 19.7 by log-rank test), but both predicted it well (P<0.001 by log-rank test). Comparison: binary diagnosis versus fibrosis classification, respectively, overall accuracy: CirrhoMeter: 79.2% versus 88.8% (P<0.001); Fibroscan: 85.4% versus 88.2% (P=0.127); positive predictive value for cirrhosis by Fibroscan: Youden cutoff (11.1 kPa): 49.1% versus cutoffs of F3/4 (17.6 kPa): 67.6% and F4 classes (25.7 kPa): 82.4%. Fibroscan's usual binary cutoffs for cirrhosis diagnosis are not sufficiently accurate. Fibrosis classification should be preferred over binary diagnosis. A cirrhosis-specific blood test markedly attenuates the accuracy deficit for cirrhosis diagnosis of usual blood tests versus transient elastometry, and may offer better prognostication.

Clinical evaluation of flowable resins in non-carious cervical lesions: two-year results.

PubMed

Celik, Cigdem; Ozgünaltay, Gül; Attar, Nuray

2007-01-01

This study evaluated the two-year clinical performance of one microhybrid composite and three different types of flowable resin materials in non-carious cervical lesions. A total of 252 noncarious cervical lesions were restored in 37 patients (12 male, 25 female) with Admira Flow, Dyract Flow, Filtek Flow and Filtek Z250, according to manufacturers' instructions. All the restorations were placed by one operator, and two other examiners evaluated the restorations clinically within one week after placement and after 6, 12, 18 and 24 months, using modified USPHS criteria. At the end of 24 months, 172 restorations were evaluated in 26 patients, with a recall rate of 68%. Statistical analysis was completed using the Pearson Chi-square and Fisher-Freeman-Halton tests (p < 0.05). Additionally, survival rates were analyzed with the Kaplan-Meier estimator and the Log-Rank test (p < 0.05). The Log-Rank test indicated statistically significant differences between the survival rates of Dyract Flow/Admira Flow and Dyract Flow/Filtek Z250 (p < 0.05). While there was a statistically significant difference between Dyract Flow and the other materials for color match at 12 and 18 months, no significant difference was observed among all of the materials tested at 24 months. Significant differences were revealed between Filtek Z250 and the other materials for marginal adaptation at 18 and 24 months (p < 0.05). With respect to marginal discoloration, secondary caries, surface texture and anatomic form, no significant differences were found between the resin materials (p > 0.05). It was concluded that different types of resin materials demonstrated acceptable clinical performance in non-carious cervical lesions, except for the retention rates of the Dyract Flow restorations.

Prevalence of hypertension and type 2 diabetes mellitus in patients with colorectal cancer and their median survival time: A cohort study.

PubMed

Ahmadi, Ali; Mobasheri, Mahmoud; Hashemi-Nazari, Seyed Saeed; Baradaran, Azar; Choobini, Zahra Molavi

2014-09-01

Type 2 diabetes mellitus (DM) and hypertension are worldwide epidemic. Association between DM and colon cancer was obtained in previous studies. Prevalence of DM and hypertension in the patients with colorectal cancer (CRC) has not been reported in Iran. The present study was aimed to investigate the prevalence of hypertension and type 2 DM and their effect on median survival time in patients with CRC. Overall, 2570 individual-year follow-ups were conducted for 1127 patients with CRC. For the diagnosis of type 2 DM, fasting blood sugar test and glycosylated hemoglobin test were used and for hypertension, blood pressure was measured in two turns. The descriptive indices were calculated, and the mean and median survival from CRC diagnosis time was calculated using survival analysis and a comparison among survival times was done through log-rank test. Stata software 12 (Stata Corp. 2011. Stata Statistical Software: Release 12. College Station, TX: Stata Corp LP) was used for data analysis. The prevalence of hypertension and type 2 DM in the patients with CRC was respectively 13.38% (95% confidence interval [CI]: 11.1-15.8) and 8.69% (95% CI: 7-10.7). Median survival time in patients with hypertension and DM were 8.52 and 4.9 years. According to log-rank test, no significant difference was observed between the survival time of CRC patients suffering from hypertension and diabetes type 2. The obtained findings in this study indicate that survival time in patients with type 2 DM less than hypertension but two metabolic diseases have the same effect on survival rate of the patients with CRC. Understanding the risk factors for CRC may guide the development of strategies targeted toward its prevention.

Self-refraction accuracy with adjustable spectacles among children in Ghana.

PubMed

Ilechie, Alex Azuka; Abokyi, Samuel; Owusu-Ansah, Andrew; Boadi-Kusi, Samuel Bert; Denkyira, Andrew Kofi; Abraham, Carl Halladay

2015-04-01

To determine the accuracy of self-refraction (SR) in myopic teenagers, we compared visual and refractive outcomes of self-refracting spectacles (FocusSpecs) with those obtained using cycloplegic subjective refraction (CSR) as a gold standard. A total of 203 eligible schoolchildren (mean [±SD] age, 13.8 [±1.0] years; 59.1% were female) completed an examination consisting of SR with FocusSpecs adjustable spectacles, visual acuity with the logMAR (logarithm of the minimum angle of resolution) chart, cycloplegic retinoscopy, and CSR. Examiners were masked to the SR findings. Wilcoxon signed rank test and paired Student t test were used to compare measures across refraction methods (95% confidence intervals [CIs]). The mean (±SD) spherical equivalent refractive error measured by CSR and SR was -1.22 (±0.49) diopters (D) and -1.66 (±0.73) D, respectively, a statistically significant difference of -0.44 D (p < 0.001, t = 15.517). The greatest proportion of participants was correctable to visual acuity greater than or equal to 6/7.5 (logMAR 0.1) in the better eye by CSR (99.0%; 95% CI, 96.5 to 99.7%), followed by cycloplegic retinoscopy (94.1%; 95% CI, 90.0 to 96.6%) and SR (85.2%; 95% CI, 79.7 to 89.5%). These proportions differed significantly from each other (p < 0.001, Wilcoxon signed rank test). Myopic inaccuracy of greater than 0.50 D and greater than or equal to -1.00 D was present in 29 (15.3%) and 16 (8.4%) right eyes, respectively, with SR. In logistic regression models, failure to achieve visual acuity greater than or equal to 6/7.5 in right eyes with SR was significantly associated with age (odds ratio, 1.92; 95% CI, 1.12 to 3.28; p = 0.017) and spherical power (odds ratio, 0.017; 95% CI, 0.005 to 0.056; p < 0.001). Self-refraction offers acceptable visual and refractive results for young people in a rural setting in Ghana, although myopic inaccuracy in the more negative direction occurred in some children.

Pyrolysis g.c.-m.s. of a series of degraded woods and coalified logs that increase in rank from peat to subbituminous coal

USGS Publications Warehouse

Hatcher, P.G.; Lerch, H. E.; Kotra, R.K.; Verheyen, T.V.

1988-01-01

Xylem tissue from degraded wood and coalified logs or stems was examined by pyrolysis g.c.-m.s. to improve understanding of the coalification process. The pyrolysis data, when combined with solid-state 13C n.m.r. data for the same samples, show several stages of evolution during coalification. The first stage, microbial degradation in peat, involves the selective degradation of cellulosic components and preservation of lignin-like components. As coalification increases, the lignin structural units undergo a series of defunctionalization reactions. The first of these involve loss of methoxyl groups, with replacement by phenolic hydroxyls such that catechol-like structures are produced. As the xylem tissue is converted to subbituminous coal, the persistence of phenols and methylated phenols in pyrolysis g.c.-m.s. data of subbituminous coal suggests that the catechol-like structures are being converted to phenol-like structures. The ability to discern detailed changes in the chemical structural composition of a genetically and histologically related series of samples provides an ideal method for developing models of coal structure, especially that of low-rank coal. ?? 1988.

Rank Dynamics

NASA Astrophysics Data System (ADS)

Gershenson, Carlos

Studies of rank distributions have been popular for decades, especially since the work of Zipf. For example, if we rank words of a given language by use frequency (most used word in English is 'the', rank 1; second most common word is 'of', rank 2), the distribution can be approximated roughly with a power law. The same applies for cities (most populated city in a country ranks first), earthquakes, metabolism, the Internet, and dozens of other phenomena. We recently proposed ``rank diversity'' to measure how ranks change in time, using the Google Books Ngram dataset. Studying six languages between 1800 and 2009, we found that the rank diversity curves of languages are universal, adjusted with a sigmoid on log-normal scale. We are studying several other datasets (sports, economies, social systems, urban systems, earthquakes, artificial life). Rank diversity seems to be universal, independently of the shape of the rank distribution. I will present our work in progress towards a general description of the features of rank change in time, along with simple models which reproduce it

Prognostic roles of preoperative α-fetoprotein and des-γ-carboxy prothrombin in hepatocellular carcinoma patients

PubMed Central

Meguro, Makoto; Mizuguchi, Toru; Nishidate, Toshihiko; Okita, Kenji; Ishii, Masayuki; Ota, Shigenori; Ueki, Tomomi; Akizuki, Emi; Hirata, Koichi

2015-01-01

AIM: To clarify the utility of using des-γ-carboxy prothrombin (DCP) and α-fetoprotein (AFP) levels to predict the prognosis of hepatocellular carcinoma (HCC) in patients with hepatitis B virus (HBV) and the hepatitis C virus (HCV) infections. METHODS: A total of 205 patients with HCC (105 patients with HBV infection 100 patients with HCV infection) who underwent primary hepatectomy between January 2004 and May 2012 were enrolled retrospectively. Preoperative AFP and DCP levels were used to create interactive dot diagrams to predict recurrence within 2 years after hepatectomy, and cutoff levels were calculated. Patients in the HBV and HCV groups were classified into three groups: a group with low AFP and DCP levels (LL group), a group in which one of the two parameters was high and the other was low (HL group), and a group with high AFP and DCP levels (HH group). Liver function parameters, the postoperative recurrence-free survival rate, and postoperative overall survival were compared between groups. The survival curves were compared by log-rank test using the Kaplan-Meier method. Multivariate analysis using a Cox forward stepwise logistic regression model was conducted for a prognosis. RESULTS: The preoperative AFP cutoff levels for recurrence within 2 years after hepatectomy in the HBV and HCV groups were 529.8 ng/mL and 60 mAU/mL, respectively; for preoperative DCP levels, the cutoff levels were 21.0 ng/mL in the HBV group and 67 mAU/mL in the HCV group. The HBV group was significantly different from the other groups in terms of vascular invasion, major hepatectomy, volume of intraoperative blood loss, and surgical duration. Significant differences were found between the LL group, the HL group, and the HH group in terms of both mean disease-free survival time (MDFST) and mean overall survival time (MOST): 64.81 ± 7.47 vs 36.63 ± 7.62 vs 18.98 ± 6.17 mo (P = 0.001) and 85.30 ± 6.55 vs 59.44 ± 7.87 vs 46.57 ± 11.20 mo (P = 0.018). In contrast, the HCV group exhibited a significant difference in tumor size, vascular invasion, volume of intraoperative blood loss, and surgical duration; however, no significant difference was observed between the three groups in liver function parameters except for albumin levels. In the LL group, the HL group, and the HH group, the MDFST was 50.09 ± 5.90, 31.01 ± 7.21, and 14.81 ± 3.08 mo (log-rank test, P < 0.001), respectively, and the MOST was 79.45 ± 8.30, 58.82 ± 7.56, and 32.87 ± 6.31 mo (log-rank test, P < 0.001), respectively. CONCLUSION: In the HBV group, the prognosis was poor when either AFP or DCP levels were high. In the HCV group, the prognosis was good when either or both levels were low; however, the prognosis was poor when both levels were high. High levels of both AFP and DCP were an independent risk factor associated with tumor recurrence in the HBV and HCV groups. The relationship between tumor marker levels and prognosis was characteristic to the type of viral hepatitis. PMID:25945007

Promoted combustion of nine structural metals in high-pressure gaseous oxygen - A comparison of ranking methods

NASA Technical Reports Server (NTRS)

Steinberg, Theodore A.; Rucker, Michelle A.; Beeson, Harold D.

1989-01-01

The 316, 321, 440C, and 17-4 PH stainless steels, as well as Inconel 600, Inconel 718, Waspaloy, Monel 400, and Al 2219, have been evaluated for relative nonflammability in a high-pressure oxygen environment with a view to the comparative advantages of four different flammability-ranking methods. The effects of changes in test pressure, sample diameter, promoter type, and sample configuration on ranking method results are evaluated; ranking methods employing velocity as the primary ranking criterion are limited by diameter effects, while those which use extinguishing pressure are nonselective for metals with similar flammabilities.

A Tensor-Train accelerated solver for integral equations in complex geometries

NASA Astrophysics Data System (ADS)

Corona, Eduardo; Rahimian, Abtin; Zorin, Denis

2017-04-01

We present a framework using the Quantized Tensor Train (QTT) decomposition to accurately and efficiently solve volume and boundary integral equations in three dimensions. We describe how the QTT decomposition can be used as a hierarchical compression and inversion scheme for matrices arising from the discretization of integral equations. For a broad range of problems, computational and storage costs of the inversion scheme are extremely modest O (log ⁡ N) and once the inverse is computed, it can be applied in O (Nlog ⁡ N) . We analyze the QTT ranks for hierarchically low rank matrices and discuss its relationship to commonly used hierarchical compression techniques such as FMM and HSS. We prove that the QTT ranks are bounded for translation-invariant systems and argue that this behavior extends to non-translation invariant volume and boundary integrals. For volume integrals, the QTT decomposition provides an efficient direct solver requiring significantly less memory compared to other fast direct solvers. We present results demonstrating the remarkable performance of the QTT-based solver when applied to both translation and non-translation invariant volume integrals in 3D. For boundary integral equations, we demonstrate that using a QTT decomposition to construct preconditioners for a Krylov subspace method leads to an efficient and robust solver with a small memory footprint. We test the QTT preconditioners in the iterative solution of an exterior elliptic boundary value problem (Laplace) formulated as a boundary integral equation in complex, multiply connected geometries.

Radiotracer properties determined by high performance liquid chromatography: a potential tool for brain radiotracer discovery.

PubMed

Tavares, Adriana Alexandre S; Lewsey, James; Dewar, Deborah; Pimlott, Sally L

2012-01-01

Previously, development of novel brain radiotracers has largely relied on simple screening tools. Improved selection methods at the early stages of radiotracer discovery and an increased understanding of the relationships between in vitro physicochemical and in vivo radiotracer properties are needed. We investigated if high performance liquid chromatography (HPLC) methodologies could provide criteria for lead candidate selection by comparing HPLC measurements with radiotracer properties in humans. Ten molecules, previously used as radiotracers in humans, were analysed to obtain the following measures: partition coefficient (Log P); permeability (P(m)); percentage of plasma protein binding (%PPB); and membrane partition coefficient (K(m)). Relationships between brain entry measurements (Log P, P(m) and %PPB) and in vivo brain percentage injected dose (%ID); and K(m) and specific binding in vivo (BP(ND)) were investigated. Log P values obtained using in silico packages and flask methods were compared with Log P values obtained using HPLC. The modelled associations with %ID were stronger for %PPB (r(2)=0.65) and P(m) (r(2)=0.77) than for Log P (r(2)=0.47) while 86% of BP(ND) variance was explained by K(m). Log P values were variable dependant on the methodology used. Log P should not be relied upon as a predictor of blood-brain barrier penetration during brain radiotracer discovery. HPLC measurements of permeability, %PPB and membrane interactions may be potentially useful in predicting in vivo performance and hence allow evaluation and ranking of compound libraries for the selection of lead radiotracer candidates at early stages of radiotracer discovery. Copyright © 2012 Elsevier Inc. All rights reserved.

Zipf law: an extreme perspective

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2016-04-01

Extreme value theory (EVT) asserts that the Fréchet law emerges universally from linearly scaled maxima of collections of independent and identically distributed random variables that are positive-valued. Observations of many real-world sizes, e.g. city-sizes, give rise to the Zipf law: if we rank the sizes decreasingly, and plot the log-sizes versus the log-ranks, then an affine line emerges. In this paper we present an EVT approach to the Zipf law. Specifically, we establish that whenever the Fréchet law emerges from the EVT setting, then the Zipf law follows. The EVT generation of the Zipf law, its universality, and its associated phase transition, are analyzed and described in detail.

Sawing SHOLO logs: three methods

Treesearch

Ronald E. Coleman; Hugh W. Reynolds

1973-01-01

Three different methods of sawing the SHOLO log were compared on a board-foot yield basis. Using sawmill simulation, all three methods of sawing were performed on the same sample of logs, eliminating differences due to sapling. A statistical test was made to determine whether or not there were any real differences between the board-foot yields. Two of the sawing...

Evaluating the Rank-Ordering Method for Standard Maintaining

ERIC Educational Resources Information Center

Bramley, Tom; Gill, Tim

2010-01-01

The rank-ordering method for standard maintaining was designed for the purpose of mapping a known cut-score (e.g. a grade boundary mark) on one test to an equivalent point on the test score scale of another test, using holistic expert judgements about the quality of exemplars of examinees' work (scripts). It is a novel application of an old…

Prognosis Related to Metastatic Burden Measured by 18F-Fluorocholine PET/CT in Castrate Resistant Prostate Cancer

PubMed Central

Kwee, Sandi A.; Lim, John; Watanabe, Alex; Kromer-Baker, Kathleen; Coel, Marc N.

2015-01-01

This study investigates the prognostic significance of metabolically active tumor volume (MATV) measurements applied to fluorine-18 fluorocholine (FC) PET/CT in castrate-resistant prostate cancer (CRPC). Methods FC PET/CT imaging was performed in 30 patients with CRPC. Metastatic disease was quantified on the basis of maximum standardized uptake value (SUVmax), MATV, and total lesion activity (TLA = MATV × mean SUV). Tumor burden indices derived from whole-body summation of PET tumor volume measurements (ie. net MATV and net TLA) were evaluated as variables in Cox regression and Kaplan-Meier survival analyses. Results Net MATV ranged from 0.12 cm3 to 1543.9 cm3 (median 52.6 cm3). Net TLA ranged from 0.40g to 6688.7g (median 225.1g). PSA level at the time of PET correlated significantly with net MATV (Pearson r = 0.65, p = 0.0001) and net TLA (r = 0.60, p = 0.0005) but not highest lesional SUVmax of each scan. Survivors were followed for a median 23 months (range 6 – 38 months). On Cox regression analyses, overall survival was significantly associated with net MATV (p = 0.0068), net TLA (p = 0.0072), and highest lesion SUVmax (p = 0.0173), and borderline associated with PSA level (p = 0.0458). Only net MATV and net TLA remained significant in univariate-adjusted survival analyses. Kaplan-Meier analysis demonstrated significant differences in survival between groups stratified by median net MATV (log-rank P = 0.0371), net TLA (log-rank P = 0.0371), and highest lesion SUVmax (log-rank P = 0.0223). Conclusions Metastatic prostate cancer detected by FC PET/CT can be quantified based on volumetric measurements of tumor metabolic activity. The prognostic value of FC PET/CT may stem from this capacity to assess whole-body tumor burden. With further clinical validation, FC PET-based indices of global disease activity and mortality risk could prove useful in patient-individualized treatment of CRPC. PMID:24676753

Survival of two post systems--five-year results of a randomized clinical trial.

PubMed

Schmitter, Marc; Hamadi, Khaled; Rammelsberg, Peter

2011-01-01

To assess the survival rate of two different post systems after 5 years of service with a prospective randomized controlled trial. One hundred patients in need of a post were studied. Half of the patients received long glass fiber-reinforced posts, while the other half received long metal screw posts. The posts were assigned randomly. After at least 5 years (mean, 61.37 months), follow-ups were established. When a complication occurred prior to this recall, the type and time of the complication was documented. Statistical analysis was performed using the log-rank test and Kaplan-Meier analysis. Additionally, a Cox regression was performed to analyze risk factors. The survival rate of fiber-reinforced posts was 71.8%. In the metal screw post group, the survival rate was significantly lower, 50.0% (log-rank test, P = .026). Metal posts resulted more often in more unfavorable complications (eg, root fractures); consequently, more teeth (n = 17) had to be extracted. The Cox regression identified the following risk factors: position of the tooth (anterior vs posterior teeth), degree of coronal tooth destruction, and the post system (fiber-reinforced post vs metal screw post). Fiber-reinforced restorations loosened in several patients; in some of these cases (n = 6), patients did not notice this, leading to the extraction of teeth. Long metal screw posts should be used with great care in endodontically treated teeth. Besides the selection of the post system, other factors influence the survival of the restoration.

Procedural revision to the use-dilution methods: establishment of maximum log density value for test microbes on inoculated carriers.

PubMed

Tomasino, Stephen F; Pines, Rebecca M; Hamilton, Gordon C

2012-01-01

(Staphylococcus aureus) and 964.02 (Pseudomonas aeruginosa), were revised in 2009 to include a standardized procedure to measure the log density of the test microbe and to establish a minimum mean log density value of 6.0 (geometric mean of 1.0 x 10(6) CFU/carrier) to qualify the test results. This report proposes setting a maximum mean log density value of 7.0 (geometric mean of 1.0 x 10(7) CFU/carrier) to further standardize the procedure. The minimum value was based on carrier count data collected by four laboratories over an 8-year period (1999-2006). The data have been updated to include an additional 4 years' worth of data (2006-2010) collected by the same laboratories. A total of 512 tests were conducted on products bearing claims against P. aeruginosa and S. aureus with and without an organic soil load (OSL) added to the inoculum (as specified on the product label claim). Six carriers were assayed in each test, for a total of 3072 carriers. Mean log densities for each of the 512 tests were at least 6.0. With the exception of two tests, one for P. aeruginosa without OSL and one for S. aureus with OSL, the mean log densities did not exceed 7.5 (geometric mean of 3.2 x 10(7) CFU/carrier). Across microbes and OSL treatments, the mean log density (+/- SEM) was 6.80 (+/- 0.07) per carrier (a geometric mean of 6.32 x 10(6) CFUlcarrier) and acceptable repeatability (0.28) and reproducibility (0.31) SDs were exhibited. A maximum mean log density per carrier of 7.0 is being proposed here as a validity requirement for S. aureus and P. aeruginosa. A modification to the method to allow for dilution of the final test cultures to achieve carrier counts within 6.0-7.0 logs is also being proposed. Establishing a range of 6.0-7.0 logs will help improve the reliability of the method and should allow for more consistent results within and among laboratories.

A Spreadsheet for a 2 x 3 x 2 Log-Linear Analysis. AIR 1991 Annual Forum Paper.

ERIC Educational Resources Information Center

Saupe, Joe L.

This paper describes a personal computer spreadsheet set up to carry out hierarchical log-linear analyses, a type of analysis useful for institutional research into multidimensional frequency tables formed from categorical variables such as faculty rank, student class level, gender, or retention status. The spreadsheet provides a concrete vehicle…

Randomization in cancer clinical trials: permutation test and development of a computer program.

PubMed Central

Ohashi, Y

1990-01-01

When analyzing cancer clinical trial data where the treatment allocation is done using dynamic balancing methods such as the minimization method for balancing the distribution of important prognostic factors in each arm, conservativeness occurs if such a randomization scheme is ignored and a simple unstratified analysis is carried out. In this paper, the above conservativeness is demonstrated by computer simulation, and the development of a computer program that carries out permutation tests of the log-rank statistics for clinical trial data where the allocation is done by the minimization method or a stratified permuted block design is introduced. We are planning to use this program in practice to supplement a usual stratified analysis and model-based methods such as the Cox regression. The most serious problem in cancer clinical trials in Japan is how to carry out the quality control or data management in trials that are initiated and conducted by researchers without support from pharmaceutical companies. In the final section of this paper, one international collaborative work for developing international guidelines on data management in clinical trials of bladder cancer is briefly introduced, and the differences between the system adopted in US/European statistical centers and the Japanese system is described. PMID:2269216

Relationships between hydrophobicity, reactivity, accumulation and peripheral nerve toxicity of a series of platinum drugs

PubMed Central

Screnci, D; McKeage, M J; Galettis, P; Hambley, T W; Palmer, B D; Baguley, B C

2000-01-01

Previous work has shown platinum drugs to differ in their effects on the peripheral nervous system. To test whether their differential toxicity was due to differences in their partitioning into the peripheral nervous system, we correlated the hydrophobicity, reactivity, tissue accumulation and neurotoxicity of a series of eight platinum analogues. Neurotoxicity was detected by measuring sensory nerve conduction velocity (SNCV) in Wistar rats treated twice per week at the maximum tolerated dose. Tissue platinum concentrations were measured by inductively coupled plasma mass spectrometry. Hydrophobicity (log P) was measured using an octanol-aqueous shake-flask method. The half-life of platinum drug binding to plasma proteins in vitro was determined. The cumulative dose causing altered SNCV ranged from 15 to > 2050 μmol kg−1. Ranking of the compounds by their neurotoxic potency in rats (oxaliplatin >R,R -(DACH)PtC4> ormaplatin >S,S -(DACH)PtCl4>S,S -(DACH)Pt oxalato > cisplatin > carboplatin > JM216) correlated with the frequency of neurotoxicity in patients (r> 0.99;P< 0.05). Ranking the compounds by their peripheral nerve accumulation was cisplatin > carboplatin > oxaliplatin >R,R -(DACH)PtCl4≈S,S -(DACH)PtCl4and did not correlate with neurotoxicity. Log P ranged from – 2.53 to –0.16 but did not correlate with neurotoxicity. Log P correlated inversely with platinum accumulation in dorsal root ganglia (r2= 0.99;P = 0.04), sural nerve (r2= 0.85;P = 0.025), sciatic nerve (r2= 0.98;P = 0.0012), spinal cord (r2= 0.97, P = 0.018) and brain (r2= 0.98, P = 0.001). Reactivity correlated with neurotoxicity potency in rats (r2= 0.89, P = 0.0005) and with the frequency of neurotoxicity in patients (r2= 0.99, P = 0.0002). The hydrophilicity of platinum drugs correlates with platinum sequestration in the peripheral nervous system but not with neurotoxicity. Differences in the reactivity of platinum complexes accounts for some of the variation in their neurotoxicity. © 2000 Cancer Research Campaign PMID:10732773

Importance of the ITF Junior Girls' Circuit in the development of women professional tennis players.

PubMed

Reid, Machar; Crespo, Miguel; Santilli, Luca

2009-11-01

In this study, we examined the extent to which ranking in professional women's tennis can be predicted by that in the top 20 International Tennis Federation's Junior Circuit. The names, nationalities, and birth dates of all players who achieved a top-20 girls' year-end ranking from 1995 to 2002 were recorded, with their progress through the professional ranks tracked to March 2008. Ninety-nine percent of top-20 ranked girls achieved a professional women's ranking. Stepwise regression analysis revealed peak junior ranking and the age at which that rank was achieved to be predictors of future professional ranking (r(2) = 0.133, P < 0.05). The following regression equation showed the achievement of a top-20 junior rank as a reasonable benchmark in the development of professional women players: log-transformed predicted professional rank = -0.552 + (0.032 x junior rank + 0.116 x age at junior rank). The predominant court surface on which junior players honed their skills was also implicated in professional ranking success, with clay-court play linked to the development of higher-ranked players (P < or = 0.01).

Weighted Discriminative Dictionary Learning based on Low-rank Representation

NASA Astrophysics Data System (ADS)

Chang, Heyou; Zheng, Hao

2017-01-01

Low-rank representation has been widely used in the field of pattern classification, especially when both training and testing images are corrupted with large noise. Dictionary plays an important role in low-rank representation. With respect to the semantic dictionary, the optimal representation matrix should be block-diagonal. However, traditional low-rank representation based dictionary learning methods cannot effectively exploit the discriminative information between data and dictionary. To address this problem, this paper proposed weighted discriminative dictionary learning based on low-rank representation, where a weighted representation regularization term is constructed. The regularization associates label information of both training samples and dictionary atoms, and encourages to generate a discriminative representation with class-wise block-diagonal structure, which can further improve the classification performance where both training and testing images are corrupted with large noise. Experimental results demonstrate advantages of the proposed method over the state-of-the-art methods.

Assessment of subjective intraocular forward scattering and quality of vision after posterior chamber phakic intraocular lens with a central hole (Hole ICL) implantation.

PubMed

Iijima, Ayaka; Shimizu, Kimiya; Yamagishi, Mayumi; Kobashi, Hidenaga; Igarashi, Akihito; Kamiya, Kazutaka

2016-12-01

To evaluate the subjective intraocular forward scattering and quality of vision after posterior chamber phakic intraocular lens with a central hole (Hole ICL, STAAR Surgical) implantation. We prospectively examined 29 eyes of 29 consecutive patients (15 men and 14 women; ages, 37.2 ± 8.8 years) undergoing Hole ICL implantation. We assessed the values of the logarithmic straylight value [log (s)] using a straylight meter (C-Quant ™ , Oculus) preoperatively and 3 months postoperatively. The patients completed a questionnaire detailing symptoms on a quantitative grading scale (National Eye Institute Refractive Error Quality of Life Instrument-42; NEI RQL-42) 3 months postoperatively. We compared the preoperative and postoperative values of the log(s) and evaluated the correlation of these values with patient subjective symptoms. The mean log(s) was not significantly changed, from 1.07 ± 0.20 preoperatively, to 1.06 ± 0.17 postoperatively (Wilcoxon signed-rank test, p = 0.641). There was a significant correlation between the preoperative and postoperative log(s) (Spearman's correlation coefficient r = 0.695, p < 0.001). The postoperative log(s) was significantly associated with the scores of glare in the questionnaire (Spearman's correlation coefficient r = -0.575, p = 0.017). According to our experience, Hole ICL implantation does not induce a significant additional change in the subjective intraocular forward scattering. The symptom of glare after Hole ICL implantation was significantly correlated with the postoperative intraocular forward scattering in relation to the preoperative one. © 2016 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model

NASA Astrophysics Data System (ADS)

Diaz-Rodriguez, Sebastian; Bozada, Samantha M.; Phifer, Jeremy R.; Paluch, Andrew S.

2016-11-01

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of 2.2± 0.2 log units (ranking 15 out of 62 entries), the correlation coefficient ( R) was 0.6± 0.1 (ranking 35), and 72± 6 % of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

RRCRank: a fusion method using rank strategy for residue-residue contact prediction.

PubMed

Jing, Xiaoyang; Dong, Qiwen; Lu, Ruqian

2017-09-02

In structural biology area, protein residue-residue contacts play a crucial role in protein structure prediction. Some researchers have found that the predicted residue-residue contacts could effectively constrain the conformational search space, which is significant for de novo protein structure prediction. In the last few decades, related researchers have developed various methods to predict residue-residue contacts, especially, significant performance has been achieved by using fusion methods in recent years. In this work, a novel fusion method based on rank strategy has been proposed to predict contacts. Unlike the traditional regression or classification strategies, the contact prediction task is regarded as a ranking task. First, two kinds of features are extracted from correlated mutations methods and ensemble machine-learning classifiers, and then the proposed method uses the learning-to-rank algorithm to predict contact probability of each residue pair. First, we perform two benchmark tests for the proposed fusion method (RRCRank) on CASP11 dataset and CASP12 dataset respectively. The test results show that the RRCRank method outperforms other well-developed methods, especially for medium and short range contacts. Second, in order to verify the superiority of ranking strategy, we predict contacts by using the traditional regression and classification strategies based on the same features as ranking strategy. Compared with these two traditional strategies, the proposed ranking strategy shows better performance for three contact types, in particular for long range contacts. Third, the proposed RRCRank has been compared with several state-of-the-art methods in CASP11 and CASP12. The results show that the RRCRank could achieve comparable prediction precisions and is better than three methods in most assessment metrics. The learning-to-rank algorithm is introduced to develop a novel rank-based method for the residue-residue contact prediction of proteins, which achieves state-of-the-art performance based on the extensive assessment.

The effects of ionizing irradiation on Salmonella inoculated on almonds and changes in sensory properties

NASA Astrophysics Data System (ADS)

Prakash, A.; Lim, F. T.; Duong, C.; Caporaso, F.; Foley, D.

2010-04-01

The goal of this study was to test the efficacy of irradiation on destroying Salmonella on raw almonds and evaluating the resultant sensory changes in the almonds. Raw almonds inoculated with various strains of Salmonella were irradiated at 5 dose levels up to 3 kGy and the D value was determined. The strain SEPT30 was the most resistant strain with a D value of 1.25 kGy indicating that a 4 log CFU/g reduction would require a dose of 5.0 kGy. Irradiation at 2.98 and 5.25 kGy induced significant sensory changes in almond nuts as manifested by intensity of chemical/metallic/rancid flavor ranked by a trained panel. A consumer panel found that samples treated with 5.25 kGy irradiation rendered the almonds unacceptable. Thus, irradiation by itself is unlikely to be a feasible method to eliminate Salmonella from raw almonds.

Effects of electrical stimulation in the treatment of osteonecrosis of the femoral head.

PubMed

Fornell, Salvador; Ribera, Juan; Mella, Mario; Carranza, Andrés; Serrano-Toledano, David; Domecq, Gabriel

2017-10-16

The aim of this study was to examine whether the use of an internal electrostimulator could improve the results obtained with core decompression alone in the treatment of osteonecrosis of the femoral head. We performed a retrospective study of 41 patients (55 hips) treated for osteonecrosis of the femoral head between 2005 and 2014. Mean follow-up time was 56 (12-108) months. We recorded 3 parameters: time to recurrence of pain, time to conversion to arthroplasty and time to radiographic failure. Survival was estimated using the Kaplan-Meier method. The equality of the survival distributions was determined by the Log rank test. Implanted electrostimulator was a factor that increased the survival of hips in a pre-op Steinberg stage of II or below, while it remained unchanged if the stage was III or higher. The addition of an internal electrostimulator provides increased survival compared to core decompression alone at stages below III.

The impact of a personal digital assistant (PDA) case log in a medical student clerkship.

PubMed

Ho, Kendall; Lauscher, Helen Novak; Broudo, Marc; Jarvis-Selinger, Sandra; Fraser, Joan; Hewes, Deborah; Scott, Ian

2009-10-01

Medical education literature emphasizes that reflection and self-audit are pivotal steps in learning and that personal digital assistants (PDAs) have potential as decision support tools. The purpose was to examine the efficacy of PDA-based resources and patient-encounter logging systems among 3rd-year medical clerks during pediatrics rotations. Students in rotations were assigned to control (using paper-based logs and references) or intervention groups (using PDA-based logs and resources). Students completed pre- and postrotation Paediatrics Competency Surveys, participated in focus groups, and were compared on year-end examination grades. Use of PDA logs far outweighed that of paper logs (1,020 PDA logs and 87 paper logs). PDA logs were ranked significantly higher in enhancing learning and reflection than paper logs (t = 2.52, p < .01). PDA logs also facilitated specific learning experiences. PDA-based patient-encounter logs appear to be effective case documentation and reflection tools. The difference in number of logs between control and intervention groups demonstrates the utility of the PDA for "point-of-care" patient logging.

Estimation of hazard function and its associated factors in gastric cancer patients using wavelet and kernel smoothing methods.

PubMed

Ahmadi, Azadeh; Roudbari, Masoud; Gohari, Mahmood Reza; Hosseini, Bistoon

2012-01-01

Increase of mortality rates of gastric cancer in Iran and the world in recent years reveal necessity of studies on this disease. Here, hazard function for gastric cancer patients was estimated using Wavelet and Kernel methods and some related factors were assessed. Ninety- five gastric cancer patients in Fayazbakhsh Hospital between 1996 and 2003 were studied. The effects of age of patients, gender, stage of disease and treatment method on patient's lifetime were assessed. For data analyses, survival analyses using Wavelet method and Log-rank test in R software were used. Nearly 25.3% of patients were female. Fourteen percent had surgery treatment and the rest had treatment without surgery. Three fourths died and the rest were censored. Almost 9.5% of patients were in early stages of the disease, 53.7% in locally advance stage and 36.8% in metastatic stage. Hazard function estimation with the wavelet method showed significant difference for stages of disease (P<0.001) and did not reveal any significant difference for age, gender and treatment method. Only stage of disease had effects on hazard and most patients were diagnosed in late stages of disease, which is possibly one of the most reasons for high hazard rate and low survival. Therefore, it seems to be necessary a public education about symptoms of disease by media and regular tests and screening for early diagnosis.

Arkansas' timber industry - an assessment of timber product output and use, 1996

Treesearch

Michael Howell; Robert Levins

1998-01-01

In 1996, roundwood output from Arkansas forests totaled 636 million cubic feet. Mill byproducts generated from primary manufacturers was 286 million cubic feet. Almost all plant residues were used primarily for fuel and fiber products. Saw logs were the leading roundwood product at 315 million cubic feet; pulpwood ranked second at 242 million cubic feet; veneer logs...

Sensitivity analysis of gene ranking methods in phenotype prediction.

PubMed

deAndrés-Galiana, Enrique J; Fernández-Martínez, Juan L; Sonis, Stephen T

2016-12-01

It has become clear that noise generated during the assay and analytical processes has the ability to disrupt accurate interpretation of genomic studies. Not only does such noise impact the scientific validity and costs of studies, but when assessed in the context of clinically translatable indications such as phenotype prediction, it can lead to inaccurate conclusions that could ultimately impact patients. We applied a sequence of ranking methods to damp noise associated with microarray outputs, and then tested the utility of the approach in three disease indications using publically available datasets. This study was performed in three phases. We first theoretically analyzed the effect of noise in phenotype prediction problems showing that it can be expressed as a modeling error that partially falsifies the pathways. Secondly, via synthetic modeling, we performed the sensitivity analysis for the main gene ranking methods to different types of noise. Finally, we studied the predictive accuracy of the gene lists provided by these ranking methods in synthetic data and in three different datasets related to cancer, rare and neurodegenerative diseases to better understand the translational aspects of our findings. In the case of synthetic modeling, we showed that Fisher's Ratio (FR) was the most robust gene ranking method in terms of precision for all the types of noise at different levels. Significance Analysis of Microarrays (SAM) provided slightly lower performance and the rest of the methods (fold change, entropy and maximum percentile distance) were much less precise and accurate. The predictive accuracy of the smallest set of high discriminatory probes was similar for all the methods in the case of Gaussian and Log-Gaussian noise. In the case of class assignment noise, the predictive accuracy of SAM and FR is higher. Finally, for real datasets (Chronic Lymphocytic Leukemia, Inclusion Body Myositis and Amyotrophic Lateral Sclerosis) we found that FR and SAM provided the highest predictive accuracies with the smallest number of genes. Biological pathways were found with an expanded list of genes whose discriminatory power has been established via FR. We have shown that noise in expression data and class assignment partially falsifies the sets of discriminatory probes in phenotype prediction problems. FR and SAM better exploit the principle of parsimony and are able to find subsets with less number of high discriminatory genes. The predictive accuracy and the precision are two different metrics to select the important genes, since in the presence of noise the most predictive genes do not completely coincide with those that are related to the phenotype. Based on the synthetic results, FR and SAM are recommended to unravel the biological pathways that are involved in the disease development. Copyright © 2016 Elsevier Inc. All rights reserved.

Personalized pulmonary rehabilitation and occupational therapy based on cardiopulmonary exercise testing for patients with advanced chronic obstructive pulmonary disease

PubMed Central

Maekura, Ryoji; Hiraga, Toru; Miki, Keisuke; Kitada, Seigo; Miki, Mari; Yoshimura, Kenji; Yamamoto, Hiroshi; Kawabe, Toshiko; Mori, Masahide

2015-01-01

Take-home summary Personalized pulmonary rehabilitation including occupational therapy improves the prognosis of patients with advanced COPD. Purpose We previously reported that patients with chronic obstructive pulmonary disease (COPD) exhibit three exercise-induced life-threatening conditions: hypoxemia, sympathetic overactivity, and respiratory acidosis. We aimed to verify whether mortality in patients with advanced COPD could be reduced by a personalized pulmonary rehabilitation (PPR) program in hospital, which determines individual safe ranges and includes occupational therapy (PPR-OT), to prevent desaturation and sympathetic nerve activation during daily activities. Patients and methods The novel PPR-OT program was evaluated in a retrospective study of patients with COPD (Global Initiative for Chronic Obstructive Lung Disease [GOLD] Grade D) who underwent cardiopulmonary exercise testing (CPET) between April 1990 and December 1999. They received regular treatment without the proposed therapy (control group: n=61; male-to-female ratio [M:F] =57:4; mean age: 68.5±6.7 years) or with the proposed therapy (PPR-OT group: n=46; M:F =44:2; mean age: 68.7±7.1 years). A prospective observational study included patients with COPD receiving home oxygen therapy (HOT) between April 1995 and March 2007 to compare the survival rates of the control group (n=47; M:F ratio =34:13; mean age: 71.3±10.0 years) and the PPR-OT group (n=85; M:F =78:7; mean age: 70.7±6.1 years) who completed the proposed therapy. Survival after CPET or HOT was analyzed using Cox proportional-hazards regression and Kaplan–Meier analyses. Results In both studies, the program significantly improved all-cause mortality (retrospective study: risk ratio =0.389 [range: 0.172–0.800]; P=0.0094; log-rank test, P=0.0094; observational study: risk ratio =0.515 [range: 0.296–0.933]; P=0.0291; log-rank test, P=0.0232]. At 5 years and 7 years, all-cause mortality was extremely low in patients in the PPR-OT group receiving HOT (18.8% and 28.2%, respectively), compared to that in the control group (34.0% and 44.7%, respectively). Survival of patients with life-threatening pathophysiological conditions also greatly improved. Conclusion The PPR-OT program improved the survival of patients with advanced COPD probably because it modified life-threatening conditions. PMID:26366071

Ranking metrics in gene set enrichment analysis: do they matter?

PubMed

Zyla, Joanna; Marczyk, Michal; Weiner, January; Polanska, Joanna

2017-05-12

There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment Analysis seems to be one of the most commonly used (over 10,000 citations). An important parameter, which could affect the final result, is the choice of a metric for the ranking of genes. Applying a default ranking metric may lead to poor results. In this work 28 benchmark data sets were used to evaluate the sensitivity and false positive rate of gene set analysis for 16 different ranking metrics including new proposals. Furthermore, the robustness of the chosen methods to sample size was tested. Using k-means clustering algorithm a group of four metrics with the highest performance in terms of overall sensitivity, overall false positive rate and computational load was established i.e. absolute value of Moderated Welch Test statistic, Minimum Significant Difference, absolute value of Signal-To-Noise ratio and Baumgartner-Weiss-Schindler test statistic. In case of false positive rate estimation, all selected ranking metrics were robust with respect to sample size. In case of sensitivity, the absolute value of Moderated Welch Test statistic and absolute value of Signal-To-Noise ratio gave stable results, while Baumgartner-Weiss-Schindler and Minimum Significant Difference showed better results for larger sample size. Finally, the Gene Set Enrichment Analysis method with all tested ranking metrics was parallelised and implemented in MATLAB, and is available at https://github.com/ZAEDPolSl/MrGSEA . Choosing a ranking metric in Gene Set Enrichment Analysis has critical impact on results of pathway enrichment analysis. The absolute value of Moderated Welch Test has the best overall sensitivity and Minimum Significant Difference has the best overall specificity of gene set analysis. When the number of non-normally distributed genes is high, using Baumgartner-Weiss-Schindler test statistic gives better outcomes. Also, it finds more enriched pathways than other tested metrics, which may induce new biological discoveries.

Evaluation of factors associated with survival in dogs with untreated nasal carcinomas: 139 cases (1993-2003).

PubMed

Rassnick, Kenneth M; Goldkamp, Carrie E; Erb, Hollis N; Scrivani, Peter V; Njaa, Bradley L; Gieger, Tracy L; Turek, Michelle M; McNiel, Elizabeth A; Proulx, David R; Chun, Ruthanne; Mauldin, Glenna E; Phillips, Brenda S; Kristal, Orna

2006-08-01

To evaluate factors associated with survival in dogs with nasal carcinomas that did not receive treatment or received only palliative treatment. Retrospective case series. 139 dogs with histologically confirmed nasal carcinomas. Medical records, computed tomography images, and biopsy specimens of nasal carcinomas were reviewed. Only dogs that were not treated with radiation, surgery, chemotherapy, or immunotherapy and that survived > or = 7 days from the date of diagnosis were included. The Kaplan-Meier method was used to estimate survival time. Factors potentially associated with survival were compared by use of log-rank and Wilcoxon rank sum tests. Multivariable survival analysis was performed by use of the Cox proportional hazards regression model. Overall median survival time was 95 days (95% confidence interval [CI], 73 to 113 days; range, 7 to 1,114 days). In dogs with epistaxis, the hazard of dying was 2.3 times that of dogs that did not have epistaxis. Median survival time of 107 dogs with epistaxis was 88 days (95% CI, 65 to 106 days) and that of 32 dogs without epistaxis was 224 days (95% CI, 54 to 467 days). The prognosis of dogs with untreated nasal carcinomas is poor. Treatment strategies to improve outcome should be pursued.

Serum/glucocorticoid-regulated kinase 1 expression in primary human prostate cancers.

PubMed

Szmulewitz, Russell Z; Chung, Elizabeth; Al-Ahmadie, Hikmat; Daniel, Silver; Kocherginsky, Masha; Razmaria, Aria; Zagaja, Gregory P; Brendler, Charles B; Stadler, Walter M; Conzen, Suzanne D

2012-02-01

Serum/glucocorticoid-regulated kinase 1 (SGK1), a known target of the androgen receptor (AR) and glucocorticoid receptor (GR), is reported to enhance cell survival. This study sought to better define the role of SGK1 and GR in prostate cancer. Immunohistochemistry was performed for AR, GR, and SGK1 on primary prostate cancers (n = 138) and 18 prostate cancers from patients treated with androgen deprivation therapy. Relative staining intensity was compared utilizing a Fisher's exact test. Univariate analyses were performed using log-rank and chi-squared tests to evaluate prostate cancer recurrence with respect to SGK1 expression. SGK1 expression was strong (3+) in 79% of untreated cancers versus 44% in androgen-deprived cancers (P = 0.003). Conversely, GR expression was present in a higher proportion of androgen-deprived versus untreated cancers (78% vs. 38%, P = 0.002). High-grade cancers were nearly twice as likely to have relatively low (0 to 2+) SGK1 staining compared to low-grade cancers (13.8% vs. 26.5%, P = 0.08). Low SGK1 expression in untreated tumors was associated with increased risk of cancer recurrence (adjusted log-rank test P = 0.077), 5-year progression-free survival 47.8% versus 72.6% (P = 0.034). SGK1 expression is high in most untreated prostate cancers and declines with androgen deprivation. However, these data suggest that relatively low expression of SGK1 is associated with higher tumor grade and increased cancer recurrence, and is a potential indicator of aberrant AR signaling in these tumors. GR expression increased with androgen deprivation, potentially providing a mechanism for the maintenance of androgen pathway signaling in these tumors. Further study of the AR/GR/SGK1 network in castration resistance. Copyright © 2011 Wiley Periodicals, Inc.

Should reporting of peri-neural invasion and extra prostatic extension be mandatory in prostate cancer biopsies? correlation with outcome in biopsy cases treated conservatively

PubMed Central

Ahmad, Amar S.; Parameshwaran, Vishnu; Beltran, Luis; Fisher, Gabrielle; North, Bernard V.; Greenberg, David; Soosay, Geraldine; Møller, Henrik; Scardino, Peter; Cuzick, Jack; Berney, Daniel M.

2018-01-01

The identification of perineural invasion (PNI) and extraprostatic extension (ECE) in prostate cancer (PC) biopsies is time consuming and can be difficult. Although this is required information in many datasets, there is little evidence on their effect on outcome in patients treated conservatively. Cases of PC were identified from three cancer registries in the UK from men with clinically localized prostate cancer diagnosed by needle biopsy from 1990–2003. The endpoint was prostate cancer death (DOD). Patients treated radically within 6 months, those with objective evidence of metastases or who had prior hormone therapy were excluded. Follow-up was through cancer registries up until 2012. Deaths were divided into those from PC and those from other causes, according to WHO criteria. 988 biopsy cases (6522 biopsy cores) were centrally reviewed by three uropathologists and assigned a Gleason score and Grade Group (GG). The presence of both PNI and ECE was recorded. Of 988 patients, PNI was present in 288 (DOD = 75) and ECE in 23 (DOD = 5). On univariable analysis PNI was highly significantly associated with DOD (hazard ratio [HR] 2.28, 95% CI: 1.68, 3.1, log-rank test p-value = 4.8 × 10–8), but ECE was not (log-rank test p-value = 0.334). On multivariable analysis with GG, serum PSA (per 10%), clinical stage and extent of disease (per 10%), PNI lost significance (HR 1.16, 95% CI: 0.83, 1.63, likelihood ratio test p-value = 0.371). The utility of routinely examining prostate biopsies for ECE and PNI is doubtful as it is not independently associated with higher grade, stage or prognosis. PMID:29755671

Should reporting of peri-neural invasion and extra prostatic extension be mandatory in prostate cancer biopsies? correlation with outcome in biopsy cases treated conservatively.

PubMed

Ahmad, Amar S; Parameshwaran, Vishnu; Beltran, Luis; Fisher, Gabrielle; North, Bernard V; Greenberg, David; Soosay, Geraldine; Møller, Henrik; Scardino, Peter; Cuzick, Jack; Berney, Daniel M

2018-04-17

The identification of perineural invasion (PNI) and extraprostatic extension (ECE) in prostate cancer (PC) biopsies is time consuming and can be difficult. Although this is required information in many datasets, there is little evidence on their effect on outcome in patients treated conservatively. Cases of PC were identified from three cancer registries in the UK from men with clinically localized prostate cancer diagnosed by needle biopsy from 1990-2003. The endpoint was prostate cancer death (DOD). Patients treated radically within 6 months, those with objective evidence of metastases or who had prior hormone therapy were excluded. Follow-up was through cancer registries up until 2012. Deaths were divided into those from PC and those from other causes, according to WHO criteria. 988 biopsy cases (6522 biopsy cores) were centrally reviewed by three uropathologists and assigned a Gleason score and Grade Group (GG). The presence of both PNI and ECE was recorded. Of 988 patients, PNI was present in 288 (DOD = 75) and ECE in 23 (DOD = 5). On univariable analysis PNI was highly significantly associated with DOD (hazard ratio [HR] 2.28, 95% CI: 1.68, 3.1, log-rank test p -value = 4.8 × 10 -8 ), but ECE was not (log-rank test p -value = 0.334). On multivariable analysis with GG, serum PSA (per 10%), clinical stage and extent of disease (per 10%), PNI lost significance (HR 1.16, 95% CI: 0.83, 1.63, likelihood ratio test p -value = 0.371). The utility of routinely examining prostate biopsies for ECE and PNI is doubtful as it is not independently associated with higher grade, stage or prognosis.

DrugE-Rank: improving drug–target interaction prediction of new candidate drugs or targets by ensemble learning to rank

PubMed Central

Yuan, Qingjun; Gao, Junning; Wu, Dongliang; Zhang, Shihua; Mamitsuka, Hiroshi; Zhu, Shanfeng

2016-01-01

Motivation: Identifying drug–target interactions is an important task in drug discovery. To reduce heavy time and financial cost in experimental way, many computational approaches have been proposed. Although these approaches have used many different principles, their performance is far from satisfactory, especially in predicting drug–target interactions of new candidate drugs or targets. Methods: Approaches based on machine learning for this problem can be divided into two types: feature-based and similarity-based methods. Learning to rank is the most powerful technique in the feature-based methods. Similarity-based methods are well accepted, due to their idea of connecting the chemical and genomic spaces, represented by drug and target similarities, respectively. We propose a new method, DrugE-Rank, to improve the prediction performance by nicely combining the advantages of the two different types of methods. That is, DrugE-Rank uses LTR, for which multiple well-known similarity-based methods can be used as components of ensemble learning. Results: The performance of DrugE-Rank is thoroughly examined by three main experiments using data from DrugBank: (i) cross-validation on FDA (US Food and Drug Administration) approved drugs before March 2014; (ii) independent test on FDA approved drugs after March 2014; and (iii) independent test on FDA experimental drugs. Experimental results show that DrugE-Rank outperforms competing methods significantly, especially achieving more than 30% improvement in Area under Prediction Recall curve for FDA approved new drugs and FDA experimental drugs. Availability: http://datamining-iip.fudan.edu.cn/service/DrugE-Rank Contact: zhusf@fudan.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307615

Comparison of Two Methods Used to Model Shape Parameters of Pareto Distributions

USGS Publications Warehouse

Liu, C.; Charpentier, R.R.; Su, J.

2011-01-01

Two methods are compared for estimating the shape parameters of Pareto field-size (or pool-size) distributions for petroleum resource assessment. Both methods assume mature exploration in which most of the larger fields have been discovered. Both methods use the sizes of larger discovered fields to estimate the numbers and sizes of smaller fields: (1) the tail-truncated method uses a plot of field size versus size rank, and (2) the log-geometric method uses data binned in field-size classes and the ratios of adjacent bin counts. Simulation experiments were conducted using discovered oil and gas pool-size distributions from four petroleum systems in Alberta, Canada and using Pareto distributions generated by Monte Carlo simulation. The estimates of the shape parameters of the Pareto distributions, calculated by both the tail-truncated and log-geometric methods, generally stabilize where discovered pool numbers are greater than 100. However, with fewer than 100 discoveries, these estimates can vary greatly with each new discovery. The estimated shape parameters of the tail-truncated method are more stable and larger than those of the log-geometric method where the number of discovered pools is more than 100. Both methods, however, tend to underestimate the shape parameter. Monte Carlo simulation was also used to create sequences of discovered pool sizes by sampling from a Pareto distribution with a discovery process model using a defined exploration efficiency (in order to show how biased the sampling was in favor of larger fields being discovered first). A higher (more biased) exploration efficiency gives better estimates of the Pareto shape parameters. ?? 2011 International Association for Mathematical Geosciences.

Long-term survivors of primary central nervous system lymphoma.

PubMed

Yamanaka, Ryuya; Morii, Ken; Sano, Masakazu; Homma, Jumpei; Yajima, Naoki; Tsukamoto, Yoshihiro; Ogura, Ryouske; Natsumeda, Manabu; Aoki, Hiroshi; Akiyama, Katsuhiko; Saitoh, Takafumi; Hondoh, Hiroaki; Kawaguchi, Atsushi; Takahashi, Hitoshi; Fujii, Yukihiko

2017-02-23

In this study, we provide long-term outcome data of patients with primary central nervous system lymphoma. The long-term outcomes of PCNSL patients diagnosed between 1982 and 2006 were reviewed. Neurological late neurotoxicity symptoms, neuroradiological brain atrophy and leukoencephalopathy were evaluated. Surviving patients completed the Quality of Life Questionnaire-30 and Brain Cancer Module-20. The differences in overall survival were assessed using the Kaplan-Meier method and log-rank test. The differences between groups in terms of each investigated parameter were analyzed using the Wilcoxon signed-rank test. Among 112 PCNSL patients, there were 33 (29.4%) long-term (> 5 years) survivors. The median survival of all long-term survivors was 105.7 months; of these, 8 (7.1%) were alive at the latest follow-up, with a mean survival time of 170.2 months (range, 121.8–286.4). Clinical assessment revealed severe neurotoxicity in 14 patients (42.4%), moderate neurotoxicity in 5 (15.1%), and normal status in 14 (42.4%). Correlations were seen between the neuroradiological imaging score changes and neurocognitive condition (P=0.0001), neurocognitive condition and the whole brain irradiation dose (P=0.0004), and atrophy and the whole brain irradiation dose (P=0.0035). A more severe clinical condition was found to be associated with increasing age and whole brain irradiation dose in long-term survivors with PCNSL. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Bo; Kowalski, Karol

The representation and storage of two-electron integral tensors are vital in large- scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this paper, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition ofmore » the two-electron integral tensor in our implementation. For the size of atomic basis set N_b ranging from ~ 100 up to ~ 2, 000, the observed numerical scaling of our implementation shows O(N_b^{2.5~3}) versus O(N_b^{3~4}) of single CD in most of other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic-orbital (AO) two-electron integral tensor from O(N_b^4) to O(N_b^2 log_{10}(N_b)) with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled- cluster formalism employing single and double excitations (CCSD) on several bench- mark systems including the C_{60} molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10^{-4} to 10^{-3} to give acceptable compromise between efficiency and accuracy.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Townsend, M., Prothro, L. B., Obi, C.

A test bed for a series of chemical explosives tests known as Source Physics Experiments (SPE) was constructed in granitic rock of the Climax stock, in northern Yucca Flat at the Nevada National Security Site in 2010-2011. These tests are sponsored by the U.S. Department of Energy, National Nuclear Security Administration's National Center for Nuclear Security. The test series is designed to study the generation and propagation of seismic waves, and will provide data that will improve the predictive capability of calculational models for detecting and characterizing underground explosions. Abundant geologic data are available for the area, primarily as amore » result of studies performed in conjunction with the three underground nuclear tests conducted in the Climax granite in the 1960s and a few later studies of various types. The SPE test bed was constructed at an elevation of approximately 1,524 meters (m), and consists of a 91.4-centimeter (cm) diameter source hole at its center, surrounded by two rings of three 20.3-cm diameter instrument holes. The inner ring of holes is positioned 10 m away from the source hole, and the outer ring of holes is positioned 20 m from the source hole. An initial 160-m deep core hole was drilled at the location of the source hole that provided information on the geology of the site and rock samples for later laboratory testing. A suite of geophysical logs was run in the core hole and all six instruments holes to obtain matrix and fracture properties. Detailed information on the character and density of fractures encountered was obtained from the borehole image logs run in the holes. A total of 2,488 fractures were identified in the seven boreholes, and these were ranked into six categories (0 through 5) on the basis of their degree of openness and continuity. The analysis presented here considered only the higher-ranked fractures (ranks 2 through 5), of which there were 1,215 (approximately 49 percent of all fractures identified from borehole image logs). The fractures were grouped into sets based on their orientation. The most ubiquitous fracture set (50 percent of all higher-ranked fractures) is a group of low-angle fractures (dips 0 to 30 degrees). Fractures with dips of 60 to 90 degrees account for 38 percent of high-ranked fractures, and the remaining 12 percent are fractures with moderate dips (30 to 60 degrees). The higher-angle fractures are further subdivided into three sets based on their dip direction: fractures of Set 1 dip to the north-northeast, fractures of Set 2 dip to the south-southwest, and Set 3 consists of high-angle fractures that dip to the southeast and strike northeast. The low-angle fractures (Set 4) dip eastward. Fracture frequency does not appear to change substantially with depth. True fracture spacing averages 0.9 to 1.2 m for high-angle Sets 1, 2, and 3, and 0.6 m for Set 4. Two significant faults were observed in the core, centered at the depths of 25.3 and 32.3 m. The upper of these two faults dips 80 degrees to the north-northeast and, thus, is related to the Set-1 fractures. The lower fault dips 79 degrees to the south-southwest and is related to SPE Set-2 fractures. Neither fault has an identifiable surface trace. Groundwater was encountered in all holes drilled on the SPE test bed, and the fluid level averaged about 15.2 to 18.3 m below ground surface. An informal study of variations in the fluid level in the holes conducted during various phases of construction of the test bed concluded that groundwater flow through the fractured granitic rocks is not uniform, and appears to be controlled by variations in the orientation and degree of interconnectedness of the fractures. It may also be possible that an aplite dike or quartz vein may be present in the test bed, which could act as a barrier to groundwater flow and, thus, could account for anisotropy seen in the groundwater recovery measurements.« less

A Prospective Trial on Initiation Factor 4E (eIF4E) Overexpression and Cancer Recurrence in Node-Positive Breast Cancer

PubMed Central

McClusky, Derek R.; Chu, Quyen; Yu, Herbert; DeBenedetti, Arrigo; Johnson, Lester W.; Meschonat, Carol; Turnage, Richard; McDonald, John C.; Abreo, Fleurette; Li, Benjamin D. L.

2005-01-01

Objective: A previous study of patients with stage I to III breast cancer showed that those patients whose tumors were in the highest tertile of eIF4E overexpression experienced a higher risk for recurrence. This study was designed to determine whether high eIF4E overexpression predicts cancer recurrence independent of nodal status by specifically targeting patients with node-positive disease. Methods: The prospective trial was designed to accrue 168 patients with node-positive breast cancer to detect a 2.5-fold increase in risk for recurrence. eIF4E level was quantified by Western blots as x-fold elevated compared with breast tissues from noncancer patients. End points measured were disease recurrence and cancer-related death. Statistical analyses performed include survival analysis by the Kaplan-Meier method, log-rank test, and Cox proportional hazard model. Results: One hundred seventy-four patients with node-positive breast cancer were accrued. All patients fulfilled study inclusion and exclusion criteria, treatment protocol, and surveillance requirements, with a compliance rate >95%. The mean eIF4E elevation was 11.0 ± 7.0-fold (range, 1.4–34.3-fold). Based on previously published data, tertile distribution was as follow: 1) lowest tertile (<7.5-fold) = 67 patients, 2) intermediate tertile (7.5–14-fold) = 54 patients, and 3) highest tertile (>14-fold) = 53 patients. At a median follow up of 32 months, patients with the highest tertile had a statistically significant higher cancer recurrence rate (log-rank test, P = 0.002) and cancer-related death rate (P = 0.036) than the lowest group. Relative risk calculations demonstrated that high eIF4E patients had a 2.4-fold increase in relative risk increase for cancer recurrence (95% confidence interval, 1.2–4.1; P = 0.01). Conclusions: In this prospective study designed to specifically address risk for recurrence in patients with node-positive breast cancer, the patients whose tumors were in the highest tertile of eIF4E overexpression had a 2.4-fold increase in relative risk for cancer recurrence. Therefore, eIF4E overexpression appears to be an independent predictor of a worse outcome in patients with breast cancer independent of nodal status. PMID:16192819

DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank.

PubMed

Yuan, Qingjun; Gao, Junning; Wu, Dongliang; Zhang, Shihua; Mamitsuka, Hiroshi; Zhu, Shanfeng

2016-06-15

Identifying drug-target interactions is an important task in drug discovery. To reduce heavy time and financial cost in experimental way, many computational approaches have been proposed. Although these approaches have used many different principles, their performance is far from satisfactory, especially in predicting drug-target interactions of new candidate drugs or targets. Approaches based on machine learning for this problem can be divided into two types: feature-based and similarity-based methods. Learning to rank is the most powerful technique in the feature-based methods. Similarity-based methods are well accepted, due to their idea of connecting the chemical and genomic spaces, represented by drug and target similarities, respectively. We propose a new method, DrugE-Rank, to improve the prediction performance by nicely combining the advantages of the two different types of methods. That is, DrugE-Rank uses LTR, for which multiple well-known similarity-based methods can be used as components of ensemble learning. The performance of DrugE-Rank is thoroughly examined by three main experiments using data from DrugBank: (i) cross-validation on FDA (US Food and Drug Administration) approved drugs before March 2014; (ii) independent test on FDA approved drugs after March 2014; and (iii) independent test on FDA experimental drugs. Experimental results show that DrugE-Rank outperforms competing methods significantly, especially achieving more than 30% improvement in Area under Prediction Recall curve for FDA approved new drugs and FDA experimental drugs. http://datamining-iip.fudan.edu.cn/service/DrugE-Rank zhusf@fudan.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

A clinically observed discrepancy between image-based and log-based MLC positions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neal, Brian, E-mail: bpn2p@virginia.edu; Ahmed, Mahmoud; Kathuria, Kunal

2016-06-15

Purpose: To present a clinical case in which real-time intratreatment imaging identified an multileaf collimator (MLC) leaf to be consistently deviating from its programmed and logged position by >1 mm. Methods: An EPID-based exit-fluence dosimetry system designed to prevent gross delivery errors was used to capture cine during treatment images. The author serendipitously visually identified a suspected MLC leaf displacement that was not otherwise detected. The leaf position as recorded on the EPID images was measured and log-files were analyzed for the treatment in question, the prior day’s treatment, and for daily MLC test patterns acquired on those treatment days.more » Additional standard test patterns were used to quantify the leaf position. Results: Whereas the log-file reported no difference between planned and recorded positions, image-based measurements showed the leaf to be 1.3 ± 0.1 mm medial from the planned position. This offset was confirmed with the test pattern irradiations. Conclusions: It has been clinically observed that log-file derived leaf positions can differ from their actual position by >1 mm, and therefore cannot be considered to be the actual leaf positions. This cautions the use of log-based methods for MLC or patient quality assurance without independent confirmation of log integrity. Frequent verification of MLC positions through independent means is a necessary precondition to trust log-file records. Intratreatment EPID imaging provides a method to capture departures from MLC planned positions.« less

An empirical method for determining average soil infiltration rates and runoff, Powder River structural basin, Wyoming

USGS Publications Warehouse

Rankl, James G.

1982-01-01

This report describes a method to estimate infiltration rates of soils for use in estimating runoff from small basins. Average rainfall intensity is plotted against storm duration on log-log paper. All rainfall events are designated as having either runoff or nonrunoff. A power-decay-type curve is visually fitted to separate the two types of rainfall events. This separation curve is an incipient-ponding curve and its equation describes infiltration parameters for a soil. For basins with more than one soil complex, only the incipient-ponding curve for the soil complex with the lowest infiltration rate can be defined using the separation technique. Incipient-ponding curves for soils with infiltration rates greater than the lowest curve are defined by ranking the soils according to their relative permeabilities and optimizing the curve position. A comparison of results for six basins produced computed total runoff for all events used ranging from 16.6 percent less to 2.3 percent more than measured total runoff. (USGS)

Punctuation effects in english and esperanto texts

NASA Astrophysics Data System (ADS)

Ausloos, M.

2010-07-01

A statistical physics study of punctuation effects on sentence lengths is presented for written texts: Alice in wonderland and Through a looking glass. The translation of the first text into esperanto is also considered as a test for the role of punctuation in defining a style, and for contrasting natural and artificial, but written, languages. Several log-log plots of the sentence-length-rank relationship are presented for the major punctuation marks. Different power laws are observed with characteristic exponents. The exponent can take a value much less than unity ( ca. 0.50 or 0.30) depending on how a sentence is defined. The texts are also mapped into time series based on the word frequencies. The quantitative differences between the original and translated texts are very minutes, at the exponent level. It is argued that sentences seem to be more reliable than word distributions in discussing an author style.

Evaluation of permeable fractures in rock aquifers

NASA Astrophysics Data System (ADS)

Bok Lee, Hang

2015-04-01

In this study, the practical usefulness and fundamental applicability of a self-potential (SP) method for identifying the permeable fractures were evaluated by a comparison of SP methods with other geophysical logging methods and hydraulic tests. At a 10 m-shallow borehole in the study site, the candidates of permeable fractures crossing the borehole were first determined by conventional geophysical methods such as an acoustic borehole televiwer, temperature, electrical conductivity and gamma-gamma loggings, which was compared to the analysis by the SP method. Constant pressure injection and recovery tests were conducted for verification of the hydraulic properties of the fractures identified by various logging methods. The acoustic borehole televiwer and gamma-gamma loggings detected the open space or weathering zone within the borehole, but they cannot prove the possibility of a groundwater flow through the detected fractures. The temperature and electrical conductivity loggings had limitations to detect the fractured zones where groundwater in the borehole flows out to the surrounding rock aquifers. Comparison of results from different methods showed that there is a best correlation between the distribution of hydraulic conductivity and the variation of the SP signals, and the SP logging can estimate accurately the hydraulic activity as well as the location of permeable fractures. Based on the results, the SP method is recommended for determining the hydraulically-active fractures rather than other conventional geophysical loggings. This self-potential method can be effectively applied in the initial stage of a site investigation which selects the optimal location and evaluates the hydrogeological property of fractures in target sites for the underground structure including the geothermal reservoir and radioactive waste disposal.

Efficacy and safety of a multiherbal formula with vitamin C and zinc (Immumax) in the management of the common cold.

PubMed

Yakoot, Mostafa; Salem, Amel

2011-01-12

To study the potential efficacy and tolerability of a natural multiherbal formula (Immumax) containing Echinacea extract 120 mg, garlic powder 100 mg, Nigella sativa oil 200 mg, and Panax ginseng extract 50 mg plus vitamin C 50 mg and elemental zinc 7.5 mg in the treatment of patients suffering from the common cold. The study was conducted in a prospective, double-blind, randomized, controlled study design in an outpatient setting. Sixty-two eligible patients with symptoms of the common cold were randomized to either Immumax or placebo treatment groups for the duration of their symptoms or a maximum of 14 days. Resolution rates were estimated using Kaplan-Meier analysis, and resolution profiles were compared between groups using the log-rank test. The mean percentage change in total symptom severity scores at days 4 and 8 from baseline were compared between the two groups by one-way analysis of variance (ANOVA). The median (interquartile range) time to resolution of all symptoms was 8 (5-9) days in the placebo group and 4 (3-6) days in the Immumax group. The results of the log-rank test indicate that symptoms resolved significantly faster in the Immumax group than in the placebo group (P < 0.001). The mean percentage reduction in total symptom severity scores from baseline at days 4 and 8 was significantly greater in the Immumax group than in the placebo group by one-way ANOVA (P < 0.01). We can conclude from our study that Immumax is helpful in reducing the duration and severity of common cold symptoms.

Radical Surgery Improves Survival in Patients with Stage 4 Neuroblastoma.

PubMed

Vollmer, Katherin; Gfroerer, Stefan; Theilen, Till-Martin; Bochennek, Konrad; Klingebiel, Thomas; Rolle, Udo; Fiegel, Henning

2018-06-01

Neuroblastoma (NBL) is the most common extracranial solid tumor in children. Despite a good overall prognosis in NBL patients, the outcome of children with stage 4 disease, even with multimodal intensive therapy, remains poor. The role of extended surgical resection of the primary tumor is in numerous studies controversial. The aim of this study was to retrospectively analyze the impact of radical surgical resection on the overall- and event-free survival of stage 4 NBL patients. We retrospectively analyzed patient charts of 40 patients with stage 4 NBL treated in our institution between January 1990 and May 2012. All clinical and pathological findings of stage 4 NBL patients were included. Extent of surgery was assessed from the operation records and was classified as non-radical (tumor biopsy, partial 50-90% resection) or radical (near-complete >90% resection, complete resection). Overall- (OS) and event-free (EFS) survival was assessed using the Kaplan-Meier analysis and log-rank test. A multivariate Cox regression analysis was used to demonstrate independency. In total, 29/40 patients were operated radically (>90% resection), whereas 11 patients received subtotal resection or biopsy only. OS and EFS were significantly increased in patients with radical operation compared with non-radical resection (p = 0.0003 for OS, p = 0.004 for EFS; log-rank test). A multivariate Cox regression analysis revealed radical operation as a significant and independent parameter for OS and EFS. Our data indicate that radical (over 90% resection) surgery improves OS and EFS in stage 4 NBL patients.

Conservative management or gamma knife radiosurgery for vestibular schwannoma: tumor growth, symptoms, and quality of life.

PubMed

Breivik, Cathrine Nansdal; Nilsen, Roy Miodini; Myrseth, Erling; Pedersen, Paal Henning; Varughese, Jobin K; Chaudhry, Aqeel Asghar; Lund-Johansen, Morten

2013-07-01

There are few reports about the course of vestibular schwannoma (VS) patients following gamma knife radiosurgery (GKRS) compared with the course following conservative management (CM). In this study, we present prospectively collected data of 237 patients with unilateral VS extending outside the internal acoustic canal who received either GKRS (113) or CM (124). The aim was to measure the effect of GKRS compared with the natural course on tumor growth rate and hearing loss. Secondary end points were postinclusion additional treatment, quality of life (QoL), and symptom development. The patients underwent magnetic resonance imaging scans, clinical examination, and QoL assessment by SF-36 questionnaire. Statistics were performed by using Spearman correlation coefficient, Kaplan-Meier plot, Poisson regression model, mixed linear regression models, and mixed logistic regression models. Mean follow-up time was 55.0 months (26.1 standard deviation, range 10-132). Thirteen patients were lost to follow-up. Serviceable hearing was lost in 54 of 71 (76%) (CM) and 34 of 53 (64%) (GKRS) patients during the study period (not significant, log-rank test). There was a significant reduction in tumor volume over time in the GKRS group. The need for treatment following initial GKRS or CM differed at highly significant levels (log-rank test, P < .001). Symptom and QoL development did not differ significantly between the groups. In VS patients, GKRS reduces the tumor growth rate and thereby the incidence rate of new treatment about tenfold. Hearing is lost at similar rates in both groups. Symptoms and QoL seem not to be significantly affected by GKRS.

Delivering tertiary centre specialty care to ALS patients via telemedicine: a retrospective cohort analysis.

PubMed

Selkirk, Stephen M; Washington, Monique O; McClellan, Frances; Flynn, Broderick; Seton, Jacinta M; Strozewski, Richard

2017-08-01

This study was undertaken to determine if ALS patients evaluated via telemedicine received the same quality of care as patients evaluated by traditional face-to-face encounters. A retrospective cohort study design was used. Participants were patients diagnosed with ALS that received multidisciplinary care at the tertiary Cleveland VA ALS Centre between 1 March 2008- and 31 anuary 2015. Participants were not randomised, but chose telemedicine based on preference, disability level or distance from the clinic. Telemedicine in this study consisted of a video conferencing platform enabling remote rather than face-to-face encounters with participants. There was no significant association between receiving quality ALS care and the mode of care. There was a trend for telemedicine patients to utilise home health care less often than those that received clinic care (AOR 0.50; 95% CI 0.16-1.59). There was no significant difference in survival time between the two groups (log-rank test χ 2  = 3.62, df = 1, p = 0.05). Patients receiving telemedicine had a higher probability of remaining stable or having <30% decrease in ALSFRS-R over time (log-rank test χ 2  = 4.46, df = 1, p = 0.03). There was a significantly lower risk of disease progression for patients receiving telemedicine (HR = 0.39, 95% CI = 0.16-0.93). Patients managed by telemedicine received the same quality of care and had similar outcomes to those patients seen via traditional face-to-face encounters. Telemedicine is an effective platform for delivering high quality tertiary ALS care.

Comparison of the Risk of Gastrointestinal Bleeding among Different Statin Exposures with Concomitant Administration of Warfarin: Electronic Health Record-Based Retrospective Cohort Study.

PubMed

Shin, Dahye; Yoon, Dukyong; Lim, Sun Gyo; Hong, Ji Man; Park, Rae Woong; Lee, Jin Soo

2016-01-01

Patients who should be treated with both warfarin and a statin are frequently seen in vascular clinics. The risk for bleeding and potential drug interactions should be considered when prescribing both medications together. This study aimed to compare the risk for gastrointestinal bleeding among different statin exposures with concomitant administration of warfarin. This is a single-hospital retrospective cohort study. We included patients who were concomitantly exposed to one of four statins (pravastatin, simvastatin, atorvastatin, and rosuvastatin) and warfarin for up to 2 years (730 days). The observation period ended when a gastrointestinal bleeding event occurred or the observation was censored. Within-class comparisons were used, and 1:1 matching using a propensity score was performed for comparisons between each statin and all of the other statins. Kaplan-Meier analyses with log-rank tests and Cox proportional hazard regression analyses were conducted to determine associations with the risk of gastrointestinal bleeding. Data were analyzed for 1,686 patients who were concomitantly administered a statin and warfarin. Log-rank tests for the gastrointestinal bleeding-free survival rate showed that the risk for gastrointestinal bleeding was significantly lower in the pravastatin group (p = 0.0499) and higher in the rosuvastatin group (p = 0.009). In the Cox proportional hazard regression analysis, the hazard ratio of 5.394 for gastrointestinal bleeding based on statin exposure in the rosuvastatin group was significant (95% confidence interval, 1.168-24.916). There was a relatively high risk of gastrointestinal bleeding with rosuvastatin when administered concomitantly with warfarin.

Grindability measurements on low-rank fuels. [Prediction of large pulverizer performance from small scale test equipment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peipho, R.R.; Dougan, D.R.

1981-01-01

Experience has shown that the grinding characteristics of low rank coals are best determined by testing them in a pulverizer. Test results from a small MPS-32 Babcock and Wilcox pulverizer to predict large, full-scale pulverizer performance are presented. The MPS-32 apparatus, test procedure and evaluation of test results is described. The test data show that the Hardgrove apparatus and the ASTM test method must be used with great caution when considering low-rank fuels. The MPS-32 meets the needs for real-machine simulation but with some disadvantages. A smaller pulverizer is desirable. 1 ref.

Combining evidence and values in priority setting: testing the balance sheet method in a low-income country.

PubMed

Makundi, Emmanuel; Kapiriri, Lydia; Norheim, Ole Frithjof

2007-09-24

Procedures for priority setting need to incorporate both scientific evidence and public values. The aim of this study was to test out a model for priority setting which incorporates both scientific evidence and public values, and to explore use of evidence by a selection of stakeholders and to study reasons for the relative ranking of health care interventions in a setting of extreme resource scarcity. Systematic search for and assessment of relevant evidence for priority setting in a low-income country. Development of a balance sheet according to Eddy's explicit method. Eight group interviews (n-85), using a modified nominal group technique for eliciting individual and group rankings of a given set of health interventions. The study procedure made it possible to compare the groups' ranking before and after all the evidence was provided to participants. A rank deviation is significant if the rank order of the same intervention differed by two or more points on the ordinal scale. A comparison between the initial rank and the final rank (before deliberation) showed a rank deviation of 67%. The difference between the initial rank and the final rank after discussion and voting gave a rank deviation of 78%. Evidence-based and deliberative decision-making does change priorities significantly in an experimental setting. Our use of the balance sheet method was meant as a demonstration project, but could if properly developed be feasible for health planners, experts and health workers, although more work is needed before it can be used for laypersons.

Locomotor ecology of wild orangutans (Pongo pygmaeus abelii) in the Gunung Leuser Ecosystem, Sumatra, Indonesia: a multivariate analysis using log-linear modelling.

PubMed

Thorpe, Susannah K S; Crompton, Robin H

2005-05-01

The large body mass and exclusively arboreal lifestyle of Sumatran orangutans identify them as a key species in understanding the dynamic between primates and their environment. Increased knowledge of primate locomotor ecology, coupled with recent developments in the standardization of positional mode classifications (Hunt et al. [1996] Primates 37:363-387), opened the way for sophisticated multivariate statistical approaches, clarifying complex associations between multiple influences on locomotion. In this study we present a log-linear modelling approach used to identify key associations between orangutan locomotion, canopy level, support use, and contextual behavior. Log-linear modelling is particularly appropriate because it is designed for categorical data, provides a systematic method for testing alternative hypotheses regarding interactions between variables, and allows interactions to be ranked numerically in terms of relative importance. Support diameter and type were found to have the strongest associations with locomotor repertoire, suggesting that orangutans have evolved distinct locomotor modes to solve a variety of complex habitat problems. However, height in the canopy and contextual behavior do not directly influence locomotion: instead, their effect is modified by support type and support diameter, respectively. Contrary to classic predictions, age-sex category has only limited influence on orangutan support use and locomotion, perhaps reflecting the presence of arboreal pathways which individuals of all age-sex categories follow. Effects are primarily related to a tendency for adult, parous females to adopt a more cautious approach to locomotion than adult males and immature subjects. Copyright 2004 Wiley-Liss, Inc.

Treatment Outcomes for T4 Oropharyngeal Squamous Cell Carcinoma.

PubMed

Zenga, Joseph; Wilson, Michael; Adkins, Douglas R; Gay, Hiram A; Haughey, Bruce H; Kallogjeri, Dorina; Michel, Loren S; Paniello, Randal C; Rich, Jason T; Thorstad, Wade L; Nussenbaum, Brian

2015-12-01

Little is known about treatment outcomes for T4 oropharyngeal squamous cell carcinoma (OPSCC), particularly in the era of human papillomavirus (HPV)-related disease. To evaluate oncologic outcomes for T4 OPSCC treated with primary surgical and nonsurgical therapies. Retrospective cohort study of 131 patients from a single academic hospital, who were treated for T4a or T4b OPSCC (with any N stage and without distant metastatic disease at presentation) between 1998 and 2012 and had a minimum 2-year follow-up (the median follow-up time was 34.6 months). This study was conducted between January 1, 1998, and November 1, 2012. Sixty-nine patients underwent nonsurgical therapy, 47 (68%) of whom had p16-positive tumors. Nonsurgical treatment paradigms included induction chemotherapy followed by chemoradiotherapy (n = 36 [54%]), concurrent chemoradiotherapy (n = 29 [43%]), and induction chemotherapy followed by radiation therapy alone (n = 2 [3%]). Sixty-two patients underwent surgical treatment, 50 (81%) of whom had p16-positive tumors. Fifty-seven surgical patients (92%) received adjuvant therapy. Overall survival (OS) was the primary outcome measure. Secondary outcome measures included disease-specific survival (DSS), disease-free survival (DFS), 2-year gastrostomy and tracheostomy tube rates, and major complication rates. Significant baseline differences between the surgical vs nonsurgical groups included age (mean 59.8 vs 55.4 years [P = .005]), sex (male, 95% vs 84% [P = .04]), body mass index (<18.5 [calculated as weight in kilograms divided by height in meters squared], 3% vs 16% [P = .02]), and smoking history of 10 or more pack-years (48% vs 77% [P = .003]). For p16-positive patients, Kaplan-Meier estimates of OS, DSS, and DFS were significantly higher for surgically treated patients than for the nonsurgical group (χ(2)(1) = 7.335 for log-rank P = .007, χ(2)(1) = 8.607 for log-rank P = .003, and χ(2)(1) = 7.763 for log-rank P = .005, respectively). For p16-negative patients, Kaplan-Meier estimates of OS and DSS were higher for the surgical group but did not reach statistical significance (χ(2)(1) = 2.649 for log-rank P = .10 and χ(2)(1) = 2.077 for log-rank P = .15, respectively), while estimates of DFS were significantly higher for patients treated with primary surgery (χ(2)(1)= 3.869 for log-rank P = .049. In a multivariable Cox survival analysis, p16-positive immunohistochemical status had a significant positive association with OS (hazard ratio [HR], 0.55; 95% CI, 0.32-0.95 [P = .03]), DSS (HR, 0.45; 95% CI, 0.22-0.92 [P = .03]), and DFS (HR, 0.55; 95% CI, 0.32-0.95 [P = .03]), and nonsurgical treatment had a significant negative association with OS (HR, 2.79; 95% CI, 1.51-5.16 [P = .001]), DSS (HR, 3.38; 95% CI, 1.59-7.16 [P = .002]), and DFS (HR, 2.59; 95% CI, 1.51-4.45 [P = .001]). Primary surgical treatment may be associated with improved outcomes in patients with T4 OPSCC. p16 Immunohistochemical status remains a strong prognostic indicator even in patients with locally advanced disease.

Number of negative lymph nodes should be considered for incorporation into staging for breast cancer

PubMed Central

Wu, San-Gang; Wang, Yan; Zhou, Juan; Sun, Jia-Yuan; Li, Feng-Yan; Lin, Huan-Xin; He, Zhen-Yu

2015-01-01

This study aimed to investigate the prognostic value of the number of involved lymph nodes (pN), number of removed lymph nodes (RLNs), lymph node ratio (LNR), number of negative lymph nodes (NLNs), and log odds of positive lymph nodes (LODDS) in breast cancer patients. The records of 2,515 breast cancer patients who received a mastectomy or breast-conserving surgery were retrospectively reviewed. The log-rank test was used to compare survival curves, and Cox regression analysis was performed to identify prognostic factors. The median follow-up time was 64.2 months, and the 8-year disease-free survival (DFS) and overall survival (OS) were 74.6% and 82.3%, respectively. Univariate analysis showed that pN stage, LNR, number of RLNs, and number of NLNs were significant prognostic factors for DFS and OS (all, P < 0.05). LODDS was a significant prognostic factor for OS (P = 0.021). Multivariate analysis indicated that pN stage and the number of NLNs were independent prognostic factors for DFS and OS. A higher number of NLNs was associated with higher DFS and OS, and a higher number of involved lymph nodes were associated with poorer DFS and OS. Patients with a NLNs count > 9 had better survival (P < 0.001). Subgroup analysis showed that the NLNs count had a prognostic value in patients with different pT stages and different lymph node status (log-rank P < 0.05). For breast cancer, pN stage and NLNs count have a better prognostic value compared to the RLNs count, LNR, and LODDS. Number of negative lymph nodes should be considered for incorporation into staging for breast cancer. PMID:25973321

Cyclin D1 and epidermal growth factor polymorphisms associated with survival in patients with advanced colorectal cancer treated with Cetuximab.

PubMed

Zhang, Wu; Gordon, Michael; Press, Oliver A; Rhodes, Katrin; Vallböhmer, Daniel; Yang, Dong Yun; Park, David; Fazzone, William; Schultheis, Anne; Sherrod, Andy E; Iqbal, Syma; Groshen, Susan; Lenz, Heinz-Josef

2006-07-01

The study aimed to investigate whether polymorphisms in genes of the EGFR signaling pathway are associated with clinical outcome in advanced colorectal cancer (CRC) patients treated with single-agent Cetuximab. Polymorphisms of interest in the EGFR pathway include: cyclin D1 (CCND1) A870G, cyclooxygenase 2 (Cox-2) G-765C, epidermal growth factor (EGF) A61G, epidermal growth factor receptor (EGFR) codon R497 K, EGFR CA dinucleotide repeat in intron 1, interleukin (IL)-8 T-251A and vascular endothelial growth factor (VEGF) C936 T gene polymorphisms. Thirty-nine metastatic CRC patients were enrolled in the IMCL-0144 trial and treated with single-agent Cetuximab. Using the polymerase chain reaction-restriction fragment length polymorphism method, gene polymorphisms of CCND1, COX-2, EGF, EGFR, IL-8 and VEGF were assessed from genomic DNA extracted from blood samples. A significant association was found between the CCND1 A870G polymorphism and overall survival in our 39 CRC subjects. Patients with the AA homozygous genotype survived for a median of 2.3 months [95% confidence interval (CI)=2.1-5.7], whereas those with any G allele (AG, GG genotype) survived for a median of 8.7 months (95% CI=4.4-13.5) (P=0.019, log-rank test). When we analysed the cyclin D1 and EGF polymorphisms together, patients with favourable genotypes (EGF any A allele and CCND1 any G allele) showed a median survival time of 12 months (95% CI=4.8-15.2), whereas patients with any two unfavourable genotypes (EGF GG or CCND1 AA) showed a median survived time of 4.4 months (95% CI=2.1-5.7) (P=0.004, log-rank test). The findings of this pilot study suggest that the cyclin D1 A870G and the EGF A61G polymorphisms may be useful molecular markers for predicting clinical outcome in CRC patients treated with single-agent Cetuximab.

Lunar phases and survival of breast cancer patients--a statistical analysis of 3,757 cases.

PubMed

Peters-Engl, C; Frank, W; Kerschbaum, F; Denison, U; Medl, M; Sevelda, P

2001-11-01

The potential influence of lunar phases on human life has been widely discussed by the lay press. The purpose of this study was to find out whether the timing of surgery during particular lunar phases influences the survival of breast cancer patients. It has been postulated that breast cancer surgery performed during the waxing moon, or particularly at full moon, is associated with a poorer outcome. We tested this hypothesis by evaluating the overall survival for 3,757 consecutive patients with invasive breast cancer. All patients underwent either modified radical mastectomy or breast conserving surgery plus radiotherapy, followed by adjuvant cytotoxic or hormonal therapy. The date of definitive surgery was allocated to the lunar phases. 1,904 (50.7%) patients were operated on during the waxing moon and 1,853 (47.3%) during the waning moon. The median follow-up was 74 months (range 1-372 months). The mean age at primary surgery did not differ significantly in the two groups 58.39 (SD 13.14) versus 58.34 (12.75) (p >0.05, t-test). Breast cancer stages at initial diagnosis were evenly distributed according to the lunar phases (p = 0.325; chi-square). Survival curves were plotted according to the method of Kaplan-Meier. No significant differences were observed when timing of surgery was allocated to the lunar phases (p = 0.4841, log-rank). Subgroup analysis of premenopausal patients revealed similar results (p = 0.2950, log-rank; n = 1072). Using multivariate Cox modelling, we found a significant association between the patient's age, stage of disease and survival, whereas no association with survival was observed for the timing of surgery (RR= 1.062; 95% CI, 0.970-1.163; p = 0.1937). No significant differences in overall survival of breast cancer patients were observed when timing of breast cancer surgery during the lunar cycle was considered. Although this was not a prospective randomized trial, the statistical magnitude of the results do not support any recommendations for scheduling patients for surgery at any particular day of the lunar phase.

Proton beam therapy and concurrent chemotherapy for esophageal cancer.

PubMed

Lin, Steven H; Komaki, Ritsuko; Liao, Zhongxing; Wei, Caimiao; Myles, Bevan; Guo, Xiaomao; Palmer, Matthew; Mohan, Radhe; Swisher, Stephen G; Hofstetter, Wayne L; Ajani, Jaffer A; Cox, James D

2012-07-01

Proton beam therapy (PBT) is a promising modality for the management of thoracic malignancies. We report our preliminary experience of treating esophageal cancer patients with concurrent chemotherapy (CChT) and PBT (CChT/PBT) at MD Anderson Cancer Center. This is an analysis of 62 esophageal cancer patients enrolled on a prospective study evaluating normal tissue toxicity from CChT/PBT from 2006 to 2010. Patients were treated with passive scattering PBT with two- or three-field beam arrangement using 180 to 250 MV protons. We used the Kaplan-Meier method to assess time-to-event outcomes and compared the distributions between groups using the log-rank test. The median follow-up time was 20.1 months for survivors. The median age was 68 years (range, 38-86). Most patients were males (82%) who had adenocarcinomas (76%) and Stage II-III disease (84%). The median radiation dose was 50.4 Gy (RBE [relative biologic equivalence]) (range, 36-57.6). The most common grade 2 to 3 acute toxicities from CChT/PBT were esophagitis (46.8%), fatigue (43.6%), nausea (33.9%), anorexia (30.1%), and radiation dermatitis (16.1%). There were two cases of grade 2 and 3 radiation pneumonitis and two cases of grade 5 toxicities. A total of 29 patients (46.8%) received preoperative CChT/PBT, with one postoperative death. The pathologic complete response (pCR) rate for the surgical cohort was 28%, and the pCR and near CR rates (0%-1% residual cells) were 50%. While there were significantly fewer local-regional recurrences in the preoperative group (3/29) than in the definitive CChT/PBT group (16/33) (log-rank test, p = 0.005), there were no differences in distant metastatic (DM)-free interval or overall survival (OS) between the two groups. This is the first report of patients treated with PBT/CChT for esophageal cancer. Our data suggest that this modality is associated with a few severe toxicities, but the pathologic response and clinical outcomes are encouraging. Prospective comparison with more traditional approach is warranted. Copyright © 2012 Elsevier Inc. All rights reserved.

Quantile rank maps: a new tool for understanding individual brain development.

PubMed

Chen, Huaihou; Kelly, Clare; Castellanos, F Xavier; He, Ye; Zuo, Xi-Nian; Reiss, Philip T

2015-05-01

We propose a novel method for neurodevelopmental brain mapping that displays how an individual's values for a quantity of interest compare with age-specific norms. By estimating smoothly age-varying distributions at a set of brain regions of interest, we derive age-dependent region-wise quantile ranks for a given individual, which can be presented in the form of a brain map. Such quantile rank maps could potentially be used for clinical screening. Bootstrap-based confidence intervals are proposed for the quantile rank estimates. We also propose a recalibrated Kolmogorov-Smirnov test for detecting group differences in the age-varying distribution. This test is shown to be more robust to model misspecification than a linear regression-based test. The proposed methods are applied to brain imaging data from the Nathan Kline Institute Rockland Sample and from the Autism Brain Imaging Data Exchange (ABIDE) sample. Copyright © 2015 Elsevier Inc. All rights reserved.

An enzyme-linked immunosorbent assay for the determination of dioxins in contaminated sediment and soil samples

PubMed Central

Van Emon, Jeanette M.; Chuang, Jane C.; Lordo, Robert A.; Schrock, Mary E.; Nichkova, Mikaela; Gee, Shirley J.; Hammock, Bruce D.

2010-01-01

A 96-microwell enzyme-linked immunosorbent assay (ELISA) method was evaluated to determine PCDDs/PCDFs in sediment and soil samples from an EPA Superfund site. Samples were prepared and analyzed by both the ELISA and a gas chromatography/high resolution mass spectrometry (GC/HRMS) method. Comparable method precision, accuracy, and detection level (8 ng kg−1) were achieved by the ELISA method with respect to GC/HRMS. However, the extraction and cleanup method developed for the ELISA requires refinement for the soil type that yielded a waxy residue after sample processing. Four types of statistical analyses (Pearson correlation coefficient, paired t-test, nonparametric tests, and McNemar’s test of association) were performed to determine whether the two methods produced statistically different results. The log-transformed ELISA-derived 2,3,7,8-tetrachlorodibenzo-p-dioxin values and logtransformed GC/HRMS-derived TEQ values were significantly correlated (r = 0.79) at the 0.05 level. The median difference in values between ELISA and GC/HRMS was not significant at the 0.05 level. Low false negative and false positive rates (<10%) were observed for the ELISA when compared to the GC/HRMS at 1000 ng TEQ kg−1. The findings suggest that immunochemical technology could be a complementary monitoring tool for determining concentrations at the 1000 ng TEQ kg−1 action level for contaminated sediment and soil. The ELISA could also be used in an analytical triage approach to screen and rank samples prior to instrumental analysis. PMID:18313102

A Case-Based Reasoning Method with Rank Aggregation

NASA Astrophysics Data System (ADS)

Sun, Jinhua; Du, Jiao; Hu, Jian

2018-03-01

In order to improve the accuracy of case-based reasoning (CBR), this paper addresses a new CBR framework with the basic principle of rank aggregation. First, the ranking methods are put forward in each attribute subspace of case. The ordering relation between cases on each attribute is got between cases. Then, a sorting matrix is got. Second, the similar case retrieval process from ranking matrix is transformed into a rank aggregation optimal problem, which uses the Kemeny optimal. On the basis, a rank aggregation case-based reasoning algorithm, named RA-CBR, is designed. The experiment result on UCI data sets shows that case retrieval accuracy of RA-CBR algorithm is higher than euclidean distance CBR and mahalanobis distance CBR testing.So we can get the conclusion that RA-CBR method can increase the performance and efficiency of CBR.

Novel adiponectin-resistin (AR) and insulin resistance (IRAR) indexes are useful integrated diagnostic biomarkers for insulin resistance, type 2 diabetes and metabolic syndrome: a case control study

PubMed Central

2011-01-01

Background Adiponectin and resistin are adipokines which modulate insulin action, energy, glucose and lipid homeostasis. Meta-analyses showed that hypoadiponectinemia and hyperresistinemia are strongly associated with increased risk of insulin resistance, type 2 diabetes (T2DM), metabolic syndrome (MS) and cardiovascular disease. The aim of this study was to propose a novel adiponectin-resistin (AR) index by taking into account both adiponectin and resistin levels to povide a better indicator of the metabolic homeostasis and metabolic disorders. In addition, a novel insulin resistance (IRAR) index was proposed by integration of the AR index into an existing insulin resistance index to provide an improved diagnostic biomarker of insulin sensitivity. Methods In this case control study, anthropometric clinical and metabolic parameters including fasting serum total adiponectin and resistin levels were determined in 809 Malaysian men (208 controls, 174 MS without T2DM, 171 T2DM without MS, 256 T2DM with MS) whose ages ranged between 40-70 years old. Significant differences in continuous variables among subject groups were confirmed by ANCOVA or MANCOVA test using 1,000 stratified bootstrap samples with bias corrected and accelerated (BCa) 95% CI. Spearman's rho rank correlation test was used to test the correlation between two variables. Results The AR index was formulated as 1+log10(R0)-log10(A0). The AR index was more strongly associated with increased risk of T2DM and MS than hypoadiponectinemia and hyperresistinemia alone. The AR index was more strongly correlated with the insulin resistance indexes and key metabolic endpoints of T2DM and MS than adiponectin and resistin levels alone. The AR index was also correlated with a higher number of MS components than adiponectin and resistin levels alone. The IRAR index was formulated as log10(I0G0)+log10(I0G0)log10(R0/A0). The normal reference range of the IRAR index for insulin sensitive individuals was between 3.265 and 3.538. The minimum cut-off values of the IRAR index for insulin resistance assessment were between 3.538 and 3.955. Conclusions The novel AR and IRAR indexes are cost-effective, precise, reproducible and reliable integrated diagnostic biomarkers of insulin sensitivity for screening subjects with increased risk of future development of T2DM and MS. PMID:21251282

Empirical evaluation of interest-level criteria

NASA Astrophysics Data System (ADS)

Sahar, Sigal; Mansour, Yishay

1999-02-01

Efficient association rule mining algorithms already exist, however, as the size of databases increases, the number of patterns mined by the algorithms increases to such an extent that their manual evaluation becomes impractical. Automatic evaluation methods are, therefore, required in order to sift through the initial list of rules, which the datamining algorithm outputs. These evaluation methods, or criteria, rank the association rules mined from the dataset. We empirically examined several such statistical criteria: new criteria, as well as previously known ones. The empirical evaluation was conducted using several databases, including a large real-life dataset, acquired from an order-by-phone grocery store, a dataset composed from www proxy logs, and several datasets from the UCI repository. We were interested in discovering whether the ranking performed by the various criteria is similar or easily distinguishable. Our evaluation detected, when significant differences exist, three patterns of behavior in the eight criteria we examined. There is an obvious dilemma in determining how many association rules to choose (in accordance with support and confidence parameters). The tradeoff is between having stringent parameters and, therefore, few rules, or lenient parameters and, thus, a multitude of rules. In many cases, our empirical evaluation revealed that most of the rules found by the comparably strict parameters ranked highly according to the interestingness criteria, when using lax parameters (producing significantly more association rules). Finally, we discuss the association rules that ranked highest, explain why these results are sound, and how they direct future research.

The role of maintenance thalidomide therapy in multiple myeloma: MRC Myeloma IX results and meta-analysis.

PubMed

Morgan, Gareth J; Gregory, Walter M; Davies, Faith E; Bell, Sue E; Szubert, Alexander J; Brown, Julia M; Coy, Nuria N; Cook, Gordon; Russell, Nigel H; Rudin, Claudius; Roddie, Huw; Drayson, Mark T; Owen, Roger G; Ross, Fiona M; Jackson, Graham H; Child, J Anthony

2012-01-05

Thalidomide maintenance has the potential to modulate residual multiple myeloma (MM) after an initial response. This trial compared the effect of thalidomide maintenance and no maintenance on progression-free survival (PFS) and overall survival (OS) in MM patients. After intensive or nonintensive induction therapy, 820 newly diagnosed MM patients were randomized to open-label thalidomide maintenance until progression, or no maintenance. Interphase FISH (iFISH) analysis was performed at study entry. Median PFS was significantly longer with thalidomide maintenance (log-rank P < .001). Median OS was similar between regimens (log-rank P = .40). Patients with favorable iFISH showed improved PFS (P = .004) and a trend toward a late survival benefit. Patients with adverse iFISH receiving thalidomide showed no significant PFS benefit and worse OS (P = .009). Effective relapse therapy enhanced survival after progression, translating into a significant OS benefit. Meta-analysis of this and other studies show a significant late OS benefit (P < .001, 7-year difference hazard ratio = 12.3; 95% confidence interval, 5.5-19.0). Thalidomide maintenance significantly improves PFS and can be associated with improved OS. iFISH testing is important in assessing the clinical impact of maintenance therapy. Overview analysis demonstrated that thalidomide maintenance was associated with a significant late OS benefit. This trial was registered at www.isrctn.org as #ISRCTN68454111.

Pretreatment 18F-FDG PET Textural Features in Locally Advanced Non–Small Cell Lung Cancer: Secondary Analysis of ACRIN 6668/RTOG 0235

PubMed Central

Ohri, Nitin; Duan, Fenghai; Snyder, Bradley S.; Wei, Bo; Machtay, Mitchell; Alavi, Abass; Siegel, Barry A.; Johnson, Douglas W.; Bradley, Jeffrey D.; DeNittis, Albert; Werner-Wasik, Maria; El Naqa, Issam

2016-01-01

In a secondary analysis of American College of Radiology Imaging Network (ACRIN) 6668/RTOG 0235, high pretreatment metabolic tumor volume (MTV) on 18F-FDG PET was found to be a poor prognostic factor for patients treated with chemoradiotherapy for locally advanced non–small cell lung cancer (NSCLC). Here we utilize the same dataset to explore whether heterogeneity metrics based on PET textural features can provide additional prognostic information. Methods Patients with locally advanced NSCLC underwent 18F-FDG PET prior to treatment. A gradient-based segmentation tool was used to contour each patient’s primary tumor. MTV, maximum SUV, and 43 textural features were extracted for each tumor. To address over-fitting and high collinearity among PET features, the least absolute shrinkage and selection operator (LASSO) method was applied to identify features that were independent predictors of overall survival (OS) after adjusting for MTV. Recursive binary partitioning in a conditional inference framework was utilized to identify optimal thresholds. Kaplan–Meier curves and log-rank testing were used to compare outcomes among patient groups. Results Two hundred one patients met inclusion criteria. The LASSO procedure identified 1 textural feature (SumMean) as an independent predictor of OS. The optimal cutpoint for MTV was 93.3 cm3, and the optimal Sum-Mean cutpoint for tumors above 93.3 cm3 was 0.018. This grouped patients into three categories: low tumor MTV (n = 155; median OS, 22.6 mo), high tumor MTV and high SumMean (n = 23; median OS, 20.0 mo), and high tumor MTV and low SumMean (n = 23; median OS, 6.2 mo; log-rank P < 0.001). Conclusion We have described an appropriate methodology to evaluate the prognostic value of textural PET features in the context of established prognostic factors. We have also identified a promising feature that may have prognostic value in locally advanced NSCLC patients with large tumors who are treated with chemoradiotherapy. Validation studies are warranted. PMID:26912429

SU-F-T-469: A Clinically Observed Discrepancy Between Image-Based and Log- Based MLC Position

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neal, B; Ahmed, M; Siebers, J

2016-06-15

Purpose: To present a clinical case which challenges the base assumption of log-file based QA, by showing that the actual position of a MLC leaf can suddenly deviate from its programmed and logged position by >1 mm as observed with real-time imaging. Methods: An EPID-based exit-fluence dosimetry system designed to prevent gross delivery errors was used in cine mode to capture portal images during treatment. Visual monitoring identified an anomalous MLC leaf pair gap not otherwise detected by the automatic position verification. The position of the erred leaf was measured on EPID images and log files were analyzed for themore » treatment in question, the prior day’s treatment, and for daily MLC test patterns acquired on those treatment days. Additional standard test patterns were used to quantify the leaf position. Results: Whereas the log file reported no difference between planned and recorded positions, image-based measurements showed the leaf to be 1.3±0.1 mm medial from the planned position. This offset was confirmed with the test pattern irradiations. Conclusion: It has been clinically observed that log-file derived leaf positions can differ from their actual positions by >1 mm, and therefore cannot be considered to be the actual leaf positions. This cautions the use of log-based methods for MLC or patient quality assurance without independent confirmation of log integrity. Frequent verification of MLC positions through independent means is a necessary precondition to trusting log file records. Intra-treatment EPID imaging provides a method to capture departures from MLC planned positions. Work was supported in part by Varian Medical Systems.« less

Susceptibility screening of hyphae-forming fungi with a new, easy, and fast inoculum preparation method.

PubMed

Schmalreck, Arno; Willinger, Birgit; Czaika, Viktor; Fegeler, Wolfgang; Becker, Karsten; Blum, Gerhard; Lass-Flörl, Cornelia

2012-12-01

In vitro susceptibility testing of clinically important fungi becomes more and more essential due to the rising number of fungal infections in patients with impaired immune system. Existing standardized microbroth dilution methods for in vitro testing of molds (CLSI, EUCAST) are not intended for routine testing. These methods are very time-consuming and dependent on sporulating of hyphomycetes. In this multicentre study, a new (independent of sporulation) inoculum preparation method (containing a mixture of vegetative cells, hyphae, and conidia) was evaluated. Minimal inhibitory concentrations (MIC) of amphotericin B, posaconazole, and voriconazole of 180 molds were determined with two different culture media (YST and RPMI 1640) according to the DIN (Deutsches Institut für Normung) microdilution assay. 24 and 48 h MIC of quality control strains, tested per each test run, prepared with the new inoculum method were in the range of DIN. YST and RPMI 1640 media showed similar MIC distributions for all molds tested. MIC readings at 48 versus 24 h yield 1 log(2) higher MIC values and more than 90 % of the MICs read at 24 and 48 h were within ± 2 log(2) dilution. MIC end point reading (log(2 MIC-RPMI 1640)-log(2 MIC-YST)) of both media demonstrated a tendency to slightly lower MICs with RPMI 1640 medium. This study reports the results of a new, time-saving, and easy-to-perform method for inoculum preparation for routine susceptibility testing that can be applied for all types of spore-/non-spore and hyphae-forming fungi.

Gene polymorphisms of epidermal growth factor receptor and its downstream effector, interleukin-8, predict oxaliplatin efficacy in patients with advanced colorectal cancer.

PubMed

Zhang, Wu; Stoehlmacher, Jan; Park, David J; Yang, Dongyun; Borchard, Erin; Gil, Ji; Tsao-Wei, Denice D; Yun, Jim; Gordon, Michael; Press, Oliver A; Rhodes, Katrin; Groshen, Susan; Lenz, Heinz-Josef

2005-07-01

Researchers have recently reported an association between the epidermal growth factor receptor (EGFR) pathway and platinum-chemotherapy sensitivity in cancer patients. The (CA)(n) repeat polymorphism in intron 1 of the EGFR gene has been identified and found to alter EGFR expression in vitro as well as in vivo. A higher number of these CA repeats is associated with lower EGFR levels, whereas a low number of repeats is associated with higher EGFR levels. A second key polymorphism within the EGFR pathway (HER1 R497K) is a single nucleotide change (G-A) in codon 497 of the EGFR gene, which leads to an arginine-lysine substitution in the extracellular domain of subdomain IV. Furthermore, interleukin-8 (IL-8), recently identified as an EGFR downstream effector, plays a vital role in tumor angiogenesis and progression. Three other polymorphisms, each related to the IL-8 gene, have also been identified as playing a pivotal role in the EGFR pathway: T-251A in the promoter region of the IL-8 gene, G+2607C in exon 2 of the IL-8 receptor CXCR1 gene, and C+785T in exon 11 of the IL-8 receptor CXCR2 gene. In this study, we employed a 5'-end 33P-gATP-labeled polymerase chain reaction (PCR) protocol as well as the PCR-restriction fragment length polymorphism method in order to determine the genotypes for the previously mentioned polymorphisms in 105 patients with metastatic colorectal cancer. Tests were conducted to establish whether these polymorphisms could predict clinical outcome to 5-flourouracil/oxaliplatin chemotherapy. Among all patients assessed, those possessing < 20 EGFR CA repeats were more likely to show disease progression than were patients with >or= 20 CA repeats (P = 0.019; log-rank test). Also, patients with the CXCR1 GC genotype were found to have an increased relative risk of time to tumor progression that was 1.55 (95% CI, 0.8-3.0) times that of patients with the homozygous GG genotype (P = 0.17; log-rank test). Overall, our data suggest that gene polymorphisms active in the EGFR pathway may be associated with the sensitivity of colorectal cancer patients to platinum-based chemotherapy.

Long-term efficacy and safety of rilpivirine plus abacavir and lamivudine in HIV-1 infected patients with undetectable viral load.

PubMed

Galizzi, Nadia; Galli, Laura; Poli, Andrea; Gianotti, Nicola; Carini, Elisabetta; Bigoloni, Alba; Tambussi, Giuseppe; Nozza, Silvia; Lazzarin, Adriano; Castagna, Antonella; Mancusi, Daniela; Termini, Roberta

2018-01-01

A regimen with rilpivirine (RPV), abacavir (ABC) and lamivudine (3TC) is simple and may allow the sparing of tenofovir and protease inhibitors. However, data on use of this combination as a strategy of switch are limited. Aims of the study were to assess the long-term efficacy and safety of this regimen. Retrospective study on HIV-1 infected patients followed at the Infectious Disease Department of the San Raffaele Scientific Institute, HBsAg-negative, HLA B5701-negative, with no documented resistance to RPV, ABC and 3TC, with HIV-RNA<50 copies/mL who started RPV plus ABC/3TC from March 2013 to September 2015. The primary outcome was durability [no treatment failure (TF)]. Secondary objectives were to evaluate changes in immunological, metabolic and other safety parameters. TF was defined as the occurrence of virological failure (VF, 2 consecutive values >50 copies/mL) or discontinuation of any drug in the regimen for any reason. Patients' follow-up accrued from the date of RPV plus ABC/3TC initiation to the date of TF (VF or discontinuation of any drug in the regimen) or to the date of last available visit. Time to TF was evaluated by use of the Kaplan-Meier curves. Mixed linear models were applied to evaluate changes in immunological, metabolic and other safety parameters. In this analysis, 100 patients starting RPV plus ABC/3TC were included. By 12, 24 and 36 months after switching to RPV plus ABC/3TC, the proportions of individuals without TF were 88% [95% confidence interval (CI): 79%-93%], 82% (95% CI:73%-89%) and 78% (95% CI:68%-86%), respectively. Time to TF was not significantly influenced by CD4+ nadir (≤200 vs >200 cells/μl; log-rank test: p = 0.311) or pre-ART viral load (<100000 vs ≥100000 copies/mL; log-rank test: p = 0.574) or the type of previous antiretroviral regimen (PI+2NRTIs vs NNRTI+2NRTIs vs Other; log-rank test: p = 0.942). Over a median follow-up of 2.9 years (IQR: 1.9-3.5), 26 subjects discontinued the treatment [10 due to toxicity, 7 for interactions with other drugs, 3 due to cardiovascular risk concern, 2 due to single viral blip, 1 due to VF, 1 for asthma, 1 patient's decision, 1 due to enrolment in a study protocol]. In this retrospective study, long-term use of RPV plus ABC/3TC regimen is effective and safe. Efficacy of this regimen was not found to be affected by low CD4+ nadir or high pre-ART viral load.

Abridged geriatric assessment is a better predictor of overall survival than the Karnofsky Performance Scale and Physical Performance Test in elderly patients with cancer.

PubMed

Ghosn, Marwan; Ibrahim, Tony; El Rassy, Elie; Nassani, Najib; Ghanem, Sassine; Assi, Tarek

2017-03-01

Comprehensive geriatric assessment (CGA) is a complex and interdisciplinary approach to evaluate the health status of elderly patients. The Karnofsky Performance Scale (KPS) and Physical Performance Test (PPT) are less time-consuming tools that measure functional status. This study was designed to assess and compare abridged geriatric assessment (GA), KPS and PPT as predictive tools of mortality in elderly patients with cancer. This prospective interventional study included all individuals aged >70years who were diagnosed with cancer during the study period. Subjects were interviewed directly using a procedure that included a clinical test and a questionnaire composed of the KPS, PPT and abridged GCA. Overall survival (OS) was the primary endpoint. The log rank test was used to compare survival curves, and Cox's regression model (forward procedure) was used for multivariate survival analysis. One hundred patients were included in this study. Abridged GA was the only tool found to predict mortality [median OS for unfit patients (at least two impairments) 467days vs 1030days for fit patients; p=0.04]. Patients defined as fit by mean PPT score (>20) had worse median OS (560 vs 721days); however, this difference was not significant (p=0.488 on log rank). Although median OS did not differ significantly between patients with low (≤80) and high (>80) KPS scores (467 and 795days, respectively; p=0.09), survival curves diverged after nearly 120days of follow-up. Visual and hearing impairments were the only components of abridged GA of prognostic value. Neither KPS nor PPT were shown to predict mortality in elderly patients with cancer whereas abridged GA was predictive. This study suggests a possible role for visual and hearing assessment as screening for patients requiring CGA. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microplate-Test for the Rapid Determination of Bacteriophage-Susceptibility of Campylobacter Isolates—Development and Validation

PubMed Central

Fischer, Samuel; Kittler, Sophie; Klein, Günter; Glünder, Gerhard

2013-01-01

A simple susceptibility test using 800 isolates of one Campylobacter strain with different degrees of susceptibility and four bacteriophages of the British phage typing scheme was developed and examined for its suitability. The test presented is economically cheaper and less time consuming than the conventional agar overlay plate assay and therefore enables the monitoring of changes in the susceptibility pattern during phage therapy under practical field conditions. The main objective of this study was to compare the simplified test with the conventional agar overlay plate assay. The conventional test describes for a population of Campylobacter: i. the rate of resistant isolates (0 plaques) and ii. the degree of susceptibility, also called relative efficiency of plating (EOP), for the remaining isolates. The simplified test divides the isolates into four susceptibility ranks, which are easily distinguishable to the naked eye. Ten Campylobacter isolates out of each rank were subjected to the conventional method for validation of the simplified test. Each resistance rank contained isolates showing certain degrees of susceptibility, reflecting decreasing susceptibility by an increase of the rank. Thus, the simplified test correlated well with the conventional method. Nevertheless, it can be suggested for a clear cut to summarise the first thee ranks as “high susceptible” and to mark out the fourth rank as reduced susceptible. Further test improvements will enable the monitoring of the degree of susceptibility and potentially also of resistance during phage therapy in the field. To ensure a long-lasting successful use of phage therapy, further studies on both the loss of susceptibility and the development of resistance of Campylobacter against phages combined with their impact on phage therapy will be necessary. PMID:23349761

Using multiple classifiers for predicting the risk of endovascular aortic aneurysm repair re-intervention through hybrid feature selection.

PubMed

Attallah, Omneya; Karthikesalingam, Alan; Holt, Peter Je; Thompson, Matthew M; Sayers, Rob; Bown, Matthew J; Choke, Eddie C; Ma, Xianghong

2017-11-01

Feature selection is essential in medical area; however, its process becomes complicated with the presence of censoring which is the unique character of survival analysis. Most survival feature selection methods are based on Cox's proportional hazard model, though machine learning classifiers are preferred. They are less employed in survival analysis due to censoring which prevents them from directly being used to survival data. Among the few work that employed machine learning classifiers, partial logistic artificial neural network with auto-relevance determination is a well-known method that deals with censoring and perform feature selection for survival data. However, it depends on data replication to handle censoring which leads to unbalanced and biased prediction results especially in highly censored data. Other methods cannot deal with high censoring. Therefore, in this article, a new hybrid feature selection method is proposed which presents a solution to high level censoring. It combines support vector machine, neural network, and K-nearest neighbor classifiers using simple majority voting and a new weighted majority voting method based on survival metric to construct a multiple classifier system. The new hybrid feature selection process uses multiple classifier system as a wrapper method and merges it with iterated feature ranking filter method to further reduce features. Two endovascular aortic repair datasets containing 91% censored patients collected from two centers were used to construct a multicenter study to evaluate the performance of the proposed approach. The results showed the proposed technique outperformed individual classifiers and variable selection methods based on Cox's model such as Akaike and Bayesian information criterions and least absolute shrinkage and selector operator in p values of the log-rank test, sensitivity, and concordance index. This indicates that the proposed classifier is more powerful in correctly predicting the risk of re-intervention enabling doctor in selecting patients' future follow-up plan.

Aggregate Interview Method of ranking orthopedic applicants predicts future performance.

PubMed

Geissler, Jacqueline; VanHeest, Ann; Tatman, Penny; Gioe, Terence

2013-07-01

This article evaluates and describes a process of ranking orthopedic applicants using what the authors term the Aggregate Interview Method. The authors hypothesized that higher-ranking applicants using this method at their institution would perform better than those ranked lower using multiple measures of resident performance. A retrospective review of 115 orthopedic residents was performed at the authors' institution. Residents were grouped into 3 categories by matching rank numbers: 1-5, 6-14, and 15 or higher. Each rank group was compared with resident performance as measured by faculty evaluations, the Orthopaedic In-Training Examination (OITE), and American Board of Orthopaedic Surgery (ABOS) test results. Residents ranked 1-5 scored significantly better on patient care, behavior, and overall competence by faculty evaluation (P<.05). Residents ranked 1-5 scored higher on the OITE compared with those ranked 6-14 during postgraduate years 2 and 3 (P⩽.5). Graduates who had been ranked 1-5 had a 100% pass rate on the ABOS part 1 examination on the first attempt. The most favorably ranked residents performed at or above the level of other residents in the program; they did not score inferiorly on any measure. These results support the authors' method of ranking residents. The rigorous Aggregate Interview Method for ranking applicants consistently identified orthopedic resident candidates who scored highly on the Accreditation Council for Graduate Medical Education resident core competencies as measured by faculty evaluations, performed above the national average on the OITE, and passed the ABOS part 1 examination at rates exceeding the national average. Copyright 2013, SLACK Incorporated.

Local Control After Stereotactic Body Radiation Therapy for Liver Tumors.

PubMed

Ohri, Nitin; Tomé, Wolfgang A; Méndez Romero, Alejandra; Miften, Moyed; Ten Haken, Randall K; Dawson, Laura A; Grimm, Jimm; Yorke, Ellen; Jackson, Andrew

2018-01-06

To quantitatively evaluate published experiences with hepatic stereotactic body radiation therapy (SBRT), to determine local control rates after treatment of primary and metastatic liver tumors and to examine whether outcomes are affected by SBRT dosing regimen. We identified published articles that reported local control rates after SBRT for primary or metastatic liver tumors. Biologically effective doses (BEDs) were calculated for each dosing regimen using the linear-quadratic equation. We excluded series in which a wide range of BEDs was used. Individual lesion data for local control were extracted from actuarial survival curves, and data were aggregated to form a single dataset. Actuarial local control curves were generated using the Kaplan-Meier method after grouping lesions by disease type and BED (<100 Gy 10 vs >100 Gy 10 ). Comparisons were made using log-rank testing. Thirteen articles met all inclusion criteria and formed the dataset for this analysis. The 1-, 2-, and 3-year actuarial local control rates after SBRT for primary liver tumors (n = 431) were 93%, 89%, and 86%, respectively. Lower 1- (90%), 2- (79%), and 3-year (76%) actuarial local control rates were observed for liver metastases (n = 290, log-rank P = .011). Among patients treated with SBRT for primary liver tumors, there was no evidence that local control is influenced by BED within the range of schedules used. For liver metastases, on the other hand, outcomes were significantly better for lesions treated with BEDs exceeding 100 Gy 10 (3-year local control 93%) than for those treated with BEDs of ≤100 Gy 10 (3-year local control 65%, P < .001). Stereotactic body radiation therapy for primary liver tumors provides high rates of durable local control, with no clear evidence for a dose-response relationship among commonly utilized schedules. Excellent local control rates are also seen after SBRT for liver metastases when BEDs of >100 Gy 10 are utilized. Copyright © 2018 Elsevier Inc. All rights reserved.

Perioperative and mid-term oncologic outcomes of robotic assisted radical cystectomy with totally intracorporeal neobladder: Results of a propensity score matched comparison with open cohort from a single-centre series.

PubMed

Simone, Giuseppe; Tuderti, Gabriele; Misuraca, Leonardo; Anceschi, Umberto; Ferriero, Mariaconsiglia; Minisola, Francesco; Guaglianone, Salvatore; Gallucci, Michele

2018-04-17

In this study, we compared perioperative and oncologic outcomes of patients treated with either open or robot-assisted radical cystectomy and intracorporeal neobladder at a tertiary care center. The institutional prospective bladder cancer database was queried for "cystectomy with curative intent" and "neobladder". All patients underwent robot-assisted radical cystectomy and intracorporeal neobladder or open radical cystectomy and orthotopic neobladder for high-grade non-muscle invasive bladder cancer or muscle invasive bladder cancer with a follow-up length ≥2 years were included. A 1:1 propensity score matching analysis was used. Kaplan-Meier method was performed to compare oncologic outcomes of selected cohorts. Survival rates were computed at 1,2,3 and 4 years after surgery and the log rank test was applied to assess statistical significance between the matched groups. Overall, 363 patients (299 open and 64 robotic) were included. Open radical cystectomy patients were more frequently male (p = 0.08), with higher pT stages (p = 0.003), lower incidence of urothelial histologies (p = 0.05) and lesser adoption of neoadjuvant chemotherapy (<0.001). After applying the propensity score matching, 64 robot-assisted radical cystectomy patients were matched with 46 open radical cystectomy cases (all p ≥ 0.22). Open cohort showed a higher rate of perioperative overall complications (91.3% vs 42.2%, p 0.001). At Kaplan-Meier analysis robotic and open cohorts displayed comparable disease-free survival (log-rank p = 0.746), cancer-specific survival (p = 0.753) and overall-survival rates (p = 0.909). Robot-assisted radical cystectomy and intracorporeal neobladder provides comparable oncologic outcomes of open radical cystectomy and orthotopic neobladder at intermediate term survival analysis. Copyright © 2018 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

Long-term outcomes in younger men following permanent prostate brachytherapy.

PubMed

Shapiro, Edan Y; Rais-Bahrami, Soroush; Morgenstern, Carol; Napolitano, Barbara; Richstone, Lee; Potters, Louis

2009-04-01

We reviewed the long-term outcomes in men undergoing permanent prostate brachytherapy with a focus on those presenting before age 60 years. Between 1992 and 2005 a total of 2,119 patients with clinical stage T1-T2, N0, M0 prostate cancer treated with permanent prostate brachytherapy were included in this study. Treatment regimens consisted of permanent prostate brachytherapy with or without hormone therapy, permanent prostate brachytherapy with external beam radiotherapy, or all 3 modalities. Biochemical recurrence was defined using the Phoenix definition. Multivariate analysis was performed to determine if age and/or other clinicopathological features were associated with disease progression. The Kaplan-Meier method was used to calculate rates of freedom from progression with the log rank test to compare patients younger than 60 vs 60 years or older. Median followup was 56.1 months. In the study population 237 patients were younger than 60 years at diagnosis (11%). The 5 and 10-year freedom from progression rates were 90.1% and 85.6%, respectively, for the entire population. Multivariate analysis demonstrated that prostate specific antigen (p <0.01), biopsy Gleason score (p <0.0001) and year of treatment (p <0.001) were associated with freedom from progression while age (p = 0.95) and clinical stage (p = 0.11) were not. There was no significant difference in freedom from progression between men younger than 60, or 60 years or older (log rank p = 0.46). In the younger cohort the 10-year freedom from progression for patients presenting with low, intermediate and high risk disease was 91.3%, 80.0% and 70.2% compared to 91.8%, 83.4% and 72.1%, respectively, for men 60 years or older. Our long-term results confirm favorable outcomes after permanent prostate brachytherapy in men younger than 60 years. Outcomes are impacted by disease related risk factors but not by age or clinical stage. Definitive treatment options for younger men with clinically localized prostate cancer should include permanent prostate brachytherapy.

Linear accelerator-based stereotactic radiosurgery for brainstem metastases: the Dana-Farber/Brigham and Women's Cancer Center experience.

PubMed

Kelly, Paul J; Lin, Yijie Brittany; Yu, Alvin Y C; Ropper, Alexander E; Nguyen, Paul L; Marcus, Karen J; Hacker, Fred L; Weiss, Stephanie E

2011-09-01

To review the safety and efficacy of linear accelerator-based stereotactic radiosurgery (SRS) for brainstem metastases. We reviewed all patients with brain metastases treated with SRS at DF/BWCC from 2001 to 2009 to identify patients who had SRS to a single brainstem metastasis. Overall survival and freedom-from-local failure rates were calculated from the date of SRS using the Kaplan-Meier method. Prognostic factors were evaluated using the log-rank test and Cox proportional hazards model. A total of 24 consecutive patients with brainstem metastases had SRS. At the time of SRS, 21/24 had metastatic lesions elsewhere within the brain. 23/24 had undergone prior WBRT. Primary diagnoses included eight NSCLC, eight breast cancer, three melanoma, three renal cell carcinoma and two others. Median dose was 13 Gy (range, 8-16). One patient had fractionated SRS 5 Gy ×5. Median target volume was 0.2 cc (range, 0.02-2.39). The median age was 57 years (range, 42-92). Follow-up information was available in 22/24 cases. At the time of analysis, 18/22 patients (82%) had died. The median overall survival time was 5.3 months (range, 0.8-21.1 months). The only prognostic factor that trended toward statistical significance for overall survival was the absence of synchronous brain metastasis at the time of SRS; 1-year overall survival was 31% with versus 67% without synchronous brain metastasis (log rank P = 0.11). Non-significant factors included primary tumor histology and status of extracranial disease (progressing vs. stable/absent). Local failure occurred in 4/22 cases (18%). Actuarial freedom from local failure for all cases was 78.6% at 1 year. RTOG grade 3 toxicities were recorded in two patients (ataxia, confusion). Linac-based SRS for small volume brainstem metastases using a median dose of 13 Gy is associated with acceptable local control and low morbidity.

Watchful waiting and factors predictive of secondary treatment of localized prostate cancer.

PubMed

Wu, Hongyan; Sun, Leon; Moul, Judd W; Wu, Hong Yu; McLeod, David G; Amling, Christopher; Lance, Raymond; Kusuda, Leo; Donahue, Timothy; Foley, John; Chung, Andrew; Sexton, Wade; Soderdahl, Douglas

2004-03-01

Watchful waiting remains an important treatment option for some patients with localized prostate cancer. We defined the demographic, clinical and outcome features of men selecting watchful waiting as an initial treatment strategy, and determined factors predictive of eventual progression to secondary treatment. Of 8390 patients diagnosed with prostate cancer from 1990 to 2001 in the Department of Defense Center for Prostate Disease Research Database, 1158 patients chose watchful waiting as initial treatment. The demographic and clinical differences between patients on watchful waiting and those choosing other initial treatments were compared using the chi-square test. Secondary treatment-free survival according to various prognostic factors was plotted using the Kaplan-Meier method and differences were tested using the log rank test. A multivariate Cox proportional hazards regression analysis was performed to determine which factors were independent predictors of secondary treatment. Compared to other patients, those selecting watchful waiting were older, had lower prostate specific antigen (PSA) at diagnosis, and were more likely to have lower stage (cT1) and lower grade (Gleason sum 7 or less) cancers. Age, PSA and clinical stage were all significant and independent predictors of secondary treatment. The relative risk of secondary treatment can be expressed as EXP (-0.034 x age at diagnosis + 0.284 x LOG (diagnostic PSA) + 0.271 x clinical stage T2 + 0.264 x clinical stage T3). Men who elect watchful waiting as initial management for prostate cancer are older with lower Gleason sums and serum PSA. In these men, age at diagnosis, serum PSA and clinical stage are the most significant predictors of requiring or selecting secondary treatment.

Using Trained Pixel Classifiers to Select Images of Interest

NASA Technical Reports Server (NTRS)

Mazzoni, D.; Wagstaff, K.; Castano, R.

2004-01-01

We present a machine-learning-based approach to ranking images based on learned priorities. Unlike previous methods for image evaluation, which typically assess the value of each image based on the presence of predetermined specific features, this method involves using two levels of machine-learning classifiers: one level is used to classify each pixel as belonging to one of a group of rather generic classes, and another level is used to rank the images based on these pixel classifications, given some example rankings from a scientist as a guide. Initial results indicate that the technique works well, producing new rankings that match the scientist's rankings significantly better than would be expected by chance. The method is demonstrated for a set of images collected by a Mars field-test rover.

The South’s timber industry - an assessment of timber product output and use, 2009

Treesearch

Tony G. Johnson; James W. Bentley; Mike Howell

2011-01-01

In 2009, industrial roundwood output from the South’s forests totaled 6.56 billion cubic feet, 20 percent less than in 2007. Pulpwood was the leading roundwood product at 3.43 billion cubic feet; saw logs ranked second at 2.26 billion cubic feet; veneer logs were third at 384.4 million cubic feet. Total receipts declined 21 percent to 6.55 billion cubic feet. Mill...

Standardized likelihood ratio test for comparing several log-normal means and confidence interval for the common mean.

PubMed

Krishnamoorthy, K; Oral, Evrim

2017-12-01

Standardized likelihood ratio test (SLRT) for testing the equality of means of several log-normal distributions is proposed. The properties of the SLRT and an available modified likelihood ratio test (MLRT) and a generalized variable (GV) test are evaluated by Monte Carlo simulation and compared. Evaluation studies indicate that the SLRT is accurate even for small samples, whereas the MLRT could be quite liberal for some parameter values, and the GV test is in general conservative and less powerful than the SLRT. Furthermore, a closed-form approximate confidence interval for the common mean of several log-normal distributions is developed using the method of variance estimate recovery, and compared with the generalized confidence interval with respect to coverage probabilities and precision. Simulation studies indicate that the proposed confidence interval is accurate and better than the generalized confidence interval in terms of coverage probabilities. The methods are illustrated using two examples.

Performance of the AOAC use-dilution method with targeted modifications: collaborative study.

PubMed

Tomasino, Stephen F; Parker, Albert E; Hamilton, Martin A; Hamilton, Gordon C

2012-01-01

The U.S. Environmental Protection Agency (EPA), in collaboration with an industry work group, spearheaded a collaborative study designed to further enhance the AOAC use-dilution method (UDM). Based on feedback from laboratories that routinely conduct the UDM, improvements to the test culture preparation steps were prioritized. A set of modifications, largely based on culturing the test microbes on agar as specified in the AOAC hard surface carrier test method, were evaluated in a five-laboratory trial. The modifications targeted the preparation of the Pseudomonas aeruginosa test culture due to the difficulty in separating the pellicle from the broth in the current UDM. The proposed modifications (i.e., the modified UDM) were compared to the current UDM methodology for P. aeruginosa and Staphylococcus aureus. Salmonella choleraesuis was not included in the study. The goal was to determine if the modifications reduced method variability. Three efficacy response variables were statistically analyzed: the number of positive carriers, the log reduction, and the pass/fail outcome. The scope of the collaborative study was limited to testing one liquid disinfectant (an EPA-registered quaternary ammonium product) at two levels of presumed product efficacies, high and low. Test conditions included use of 400 ppm hard water as the product diluent and a 5% organic soil load (horse serum) added to the inoculum. Unfortunately, the study failed to support the adoption of the major modification (use of an agar-based approach to grow the test cultures) based on an analysis of method's variability. The repeatability and reproducibility standard deviations for the modified method were equal to or greater than those for the current method across the various test variables. However, the authors propose retaining the frozen stock preparation step of the modified method, and based on the statistical equivalency of the control log densities, support its adoption as a procedural change to the current UDM. The current UDM displayed acceptable responsiveness to changes in product efficacy; acceptable repeatability across multiple tests in each laboratory for the control counts and log reductions; and acceptable reproducibility across multiple laboratories for the control log density values and log reductions. Although the data do not support the adoption of all modifications, the UDM collaborative study data are valuable for assessing sources of method variability and a reassessment of the performance standard for the UDM.

A sampling-based method for ranking protein structural models by integrating multiple scores and features.

PubMed

Shi, Xiaohu; Zhang, Jingfen; He, Zhiquan; Shang, Yi; Xu, Dong

2011-09-01

One of the major challenges in protein tertiary structure prediction is structure quality assessment. In many cases, protein structure prediction tools generate good structural models, but fail to select the best models from a huge number of candidates as the final output. In this study, we developed a sampling-based machine-learning method to rank protein structural models by integrating multiple scores and features. First, features such as predicted secondary structure, solvent accessibility and residue-residue contact information are integrated by two Radial Basis Function (RBF) models trained from different datasets. Then, the two RBF scores and five selected scoring functions developed by others, i.e., Opus-CA, Opus-PSP, DFIRE, RAPDF, and Cheng Score are synthesized by a sampling method. At last, another integrated RBF model ranks the structural models according to the features of sampling distribution. We tested the proposed method by using two different datasets, including the CASP server prediction models of all CASP8 targets and a set of models generated by our in-house software MUFOLD. The test result shows that our method outperforms any individual scoring function on both best model selection, and overall correlation between the predicted ranking and the actual ranking of structural quality.

Randomized comparison of two Internet-supported fertility-awareness-based methods of family planning.

PubMed

Fehring, Richard J; Schneider, Mary; Raviele, Kathleen; Rodriguez, Dana; Pruszynski, Jessica

2013-07-01

The aim was to compare the efficacy and acceptability of two Internet-supported fertility-awareness-based methods of family planning. Six hundred and sixty-seven women and their male partners were randomized into either an electronic hormonal fertility monitor (EHFM) group or a cervical mucus monitoring (CMM) group. Both groups utilized a Web site with instructions, charts and support. Acceptability was assessed online at 1, 3 and 6 months. Pregnancy rates were determined by survival analysis. The EHFM participants (N=197) had a total pregnancy rate of 7 per 100 users over 12 months of use compared with 18.5 for the CMM group (N=164). The log rank survival test showed a significant difference (p<.01) in survival functions. Mean acceptability for both groups increased significantly over time (p<.0001). Continuation rates at 12 months were 40.6% for the monitor group and 36.6% for the mucus group. In comparison with the CMM, the EHFM method of family planning was more effective. All users had an increase in acceptability over time. Results are tempered by the high dropout rate. Copyright © 2013 Elsevier Inc. All rights reserved.

Assessment of Mudrock Brittleness with Micro-scratch Testing

NASA Astrophysics Data System (ADS)

Hernandez-Uribe, Luis Alberto; Aman, Michael; Espinoza, D. Nicolas

2017-11-01

Mechanical properties are essential for understanding natural and induced deformational behavior of geological formations. Brittleness characterizes energy dissipation rate and strain localization at failure. Brittleness has been investigated in hydrocarbon-bearing mudrocks in order to quantify the impact of hydraulic fracturing on the creation of complex fracture networks and surface area for reservoir drainage. Typical well logging correlations associate brittleness with carbonate content or dynamic elastic properties. However, an index of rock brittleness should involve actual rock failure and have a consistent method to quantify it. Here, we present a systematic method to quantify mudrock brittleness based on micro-mechanical measurements from the scratch test. Brittleness is formulated as the ratio of energy associated with brittle failure to the total energy required to perform a scratch. Soda lime glass and polycarbonate are used for comparison to identify failure in brittle and ductile mode and validate the developed method. Scratch testing results on mudrocks indicate that it is possible to use the recorded transverse force to estimate brittleness. Results show that tested samples rank as follows in increasing degree of brittleness: Woodford, Eagle Ford, Marcellus, Mancos, and Vaca Muerta. Eagle Ford samples show mixed ductile/brittle failure characteristics. There appears to be no definite correlation between micro-scratch brittleness and quartz or total carbonate content. Dolomite content shows a stronger correlation with brittleness than any other major mineral group. The scratch brittleness index correlates positively with increasing Young's modulus and decreasing Poisson's ratio, but shows deviations in rocks with distinct porosity and with stress-sensitive brittle/ductile behavior (Eagle Ford). The results of our study demonstrate that the micro-scratch test method can be used to investigate mudrock brittleness. The method is particularly useful for reservoir characterization methods that take advantage of drill cuttings or whenever large samples for triaxial testing or fracture mechanics testing cannot be recovered.

QSAR models for predicting octanol/water and organic carbon/water partition coefficients of polychlorinated biphenyls.

PubMed

Yu, S; Gao, S; Gan, Y; Zhang, Y; Ruan, X; Wang, Y; Yang, L; Shi, J

2016-04-01

Quantitative structure-property relationship modelling can be a valuable alternative method to replace or reduce experimental testing. In particular, some endpoints such as octanol-water (KOW) and organic carbon-water (KOC) partition coefficients of polychlorinated biphenyls (PCBs) are easier to predict and various models have been already developed. In this paper, two different methods, which are multiple linear regression based on the descriptors generated using Dragon software and hologram quantitative structure-activity relationships, were employed to predict suspended particulate matter (SPM) derived log KOC and generator column, shake flask and slow stirring method derived log KOW values of 209 PCBs. The predictive ability of the derived models was validated using a test set. The performances of all these models were compared with EPI Suite™ software. The results indicated that the proposed models were robust and satisfactory, and could provide feasible and promising tools for the rapid assessment of the SPM derived log KOC and generator column, shake flask and slow stirring method derived log KOW values of PCBs.

Hazard Ranking Method for Populations Exposed to Arsenic in Private Water Supplies: Relation to Bedrock Geology.

PubMed

Crabbe, Helen; Fletcher, Tony; Close, Rebecca; Watts, Michael J; Ander, E Louise; Smedley, Pauline L; Verlander, Neville Q; Gregory, Martin; Middleton, Daniel R S; Polya, David A; Studden, Mike; Leonardi, Giovanni S

2017-12-01

Approximately one million people in the UK are served by private water supplies (PWS) where main municipal water supply system connection is not practical or where PWS is the preferred option. Chronic exposure to contaminants in PWS may have adverse effects on health. South West England is an area with elevated arsenic concentrations in groundwater and over 9000 domestic dwellings here are supplied by PWS. There remains uncertainty as to the extent of the population exposed to arsenic (As), and the factors predicting such exposure. We describe a hazard assessment model based on simplified geology with the potential to predict exposure to As in PWS. Households with a recorded PWS in Cornwall were recruited to take part in a water sampling programme from 2011 to 2013. Bedrock geologies were aggregated and classified into nine Simplified Bedrock Geological Categories (SBGC), plus a cross-cutting "mineralized" area. PWS were sampled by random selection within SBGCs and some 508 households volunteered for the study. Transformations of the data were explored to estimate the distribution of As concentrations for PWS by SBGC. Using the distribution per SBGC, we predict the proportion of dwellings that would be affected by high concentrations and rank the geologies according to hazard. Within most SBGCs, As concentrations were found to have log-normal distributions. Across these areas, the proportion of dwellings predicted to have drinking water over the prescribed concentration value (PCV) for As ranged from 0% to 20%. From these results, a pilot predictive model was developed calculating the proportion of PWS above the PCV for As and hazard ranking supports local decision making and prioritization. With further development and testing, this can help local authorities predict the number of dwellings that might fail the PCV for As, based on bedrock geology. The model presented here for Cornwall could be applied in areas with similar geologies. Application of the method requires independent validation and further groundwater-derived PWS sampling on other geological formations.

Decontamination of materials contaminated with Francisella philomiragia or MS2 bacteriophage using PES-Solid, a solid source of peracetic acid.

PubMed

Buhr, T L; Young, A A; Johnson, C A; Minter, Z A; Wells, C M

2014-08-01

The aim of the study was to develop test methods and evaluate survival of Francisella philomiragia cells and MS2 bacteriophage after exposure to PES-Solid (a solid source of peracetic acid) formulations with or without surfactants. Francisella philomiragia cells (≥7·6 log10 CFU) or MS2 bacteriophage (≥6·8 log10 PFU) were deposited on seven different test materials and treated with three different PES-Solid formulations, three different preneutralized samples and filter controls at room temperature for 15 min. There were 0-1·3 log10 CFU (<20 cells) of cell survival, or 0-1·7 log10 (<51 PFU) of bacteriophage survival in all 21 test combinations (organism, formulation and substrate) containing reactive PES-Solid. In addition, the microemulsion (Dahlgren Surfactant System) showed ≤2 log10 (100 cells) of viable F. philomiragia cells, indicating the microemulsion achieved <2 log10 CFU on its own. Three PES-Solid formulations and one microemulsion system (DSS) inactivated F. philomiragia cells and/or MS2 bacteriophage that were deposited on seven different materials. A test method was developed to show that reactive PES-Solid formulations and a microemulsion system (DSS) inactivated >6 log10 CFU/PFU F. philomiragia cells and/or MS2 bacteriophage on different materials. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Lithology identification of aquifers from geophysical well logs and fuzzy logic analysis: Shui-Lin Area, Taiwan

NASA Astrophysics Data System (ADS)

Hsieh, Bieng-Zih; Lewis, Charles; Lin, Zsay-Shing

2005-04-01

The purpose of this study is to construct a fuzzy lithology system from well logs to identify formation lithology of a groundwater aquifer system in order to better apply conventional well logging interpretation in hydro-geologic studies because well log responses of aquifers are sometimes different from those of conventional oil and gas reservoirs. The input variables for this system are the gamma-ray log reading, the separation between the spherically focused resistivity and the deep very-enhanced resistivity curves, and the borehole compensated sonic log reading. The output variable is groundwater formation lithology. All linguistic variables are based on five linguistic terms with a trapezoidal membership function. In this study, 50 data sets are clustered into 40 training sets and 10 testing sets for constructing the fuzzy lithology system and validating the ability of system prediction, respectively. The rule-based database containing 12 fuzzy lithology rules is developed from the training data sets, and the rule strength is weighted. A Madani inference system and the bisector of area defuzzification method are used for fuzzy inference and defuzzification. The success of training performance and the prediction ability were both 90%, with the calculated correlation of training and testing equal to 0.925 and 0.928, respectively. Well logs and core data from a clastic aquifer (depths 100-198 m) in the Shui-Lin area of west-central Taiwan are used for testing the system's construction. Comparison of results from core analysis, well logging and the fuzzy lithology system indicates that even though the well logging method can easily define a permeable sand formation, distinguishing between silts and sands and determining grain size variation in sands is more subjective. These shortcomings can be improved by a fuzzy lithology system that is able to yield more objective decisions than some conventional methods of log interpretation.

Efficacy of the World Health Organization-recommended handwashing technique and a modified washing technique to remove Clostridium difficile from hands.

PubMed

Deschênes, Philippe; Chano, Frédéric; Dionne, Léa-Laurence; Pittet, Didier; Longtin, Yves

2017-08-01

The efficacy of the World Health Organization (WHO)-recommended handwashing technique against Clostridium difficile is uncertain, and whether it could be improved remains unknown. Also, the benefit of using a structured technique instead of an unstructured technique remains unclear. This study was a prospective comparison of 3 techniques (unstructured, WHO, and a novel technique dubbed WHO shortened repeated [WHO-SR] technique) to remove C difficile. Ten participants were enrolled and performed each technique. Hands were contaminated with 3 × 10 6 colony forming units (CFU) of a nontoxigenic strain containing 90% spores. Efficacy was assessed using the whole-hand method. The relative efficacy of each technique and of a structured (either WHO or WHO-SR) vs an unstructured technique were assessed by Mann-Whitney U test and Wilcoxon signed-rank test. The median effectiveness of the unstructured, WHO, and WHO-SR techniques in log 10 CFU reduction was 1.30 (interquartile range [IQR], 1.27-1.43), 1.71 (IQR, 1.34-1.91), and 1.70 (IQR, 1.54-2.42), respectively. The WHO-SR technique was significantly more efficacious than the unstructured technique (P = .01). Washing hands with a structured technique was more effective than washing with an unstructured technique (median, 1.70 vs 1.30 log 10 CFU reduction, respectively; P = .007). A structured washing technique is more effective than an unstructured technique against C difficile. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Applying a "Big Data" Literature System to Recommend Antihypertensive Drugs for Hypertension Patients with Diabetes Mellitus.

PubMed

Shu, Jing-Xian; Li, Ying; He, Ting; Chen, Ling; Li, Xue; Zou, Lin-Lin; Yin, Lu; Li, Xiao-Hui; Wang, An-Li; Liu, Xing; Yuan, Hong

2018-01-07

BACKGROUND The explosive increase in medical literature has changed therapeutic strategies, but it is challenging for physicians to keep up-to-date on the medical literature. Scientific literature data mining on a large-scale of can be used to refresh physician knowledge and better improve the quality of disease treatment. MATERIAL AND METHODS This paper reports on a reformulated version of a data mining method called MedRank, which is a network-based algorithm that ranks therapy for a target disease based on the MEDLINE literature database. MedRank algorithm input for this study was a clear definition of the disease model; the algorithm output was the accurate recommendation of antihypertensive drugs. Hypertension with diabetes mellitus was chosen as the input disease model. The ranking output of antihypertensive drugs are based on the Joint National Committee (JNC) guidelines, one through eight, and the publication dates, ≤1977, ≤1980, ≤1984, ≤1988, ≤1993, ≤1997, ≤2003, and ≤2013. The McNemar's test was used to evaluate the efficacy of MedRank based on specific JNC guidelines. RESULTS The ranking order of antihypertensive drugs changed with the date of the published literature, and the MedRank algorithm drug recommendations had excellent consistency with the JNC guidelines in 2013 (P=1.00 from McNemar's test, Kappa=0.78, P=1.00). Moreover, the Kappa index increased over time. Sensitivity was better than specificity for MedRank; in addition, sensitivity was maintained at a high level, and specificity increased from 1997 to 2013. CONCLUSIONS The use of MedRank in ranking medical literature on hypertension with diabetes mellitus in our study suggests possible application in clinical practice; it is a potential method for supporting antihypertensive drug-prescription decisions.

CNS infections in Greenland: A nationwide register-based cohort study

PubMed Central

Nordholm, Anne Christine; Søborg, Bolette; Andersson, Mikael; Hoffmann, Steen; Skinhøj, Peter; Koch, Anders

2017-01-01

Background Indigenous Arctic people suffer from high rates of infectious diseases. However, the burden of central nervous system (CNS) infections is poorly documented. This study aimed to estimate incidence rates and mortality of CNS infections among Inuits and non-Inuits in Greenland and in Denmark. Methods We conducted a nationwide cohort study using the populations of Greenland and Denmark 1990–2012. Information on CNS infection hospitalizations and pathogens was retrieved from national registries and laboratories. Incidence rates were estimated as cases per 100,000 person-years. Incidence rate ratios were calculated using log-linear Poisson-regression. Mortality was estimated using Kaplan-Meier curves and Log Rank test. Results The incidence rate of CNS infections was twice as high in Greenland (35.6 per 100,000 person years) as in Denmark (17.7 per 100,000 person years), but equally high among Inuits in Greenland and Denmark (38.2 and 35.4, respectively). Mortality from CNS infections was 2 fold higher among Inuits (10.5%) than among non-Inuits (4.8%) with a fivefold higher case fatality rate in Inuit toddlers. Conclusion Overall, Inuits living in Greenland and Denmark suffer from twice the rate of CNS infections compared with non-Inuits, and Inuit toddlers carried the highest risk of mortality. Further studies regarding risk factors such as genetic susceptibility, life style and socioeconomic factors are warranted. PMID:28158207

The Need for New Donor Stratification to Predict Graft Survival in Deceased Donor Kidney Transplantation.

PubMed

Yang, Shin Seok; Yang, Jaeseok; Ahn, Curie; Min, Sang Il; Ha, Jongwon; Kim, Sung Joo; Park, Jae Berm

2017-05-01

The aim of this study was to determine whether stratification of deceased donors by the United Network for Organ Sharing (UNOS) criteria negatively impacts graft survival. We retrospectively reviewed deceased donor and recipient pretransplant variables of kidney transplantations that occurred between February 1995 and December 2009. We compared clinical outcomes between standard criteria donors (SCDs) and expanded criteria donors (ECDs). The deceased donors consisted of 369 patients. A total of 494 transplant recipients were enrolled in this study. Mean age was 41.7±11.4 year (range 18-69) and 273 patients (55.4%) were male. Mean duration of follow-up was 8.8±4.9 years. The recipients from ECD kidneys were 63 patients (12.8%). The overall mean cold ischemia time was 5.7±3.2 hours. Estimated glomerular filtration rate at 1, 2, and 3 years after transplantation were significantly lower in ECD transplants (1 year, 62.2±17.6 vs. 51.0±16.4, p<0.001; 2 year, 62.2±17.6 vs. 51.0±16.4, p=0.001; 3 year, 60.9±23.5 vs. 54.1±18.7, p=0.047). In multivariate analysis, donor age (≥40 years) was an independent risk factor for graft failure. In Kaplan-Meier analyses, there was no significant difference in death-censored graft survival (Log rank test, p>0.05), although patient survival was lower in ECDs than SCDs (Log rank test, p=0.011). Our data demonstrate that stratification by the UNOS criteria does not predict graft survival. In order to expand the donor pool, new criteria for standard/expanded donors need to be modified by regional differences. © Copyright: Yonsei University College of Medicine 2017

S-shaped versus conventional straight skin incision: Impact on primary functional maturation, stenosis and thrombosis of autogenous radiocephalic arteriovenous fistula: Impact of incision on maturation, stenosis & failure of RCAVF. Study design: Prospective observational comparative.

PubMed

Kordzadeh, Ali; Panayiotopolous, Yiannis

2017-10-01

The objective of this study is to test the null hypothesis that an S-shaped surgical incision versus conventional (straight) skin incision in the creation of autogenous radiocephalic arteriovenous fistulas (RCAVFs) have no impact on the primary end-point of primary functional maturation and secondary end points of stenosis and thrombosis. A prospective observational comparative consecutive study with intention-to-treat on individuals undergoing only radiocephalic arteriovenous fistula (RCAVFs) over a period of 12 months was conducted. Variables on patient's demographics, comorbidities, anesthesia type, mean arterial blood pressure, thrill, laterality, cephalic vein and radial artery diameter were collated. The test of probability was assessed through Chi-Square, Kaplan-Meier survival estimator and Log-Rank analysis. Total of n = 83 individuals with median age of 67 years (IQR, 20-89) and male predominance 83% during this period were subjected to RCAVF formation. Total of n = 45 patients in straight skin incision were compared to n = 38 individuals in S-shaped group. Despite equal prevalence of demographics, comorbidities, anesthesia type, mean arterial blood pressure (MAP), thrill, laterality, cephalic vein and radial artery diameter ( p  > 0.05) higher incidence of juxta-anastomotic stenosis was noted in the straight skin incision group ( p  = 0.029) in comparative and survival analysis (Log-Rank, p  = 0.036). The maturation of the entire cohort was 69% (S-shaped 76% vs. straight group 62%) (p > 0.05). The outcome of this study demonstrates that S-shaped surgical skin incision is associated with a lower incidence of stenosis in comparison to straight incision type in RCAVF formation.

Different pathological features and prognosis in gastric cancer patients coming from high-risk and low-risk areas of Italy.

PubMed

Marrelli, Daniele; Pedrazzani, Corrado; Corso, Giovanni; Neri, Alessandro; Di Martino, Marianna; Pinto, Enrico; Roviello, Franco

2009-07-01

To compare clinicopathological features and long-term outcome in gastric cancer patients coming from high-risk and low-risk areas of Italy. Better survival rates have been reported from countries with higher incidence of gastric cancer. Data regarding 829 patients coming from Tuscany (group A) and 143 patients coming from Southern Italy (group B) were analyzed. Mean follow-up time was 56 +/- 57 months; it was 85 +/- 63 months in surviving patients or not tumor-related deaths. Prognostic factors were investigated by multivariate analysis with Cox proportional hazard model after verifying the assumption of proportionality of the risk associated with covariates. Lauren diffuse-mixed histotype, younger age, extended lymphadenectomy, and advanced stages were more common in group B. Gastric cancer-related 10-year survival probability was 48% in group A versus 29% in group B (log-rank test: P < 0.001). By multivariate analysis, geographic area was confirmed as a significant prognostic factor (hazard ratio for group B vs. group A: 1.52, 95% confidence interval: 1.12-2.06, P = 0.006). The influence of this factor on long-term survival was independent from other clinical, surgical, and pathologic factors, and was notable in neoplasms involving the serosa (10-year survival probability: 15% in group A vs. 3% in group B, log-rank test: P = 0.005). Patients coming from low-risk area of Italy showed distinct pathologic features, more advanced stage, and worse prognosis when compared with patients coming from high-risk area. These findings may be indicative of different tumor biology, and may contribute to partly explain worldwide geographic variability in prognosis reported in different series.

Impact of stent length on clinical outcomes of first-generation and new-generation drug-eluting stents.

PubMed

Konishi, Hirokazu; Miyauchi, Katsumi; Dohi, Tomotaka; Tsuboi, Shuta; Ogita, Manabu; Naito, Ryo; Kasai, Takatoshi; Tamura, Hiroshi; Okazaki, Shinya; Isoda, Kikuo; Daida, Hiroyuki

2016-04-01

The aim of this study is to compare first- and new-generation drug-eluting stents (DESs) which are implanted in long lesion. Stent length is known to be a predictor of adverse events after percutaneous coronary intervention (PCI), even with the first-generation DESs. The introduction of new-generation DESs has reduced the rates of adverse clinical events. However, the impact of stent length on long-term clinical outcomes is not well known. A total of 1181 consecutive patients who underwent PCI using either a first-generation DES (n = 885) or a new-generation DES (n = 296) between 2004 and 2011 were investigated. In each of the stent groups, the patients were divided into two groups by stent length (>32 and ≤32 mm) and compared. During the follow-up period, the incidence of major adverse cardiac events (MACEs) was significantly higher for patients with long stents implanted than with short stents (P < 0.01; log-rank test) in the first-generation DES group. However, there was no difference in the incidence of MACEs between the long- and short-stent groups in the new-generation DES group (P = 0.24; log-rank test). On multivariate Cox regression analysis, stent length was not associated with adverse events in the new-generation DES groups [hazard ratio (HR) 0.87; 95 % confidence interval (95 % CI) 0.71-1.04; P = 0.14]. Implanted stent length was significantly associated with a higher risk of MACEs in patients who received first-generation DESs, but not in patients who received the new-generation DESs.

Two-year survival of Ahmed valve implantation in the first 2 years of life with and without intraoperative mitomycin-C.

PubMed

Al-Mobarak, Faisal; Khan, Arif O

2009-10-01

To evaluate the effect of intraoperative mitomycin-C (MMC) on polypropylene Ahmed glaucoma valve (AGV) survival 2 years after implantation during the first 2 years of life. Retrospective institutional comparative series (1995-2005). Thirty-one eyes of 27 patients (23 unilateral, 4 bilateral; 16 boys, 11 girls) undergoing AGV implantation at a mean age of 11.1 months (standard deviation [SD], 5.46), all of which had 2 years of regular postoperative follow-up. MMC was applied intraoperatively in those cases in the area of AGV implantation in 16 (52%) and was not applied in 15 (48%). In some eyes, MMC was applied intraoperatively in cases done by the surgeons who routinely used MMC for all AGV implantation in young children. Failure was defined as intraocular pressure (IOP) > 22 mmHg with or without glaucoma medications, the need for an additional procedure for IOP control, or the occurrence of significant complications (e.g., endophthalmitis, retinal detachment, persistent hypotony [IOP < 5 mmHg]). Survival was the absence of failure. Failure or significant complications as defined. Mean survival for the non-MMC eyes (22.15 months; standard error [SE], 1.93) was significantly longer than survival for the MMC eyes (16.25 months; SE, 2.17) by the log-rank test (P = 0.025). The difference in cumulative survival at 2 years was also significantly different by log-rank test (P = 0.001): 80.0% (SE 10.3) and 31.3% (SE 11.6), respectively. Rather than improved survival, intraoperative use of MMC was associated with shorter survival 2 years after AGV implantation during the first 2 years of life. We speculate that MMC-induced tissue death can stimulate a reactive fibrosis around the AGV in very young eyes.

Long non-coding RNA PVT1 as a novel potential biomarker for predicting the prognosis of colorectal cancer.

PubMed

Fan, Heng; Zhu, Jian-Hua; Yao, Xue-Qing

2018-05-01

Long non-coding RNA (lncRNA) plays a very important role in the occurrence and development of various tumors, and is a potential biomarker for cancer diagnosis and prognosis. The purpose of this study was to investigate the relationship between the expression of lncRNA plasmacytoma variant translocation 1 (PVT1) and the prognostic significance in patients with colorectal cancer. The expression of PVT1 was measured by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) in cancerous and adjacent tissues of 210 colorectal cancer patients. The disease-free survival and overall survival of colorectal cancer patients were evaluated by Kaplan-Meier analysis, and univariate and multivariate analysis were performed by Cox proportional-hazards model. Our results revealed that PVT1 expression in cancer tissues of colorectal cancer was significantly higher than that of adjacent tissues ( P<0.001). High PVT1 expression was increased by 51.4% (108/210), which was significantly correlated with the tumor differentiation, the depth of invasion, the stage of tumor, node, metastasis (TNM), and lymphatic metastasis. The Kaplan-Meier analysis showed that high PVT1 expression resulted in a shorter disease-free survival (Log-rank test P<0.001) and overall survival (Log-rank test P<0.001) compared with the low PVT1 expression group in colorectal cancer patients, whether at TNM I/II stage or at TNM III/IV stage. A multivariate Cox regression analysis demonstrated that high PVT1 expression was an independent predictor of poor prognosis in colorectal cancer patients. Our results suggest that high PVT1 expression might be a potential biomarker for assessing tumor recurrence and prognosis in colorectal cancer patients.

Nephron sparing surgery (NSS) for unilateral wilms tumor (UWT): the SIOP 2001 experience.

PubMed

Wilde, Jim C H; Aronson, Daniel C; Sznajder, Beata; Van Tinteren, Harm; Powis, Mark; Okoye, Bruce; Cecchetto, Giovanni; Audry, Georges; Fuchs, Jörg; Schweinitz, Dietrich Von; Heij, Hugo; Graf, Norbert; Bergeron, Christophe; Pritchard-Jones, Kathy; Van Den Heuvel-Eibrink, Marry; Carli, Modesto; Oldenburger, Foppe; Sandstedt, Bengt; De Kraker, Jan; Godzinski, Jan

2014-12-01

Total nephrectomy (TN) remains the standard treatment of unilateral Wilms tumors (uWT). The SIOP WT-2001 protocol allowed Nephron Sparing Surgery (NSS) for polar or peripherally non-infiltrating tumors. Inventory of the current SIOP NSS-experience. 2,800 patients with a unilateral, localized or metastatic and an unequivocal surgical technique recorded were included. All had neo-adjuvant chemotherapy and delayed surgery. In 91 (3%) NSS was performed and in 2709 TN. Data was retrieved from the SIOP WT 2001 database. NSS group contained 65% stage I tumours and the TN group 48%. Tumor volume (at diagnosis and surgery) was significantly smaller in the NSS group. Within stage III, after NSS, 7/12 (58%) had positive margins (M +), 5 with tumor negative lymph nodes (LN-). After TN, 355/712 (55%) had M + , 182 were LN-. Treatment of M+ in the NSS group resulted in two conversions to TN (one combined with radiotherapy), three patients had radiotherapy only and in two patients local therapy, if given, was not recorded. After NSS, four recurrences occurred. For localized disease the 5-year overall (OS) and event free survival (EFS) in NSS group was 100 and 94.8 (95% CI:89.9-99.9), respectively, while OS and EFS in the TN group were 94.4 (95% CI: 93.2-95.5, log-rank test P = 0.06) and 86.5 (95% CI:85.0-88.1, log-rank test P = 0.06), respectively. NSS was only performed in 3% of patients with uWT. Despite excellent survival with few relapses, the gain of nephrons needs to be weighed against the risk to induce stage III with intensified therapy. © 2014 Wiley Periodicals, Inc.

Two types of lacunar infarcts: further arguments from a study on prognosis.

PubMed

de Jong, G; Kessels, F; Lodder, J

2002-08-01

Earlier, we found that lacunar stroke patients with > or =1 asymptomatic lacunar infarcts on CT had leukoaraiosis and hypertension significantly more often than patients without such lesions, and we hypothesized that 2 types of small-vessel disease could be distinguished during life: arteriolosclerosis and microatheromatosis, respectively. Differences in prognosis might sustain this hypothesis of 2 lacunar stroke entities. Therefore, we performed a follow-up in 333 patients with first lacunar stroke, distinguishing those with > or =1 asymptomatic lacunar lesions (LACI+) from those without such lesions (LACI-). Cross-sectional follow-up was performed after 785+/-479 days (mean+/-SD) in 104 LACI+ patients and 865+/-545 days in 229 LACI- patients. Mortality at the end of follow-up was 33% in LACI+ and 21% in LACI- patients [odds ratio (OR), 1.74; 95% confidence interval (CI), 1.01 to 3.01]. Stroke recurrence rate was 21% in LACI+ and 11% in LACI- (OR, 2.09; 95% CI, 1.08 to 4.06). Forty percent of LACI+ and 26% of LACI- patients had unfavorable outcome at the end of follow-up (OR, 1.95; 95% CI, 1.17 to 3.26). Kaplan-Meier curves showed less favorable survival in LACI+ (log-rank test, P=0.0218) and survival free of stroke (log-rank test, P=0.0121) than in LACI-. When we restricted the analysis to patients with both silent lesions and leukoaraiosis (n=63) compared with those without (n=196), differences were even more pronounced. Prognosis for mortality, recurrent stroke, and overall functional outcome in lacunar stroke patients with > or =1 silent lacunar lesions is more unfavorable than in patients without such lesions. These findings sustain the idea of 2 lacunar stroke entities.

Relationship between mono-hydroxy-carbazepine serum concentrations and adverse effects in patients on oxcarbazepine monotherapy.

PubMed

Sattler, Annika; Schaefer, Marion; May, Theodor W

2015-09-01

To evaluate the relationship between serum concentrations of mono-hydroxy-carbazepine (MHD), the main metabolite of oxcarbazepine (OXC), and the occurrence of adverse effects (AE) in a large group of patients on OXC monotherapy. An antiepileptic drug (AED) therapeutic drug monitoring (TDM) database was analyzed especially with regard to OXC dosage, MHD serum concentration, and the occurrence of AE. In total, 893 blood samples of 442 patients were included in this retrospective study. The statistical evaluation was performed by means of Kaplan-Meier estimates, log-rank tests and generalized estimating equations (GEE). At least one AE was reported in 78 (17.6%) of the 442 patients. At MHD serum concentrations of 30.0 μg/ml and 43.7 μg/ml and OXC dosages of 33.1 mg/kg and 62.3 mg/kg, 25% and 75% of patients, respectively, experienced at least one AE. Log-rank tests indicated that younger patients (<18 years) may be able to tolerate higher MHD serum levels (p = 0.006) and higher OXC dosages per body weight (p < 0.001) compared to adult patients (≥ 18 years). Furthermore, AEs occurred at higher body-weight adjusted OXC dosages of extended release formulations compared to immediate-release formulations (p = 0.010), whereas MHD serum levels at which AEs occurred did not differ significantly between formulations (p = 0.125). Multivariate GEE confirmed the results. The occurrence of AEs is significantly (and non-linearly) dependent on MHD serum level, whereas the dependence of OXC dosage is less distinctive. But, tolerability of OXC seems to depend on age of the patients as well as on pharmaceutical formulation of OXC. Copyright © 2015 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

Prospective Randomized Trial Comparing Efficacy of Topical Loteprednol Etabonate 0.5% Versus Cyclosporine-A 0.05% for Treatment of Dry Eye Syndrome Following Hematopoietic Stem Cell Transplantation.

PubMed

Boynton, Grace E; Raoof, Duna; Niziol, Leslie M; Hussain, Munira; Mian, Shahzad I

2015-07-01

To evaluate the safety and efficacy of topical loteprednol etabonate (LE) 0.5% compared with cyclosporine A (CsA) 0.05% for the prophylaxis and treatment of dry eye syndrome (DES) after hematopoietic stem cell transplantation (HSCT). Seventy-five patients were randomized to LE (n = 76 eyes of 38 patients) or CsA (n = 74 eyes of 37 patients) pre-HSCT. Lissamine green and fluorescein staining, tear break-up time, tear osmolarity (Osm), Schirmer score (Sch), intraocular pressure, visual acuity, and Ocular Surface Disease Index were assessed pre-HSCT, 3, 6, 9, and 12 months post-HSCT. There were no differences in DES incidence (P = 0.22; log-rank test) or progression (P = 0.41; log-rank test) between the 2 treatment arms during the course of the study. Among eyes with no DES at enrollment, the Kaplan-Meier analysis yielded a 90% rate of DES development in cyclosporine-treated eyes and a 79% rate of DES development in LE-treated eyes by 12 months post-HSCT. The Kaplan-Meier analysis of eyes with DES at enrollment demonstrated a 38% rate of disease progression among cyclosporine-treated eyes and a 26% rate of disease progression among loteprednol-treated eyes by 12 months. No patient in either group had an elevation of 10 mm Hg or greater from baseline at any study visit, and no patients had their treatment discontinued for elevation in intraocular pressure. Pre-HSCT initiation of LE 0.5% appears to be safe and may be as effective as CsA 0.5% for the treatment and prophylaxis of DES following HSCT.

Characteristics of Chinese herbal medicine usage in ischemic heart disease patients among type 2 diabetes and their protection against hydrogen peroxide-mediated apoptosis in H9C2 cardiomyoblasts

PubMed Central

Cheng, Chi-Fung; Shiao, Yi-Tzone; Chien, Wen-Kuei; Chen, Jin-Hua; Liu, Xiang; Tsang, Hsinyi; Lin, Ting-Hsu; Liao, Chiu-Chu; Huang, Shao-Mei; Li, Ju-Pi; Lin, Cheng-Wen; Lin, Jaung-Geng; Lan, Yu-Ching; Liu, Yu-Huei; Hung, Chien-Hui; Lin, Jung-Chun; Lin, Chih-Chien; Lai, Chih-Ho; Liang, Wen-Miin; Lin, Ying-Ju

2017-01-01

Evidence for long-term use of Chinese herbal medicine (CHM) as an adjuvant treatment in patients with type 2 diabetes (T2D) remains limited. This study aimed to assess the frequency of use, utilization patterns, and therapeutic effects of adjuvant CHM for ischemic heart disease (IHD) in patients with T2D in Taiwan. We identified 4620 IHD patients with T2D. After matching for age, gender, and insulin use, 988 subjects each were allocated to a CHM group and a non-CHM group. There were no differences in baseline characteristics except for comorbidities. The CHM group contained more cases with chronic obstructive pulmonary disease, hepatitis, ulcer disease, and hyperlipidemia. The cumulative survival probability was higher in CHM users than in matched non-CHM users aged 60 years or older (P < .0001, log rank test) regardless of gender (P = .0046 for men, P = .0010 for women, log rank test). Among the top 12 CHM combinations, Shu-Jing-Huo-Xue-Tang and Shao-Yao-Gan-Cao-Tang (13.6%) were the most common. This dual combination improved antiapoptotic activity in H2O2-exposed H9C2 cells by enhancing phosphorylation of glycogen synthase kinase-3β and p38 mitogen-activated protein kinase and could increase the survival of myocardial cells. Our study suggests that adjuvant CHM therapy may increase the survival probability and provides a comprehensive list for future investigations of the safety and efficacy of CHM for IHD patients with T2D. PMID:28099940

Are comorbid anxiety disorders a risk factor for suicide attempts in patients with mood disorders? A two-year prospective study.

PubMed

Abreu, L N; Oquendo, M A; Galfavy, H; Burke, A; Grunebaum, M F; Sher, L; Sullivan, G M; Sublette, M E; Mann, J; Lafer, B

2018-01-01

Comorbid anxiety disorders have been considered a risk factor for suicidal behavior in patients with mood disorders, although results are controversial. The aim of this two-year prospective study was to determine if lifetime and current comorbid anxiety disorders at baseline were risk factors for suicide attempts during the two-year follow-up. We evaluated 667 patients with mood disorders (504 with major depression and 167 with bipolar disorder) divided in two groups: those with lifetime comorbid anxiety disorders (n=229) and those without (n=438). Assessments were performed at baseline and at 3, 12, and 24 months. Kaplan-Meier survival analysis and log-rank test were used to evaluate the relationship between anxiety disorders and suicide attempts. Cox proportional hazard regression was performed to investigate clinical and demographic variables that were associated with suicide attempts during follow-up. Of the initial sample of 667 patients, 480 had all three follow-up interviews. During the follow-up, 63 patients (13.1%) attempted suicide at least once. There was no significant difference in survival curves for patients with and without comorbid anxiety disorders (log-rank test=0.269; P=0.604). Female gender (HR=3.66, P=0.001), previous suicide attempts (HR=3.27, P=0.001) and higher scores in the Buss-Durkee Hostility Inventory (HR=1.05, P≤0.001) were associated with future suicide attempts. Our results suggest that comorbid anxiety disorders were not risk factors for suicide attempts. Further studies were needed to determine the role of anxiety disorders as risk factors for suicide attempts. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Methotrexate toxicity and efficacy during the consolidation phase in paediatric acute lymphoblastic leukaemia and MTHFR polymorphisms as pharmacogenetic determinants.

PubMed

D'Angelo, Velia; Ramaglia, Maria; Iannotta, Adriana; Crisci, Stefania; Indolfi, Paolo; Francese, Matteo; Affinita, Maria Carmen; Pecoraro, Giulia; Napolitano, Addolorata; Fusco, Claudia; Oreste, Matilde; Indolfi, Cristiana; Casale, Fiorina

2011-11-01

Folate-metabolizing single-nucleotide polymorphisms (SNPs) are emerging as important pharmacogenetic prognostic determinants of the response to chemotherapy. With high doses of methotrexate (MTX) in the consolidation phase, methylenetetrahydrofolate reductase (MTHFR) polymorphisms could be potential modulators of the therapeutic response to antifolate chemotherapeutics in identifying a possible correlation with the outcome. This study aims to analyse the potential role of the MTHFR C677T and A1298C genetic variants in modulating the clinical toxicity and efficacy of high doses of MTX in a cohort of paediatric ALL patients (n = 151) treated with AIEOP protocols. This work includes DNA extraction by slides and RFLP-PCR. The first observation relative to early toxicities (haematological and non-haematological), after the first doses of MTX in all protocols, was an association between the 677T and 1298C carriers and global toxicity. We found that in the 2 g/m(2) MTX group, patients harbouring 677TT homozygously exhibited a substantial 12-fold risk of developing toxicity. In this study, we demonstrate that the MTHFR 677TT variant is associated with an increased risk of relapse when compared to other genotypes. The Kaplan-Meier analysis showed that the 677TT variant had a lower 7-year DFS(disease-free survival) probability compared to the 677C carrier genotype (log-rank test P = 0.003) and OS (overall survival) and also confirms the lower probability of survival for patients with the 677TT variant (log-rank test, P = 0.006). Our study provides further evidence of the critical role played by folate pathway enzymes in the outcome of ALL, possibly through the interference of MTX.

Helicobacter pylori dupA and gastric acid secretion are negatively associated with gastric cancer development.

PubMed

Imagawa, Shinobu; Ito, Masanori; Yoshihara, Masaharu; Eguchi, Hidetaka; Tanaka, Shinji; Chayama, Kazuaki

2010-12-01

Few reports have described the cancer prevalence of peptic ulcer patients with long-term follow-up studies. We have conducted a long-term retrospective cohort study of Japanese peptic ulcer patients and evaluated the risk factors for the occurrence of gastric cancer (GCa). A total of 136 patients diagnosed with peptic ulcers from 1975 to 1983 were enrolled. These 136 cases [102 males and 34 females; 69 gastric ulcer (GU) and 67 duodenal ulcer (DU) patients at the time of enrollment; mean follow-up period of 14.4 years (range 1-30 years)] after being matched with a tumour registry database in Hiroshima prefecture were surveyed for GCa. We investigated Helicobacter pylori duodenal ulcer promoter gene A (dupA) using paraffin-embedded gastric biopsy specimens in 56 cases. Gastric acid secretion and basal acid output (BAO) in 40 cases, and maximal acid output in 68 cases, had been measured at first diagnosis of peptic ulcers. GCa was detected in 24 patients (17 with GU, 7 with DU) during the follow-up. The prevalence of GCa was significantly higher in GU patients than in DU patients (log-rank test P<0.05). dupA-positive H. pylori was detected not only in DU patients (9/20) but also in GU patients (9/36). Gastric acid output was significantly larger in quantity in patients with dupA-positive H. pylori than in those with dupA-negative H. pylori (P<0.05). The occurrence of GCa was significantly lower in patients with dupA-positive H. pylori and a high BAO level (log-rank test P<0.05). DUs, higher acid output and dupA-positive H. pylori were negatively associated with GCa.

The predictive role of E/e' on ischemic stroke and atrial fibrillation in Japanese patients without atrial fibrillation.

PubMed

Arai, Riku; Suzuki, Shinya; Semba, Hiroaki; Arita, Takuto; Yagi, Naoharu; Otsuka, Takayuki; Sagara, Koichi; Sasaki, Kenichi; Kano, Hiroto; Matsuno, Shunsuke; Kato, Yuko; Uejima, Tokuhisa; Oikawa, Yuji; Kunihara, Takashi; Yajima, Junji; Yamashita, Takeshi

2018-07-01

The predictive role of E/e' on ischemic stroke (IS) and atrial fibrillation (AF) in Japanese patients without AF are unclear. Shinken database includes all the new patients visiting the Cardiovascular Institute Hospital in Tokyo, Japan. E/e' has been routinely measured since 2007. Patients without AF for whom E/e' was measured at the initial visit between 2007 and 2014 (n=11 477, mean age 57.2 years old, men 59.5%) were divided into E/e' tertiles (<8.04, 8.04-11.00, >11.00). During the mean follow-up period of 1.8 years, 58 IS and 140 new appearances of AF were observed. High E/e' tertile was associated with more prevalence of atherothrombotic risks. The cumulative incidence of IS events and new appearance of AF at 6 years in low, middle, and high E/e' tertiles were 0.5%, 1.4%, and 3.0%/year (log-rank test, p<0.001), and 2.5%, 2.9%, and 4.2%/year (log-rank test, p=0.007), respectively. In multivariate analysis, high E/e' tertile was independently associated with IS (HR, 2.857, 95%CI 1.257-6.495, p=0.012). Although high E/e' tertile was independently associated with new appearance of AF when adjusted for coexistence of atherothrombotic risk factors (HR, 1.694, 95%CI, 1.097-2.616, p=0.017), the association was attenuated after adjustment for left atrial dimension. E/e' was significantly associated with incidence of IS and new appearance of AF in non-AF patients. Copyright © 2018 Japanese College of Cardiology. Published by Elsevier Ltd. All rights reserved.

Randomized, placebo-controlled, phase III trial of sunitinib plus prednisone versus prednisone alone in progressive, metastatic, castration-resistant prostate cancer.

PubMed

Michaelson, M Dror; Oudard, Stephane; Ou, Yen-Chuan; Sengeløv, Lisa; Saad, Fred; Houede, Nadine; Ostler, Peter; Stenzl, Arnulf; Daugaard, Gedske; Jones, Robert; Laestadius, Fredrik; Ullèn, Anders; Bahl, Amit; Castellano, Daniel; Gschwend, Juergen; Maurina, Tristan; Chow Maneval, Edna; Wang, Shaw-Ling; Lechuga, Maria Jose; Paolini, Jolanda; Chen, Isan

2014-01-10

We evaluated angiogenesis-targeted sunitinib therapy in a randomized, double-blind trial of metastatic castration-resistant prostate cancer (mCRPC). Men with progressive mCRPC after docetaxel-based chemotherapy were randomly assigned 2:1 to receive sunitinib 37.5 mg/d continuously or placebo. Patients also received oral prednisone 5 mg twice daily. The primary end point was overall survival (OS); secondary end points included progression-free survival (PFS). Two interim analyses were planned. Overall, 873 patients were randomly assigned to receive sunitinib (n = 584) or placebo (n = 289). The independent data monitoring committee stopped the study for futility after the second interim analysis. After a median overall follow-up of 8.7 months, median OS was 13.1 months and 11.8 months for sunitinib and placebo, respectively (hazard ratio [HR], 0.914; 95% CI, 0.762 to 1.097; stratified log-rank test, P = .168). PFS was significantly improved in the sunitinib arm (median 5.6 v 4.1 months; HR, 0.725; 95% CI, 0.591 to 0.890; stratified log-rank test, P < .001). Toxicity and rates of discontinuations because of adverse events (AEs; 27% v 7%) were greater with sunitinib than placebo. The most common treatment-related grade 3/4 AEs were fatigue (9% v 1%), asthenia (8% v 2%), and hand-foot syndrome (7% v 0%). Frequent treatment-emergent grade 3/4 hematologic abnormalities were lymphopenia (20% v 11%), anemia (9% v 8%), and neutropenia (6% v < 1%). The addition of sunitinib to prednisone did not improve OS compared with placebo in docetaxel-refractory mCRPC. The role of antiangiogenic therapy in mCRPC remains investigational.

Characterization of gastrointestinal hemorrhage and prediction of mortality in Asian patients with alcoholic hepatitis.

PubMed

Kim, Su Hwan; Kim, Byeong Gwan; Kim, Won; Oh, Sohee; Kim, Hwi Young; Jung, Yong Jin; Jeong, Ji Bong; Kim, Ji Won; Lee, Kook Lae

2016-04-01

Gastrointestinal bleeding (GIB) often accompanies alcoholic hepatitis (AH). The study aimed to investigate clinical characteristics of GIB in AH patients and to identify risk factors for mortality in AH patients with GIB. Data from 329 patients hospitalized with AH in a single center during 1999-2014 were retrospectively analyzed. Patients with AH were dichotomized into GIB and non-GIB groups. The GIB group was further divided into portal hypertensive bleeding (PHB) and non-PHB groups. Clinical characteristics and survival outcomes were compared between the groups. Risk factors for mortality were analyzed using Cox regression. Among the 329 AH patients, 132 experienced GIB at admission or during hospitalization. The most common cause of GIB was an esophageal varix. The GIB group had worse survival outcomes than the non-GIB group (log-rank test, P = 0.034). The PHB group had worse survival outcomes than the non-PHB group (log-rank test, P = 0.001). On multivariate analysis, alcohol consumption, ascites, encephalopathy, infection, Maddrey's discriminant function, and the model for end-stage liver disease (MELD) score independently predicted mortality in the entire AH cohort. The MELD score (hazard ratio, 1.085; 95% confidence interval, 1.052-1.120; P < 0.001) and PHB (hazard ratio, 2.162; 95% confidence interval, 1.021-4.577; P = 0.044) were significant prognosticators for patients with AH and GIB. The presence of PHB and a higher MELD score adversely affected survival in AH patients with GIB. Accordingly, prompt endoscopic examination for exploring the etiologies of GIB may alert physicians to predict the risk of death in AH patients with GIB. © 2015 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

The role of the posterior cruciate ligament in total knee replacement

PubMed Central

Ritter, M. A.; Davis, K. E.; Meding, J. B.; Farris, A.

2012-01-01

Objectives The purpose of this study was to examine the effect of posterior cruciate ligament (PCL) retention, PCL recession, and PCL excision during cruciate-retaining total knee replacement. Methods A total of 3018 anatomic graduated component total knee replacements were examined; 1846 of these retained the PCL, 455 PCLs were partially recessed, and in 717 the PCL was completely excised from the back of the tibia. Results Clinical scores between PCL groups favored excision for flexion (p < 0.0001), and recession and retention for stairs (p < 0.0001). There was a mild difference in long-term all-cause aseptic survivorship between PCL-retained (96.4% at 15 years) combined with PCL-recessed groups (96.6% at 15 years) when compared with the PCL-excised group (95.0% at 15 years) (p = 0.0411, Wilcoxon; p = 0.0042, log-rank), as well as tibial or femoral loosening, which reported prosthesis survival of 97.8% at 15 years for PCL-retained knees, 98.2% for recessed knees, and 96.4% for excised knees (p = 0.0934, Wilcoxon; p = 0.0202, log-rank). Conclusions Despite some trade off in clinical performance, if the PCL is detached at the time of operation, conversion to a posterior-stabilised prosthesis may not be necessarily required as long as stability in the anteroposterior and coronal planes is achieved. PMID:23610673

Clinical relevance of KRAS mutation detection in metastatic colorectal cancer treated by Cetuximab plus chemotherapy

PubMed Central

Di Fiore, F; Blanchard, F; Charbonnier, F; Le Pessot, F; Lamy, A; Galais, M P; Bastit, L; Killian, A; Sesboüé, R; Tuech, J J; Queuniet, A M; Paillot, B; Sabourin, J C; Michot, F; Michel, P; Frebourg, T

2007-01-01

The predictive value of KRAS mutation in metastatic colorectal cancer (MCRC) patients treated with cetuximab plus chemotherapy has recently been suggested. In our study, 59 patients with a chemotherapy-refractory MCRC treated with cetuximab plus chemotherapy were included and clinical response was evaluated according to response evaluation criteria in solid tumours (RECIST). Tumours were screened for KRAS mutations using first direct sequencing, then two sensitive methods based on SNaPshot and PCR-ligase chain reaction (LCR) assays. Clinical response was evaluated according to gene mutations using the Fisher exact test. Times to progression (TTP) were calculated using the Kaplan–Meier method and compared with log-rank test. A KRAS mutation was detected in 22 out of 59 tumours and, in six cases, was missed by sequencing analysis but detected using the SNaPshot and PCR-LCR assays. Remarkably, no KRAS mutation was found in the 12 patients with clinical response. KRAS mutation was associated with disease progression (P=0.0005) and TTP was significantly decreased in mutated KRAS patients (3 vs 5.5 months, P=0.015). Our study confirms that KRAS mutation is highly predictive of a non-response to cetuximab plus chemotherapy in MCRC and highlights the need to use sensitive molecular methods, such as SNaPshot or PCR-LCR assays, to ensure an efficient mutation detection. PMID:17375050

An exploratory data analysis of electroencephalograms using the functional boxplots approach

PubMed Central

Ngo, Duy; Sun, Ying; Genton, Marc G.; Wu, Jennifer; Srinivasan, Ramesh; Cramer, Steven C.; Ombao, Hernando

2015-01-01

Many model-based methods have been developed over the last several decades for analysis of electroencephalograms (EEGs) in order to understand electrical neural data. In this work, we propose to use the functional boxplot (FBP) to analyze log periodograms of EEG time series data in the spectral domain. The functional bloxplot approach produces a median curve—which is not equivalent to connecting medians obtained from frequency-specific boxplots. In addition, this approach identifies a functional median, summarizes variability, and detects potential outliers. By extending FBPs analysis from one-dimensional curves to surfaces, surface boxplots are also used to explore the variation of the spectral power for the alpha (8–12 Hz) and beta (16–32 Hz) frequency bands across the brain cortical surface. By using rank-based nonparametric tests, we also investigate the stationarity of EEG traces across an exam acquired during resting-state by comparing the spectrum during the early vs. late phases of a single resting-state EEG exam. PMID:26347598

Risk of invasive breast cancer and ductal carcinoma in situ in women with atypical papillary lesions of the breast.

PubMed

Cuneo, Kyle C; Dash, Rajesh C; Wilke, Lee G; Horton, Janet K; Koontz, Bridget F

2012-09-01

Benign papillary lesions of the breast include papilloma and papillomatosis. A retrospective analysis of patients with a papillary breast lesion diagnosed between October 1992 and December 2009 was performed. Patients were excluded if they had a previous or concurrent diagnosis of invasive or in situ cancer or less than 6 months of follow-up. The Kaplan-Meier method was used to determine the risk of developing subsequent malignancy. The log rank test was used to compare groups of patients. Median follow-up for the 167 patients included in the study was 4.6 years. Fifty-one patients had a papillary lesion with atypia and 116 patients had a papillary lesion without atypia. Patients with a papillary lesion with atypia were more likely to develop invasive or in situ breast cancer with a 5 year risk of 13.0% versus 4.6% in patients with no atypia (p = 0.03). © 2012 Wiley Periodicals, Inc.

Choice of Stimulus Range and Size Can Reduce Test-Retest Variability in Glaucomatous Visual Field Defects

PubMed Central

Swanson, William H.; Horner, Douglas G.; Dul, Mitchell W.; Malinovsky, Victor E.

2014-01-01

Purpose To develop guidelines for engineering perimetric stimuli to reduce test-retest variability in glaucomatous defects. Methods Perimetric testing was performed on one eye for 62 patients with glaucoma and 41 age-similar controls on size III and frequency-doubling perimetry and three custom tests with Gaussian blob and Gabor sinusoid stimuli. Stimulus range was controlled by values for ceiling (maximum sensitivity) and floor (minimum sensitivity). Bland-Altman analysis was used to derive 95% limits of agreement on test and retest, and bootstrap analysis was used to test the hypotheses about peak variability. Results Limits of agreement for the three custom stimuli were similar in width (0.72 to 0.79 log units) and peak variability (0.22 to 0.29 log units) for a stimulus range of 1.7 log units. The width of the limits of agreement for size III decreased from 1.78 to 1.37 to 0.99 log units for stimulus ranges of 3.9, 2.7, and 1.7 log units, respectively (F = 3.23, P < 0.001); peak variability was 0.99, 0.54, and 0.34 log units, respectively (P < 0.01). For a stimulus range of 1.3 log units, limits of agreement were narrowest with Gabor and widest with size III stimuli, and peak variability was lower (P < 0.01) with Gabor (0.18 log units) and frequency-doubling perimetry (0.24 log units) than with size III stimuli (0.38 log units). Conclusions Test-retest variability in glaucomatous visual field defects was substantially reduced by engineering the stimuli. Translational Relevance The guidelines should allow developers to choose from a wide range of stimuli. PMID:25371855

Identifying the greatest team and captain—A complex network approach to cricket matches

NASA Astrophysics Data System (ADS)

Mukherjee, Satyam

2012-12-01

We consider all Test matches played between 1877 and 2010 and One Day International (ODI) matches played between 1971 and 2010. We form directed and weighted networks of teams and also of their captains. The success of a team (or captain) is determined by the ‘quality’ of the wins, not simply by the number of wins. We apply the diffusion-based PageRank algorithm to the networks to assess the importance of the wins, and rank the respective teams and captains. Our analysis identifies Australia as the best team in both forms of cricket, Test and ODI. Steve Waugh is identified as the best captain in Test cricket and Ricky Ponting is the best captain in the ODI format. We also compare our ranking scheme with an existing ranking scheme, the Reliance ICC ranking. Our method does not depend on ‘external’ criteria in the ranking of teams (captains). The purpose of this paper is to introduce a revised ranking of cricket teams and to quantify the success of the captains.

Comparison of fine particle measurements from a direct-reading instrument and a gravimetric sampling method.

PubMed

Kim, Jee Young; Magari, Shannon R; Herrick, Robert F; Smith, Thomas J; Christiani, David C

2004-11-01

Particulate air pollution, specifically the fine particle fraction (PM2.5), has been associated with increased cardiopulmonary morbidity and mortality in general population studies. Occupational exposure to fine particulate matter can exceed ambient levels by a large factor. Due to increased interest in the health effects of particulate matter, many particle sampling methods have been developed In this study, two such measurement methods were used simultaneously and compared. PM2.5 was sampled using a filter-based gravimetric sampling method and a direct-reading instrument, the TSI Inc. model 8520 DUSTTRAK aerosol monitor. Both sampling methods were used to determine the PM2.5 exposure in a group of boilermakers exposed to welding fumes and residual fuel oil ash. The geometric mean PM2.5 concentration was 0.30 mg/m3 (GSD 3.25) and 0.31 mg/m3 (GSD 2.90)from the DUSTTRAK and gravimetric method, respectively. The Spearman rank correlation coefficient for the gravimetric and DUSTTRAK PM2.5 concentrations was 0.68. Linear regression models indicated that log, DUSTTRAK PM2.5 concentrations significantly predicted loge gravimetric PM2.5 concentrations (p < 0.01). The association between log(e) DUSTTRAK and log, gravimetric PM2.5 concentrations was found to be modified by surrogate measures for seasonal variation and type of aerosol. PM2.5 measurements from the DUSTTRAK are well correlated and highly predictive of measurements from the gravimetric sampling method for the aerosols in these work environments. However, results from this study suggest that aerosol particle characteristics may affect the relationship between the gravimetric and DUSTTRAK PM2.5 measurements. Recalibration of the DUSTTRAK for the specific aerosol, as recommended by the manufacturer, may be necessary to produce valid measures of airborne particulate matter.

Depressive symptoms, physical inactivity and risk of cardiovascular mortality in older adults: the Cardiovascular Health Study

PubMed Central

Win, Sithu; Parakh, Kapil; Eze-Nliam, Chete M; Gottdiener, John S; Kop, Willem J

2011-01-01

Background Depressed older individuals have a higher mortality than older persons without depression. Depression is associated with physical inactivity, and low levels of physical activity have been shown in some cohorts to be a partial mediator of the relationship between depression and cardiovascular events and mortality. Methods A cohort of 5888 individuals (mean 72.8±5.6 years, 58% female, 16% African-American) from four US communities was followed for an average of 10.3 years. Self-reported depressive symptoms (10-item Center for Epidemiological Studies Depression Scale) were assessed annually and self-reported physical activity was assessed at baseline and at 3 and 7 years. To estimate how much of the increased risk of cardiovascular mortality associated with depressive symptoms was due to physical inactivity, Cox regression with time-varying covariates was used to determine the percentage change in the log HR of depressive symptoms for cardiovascular mortality after adding physical activity variables. Results At baseline, 20% of participants scored above the cut-off for depressive symptoms. There were 2915 deaths (49.8%), of which 1176 (20.1%) were from cardiovascular causes. Depressive symptoms and physical inactivity each independently increased the risk of cardiovascular mortality and were strongly associated with each other (all p<0.001). Individuals with both depressive symptoms and physical inactivity had greater cardiovascular mortality than those with either individually (p<0.001, log rank test). Physical inactivity reduced the log HR of depressive symptoms for cardiovascular mortality by 26% after adjustment. This was similar for persons with (25%) and without (23%) established coronary heart disease. Conclusions Physical inactivity accounted for a significant proportion of the risk of cardiovascular mortality due to depressive symptoms in older adults, regardless of coronary heart disease status. PMID:21339320

Huminite reflectance measurements of Paleocene and Upper Cretaceous coals from borehole cuttings, Zavala and Dimmit counties, South Texas

USGS Publications Warehouse

Hackley, Paul C.; Hook, Robert W.; Warwick, Peter D.

2005-01-01

The reflectance of huminite in 19 cuttings samples was determined in support of ongoing investigations into the coal bed methane potential of subsurface Paleocene and Upper Cretaceous coals of South Texas. Coal cuttings were obtained from the Core Research Center of the Bureau of Economic Geology, The University of Texas at Austin. Geophysical logs, mud-gas logs, driller's logs, completion cards, and scout tickets were used to select potentially coal-bearing sample suites and to identify specific sample depths. Reflectance measurements indicate coals of subbituminous rank are present in a wider area in South Texas than previously recognized.

Empirical prediction intervals improve energy forecasting

PubMed Central

Kaack, Lynn H.; Apt, Jay; Morgan, M. Granger; McSharry, Patrick

2017-01-01

Hundreds of organizations and analysts use energy projections, such as those contained in the US Energy Information Administration (EIA)’s Annual Energy Outlook (AEO), for investment and policy decisions. Retrospective analyses of past AEO projections have shown that observed values can differ from the projection by several hundred percent, and thus a thorough treatment of uncertainty is essential. We evaluate the out-of-sample forecasting performance of several empirical density forecasting methods, using the continuous ranked probability score (CRPS). The analysis confirms that a Gaussian density, estimated on past forecasting errors, gives comparatively accurate uncertainty estimates over a variety of energy quantities in the AEO, in particular outperforming scenario projections provided in the AEO. We report probabilistic uncertainties for 18 core quantities of the AEO 2016 projections. Our work frames how to produce, evaluate, and rank probabilistic forecasts in this setting. We propose a log transformation of forecast errors for price projections and a modified nonparametric empirical density forecasting method. Our findings give guidance on how to evaluate and communicate uncertainty in future energy outlooks. PMID:28760997

Restoration of the photoreceptor layer and improvement of visual acuity in successfully treated optic disc pit maculopathy: a long follow-up study by optical coherence tomography.

PubMed

Theodossiadis, George P; Grigoropoulos, Vlassis G; Liarakos, Vasilis S; Rouvas, Alexandros; Emfietzoglou, Ioannis; Theodossiadis, Panagiotis G

2012-07-01

To investigate by optical coherence tomography (OCT) the evolution of the photoreceptor layer and its association with best-corrected visual acuity (BCVA) in optic disc pit (ODP) maculopathy after successful surgical treatment. Fourteen eyes of 14 patients were included in this study, and followed up from 36 to 95 months (mean 57.36 ± 18.32 months). The follow-up period started at the time of complete subretinal fluid absorption. Examination was performed by time-domain OCT before and after treatment. Spectral-domain OCT was used after treatment. Parameters assessed were type of elevation, central foveal thickness, time elapsed from onset to treatment, type of treatment, BCVA, and inner segment outer segment (IS/OS) junction line. The IS/OS junction was characterized after treatment as intact, interrupted, or absent (not distinguishable). Significant restoration of the IS/OS junction line was first noticed between 6 and 12 months after fluid absorption (p = 0.02; Wilcoxon signed rank test). Restoration was continuous up to the 24th month of postoperative examination after fluid absorption (p = 0.14; Wilcoxon signed rank test). BCVA was 0.99 ± 0.38 logMar before treatment, 0.81 ± 0.26 logMar (p = 0.011; paired t-test) immediately after fluid absorption and 0.61 ± 0.33 logMar (p = 0.026; one-way ANOVA) 24 months after fluid resolution. BCVA was significantly positively correlated with the integrity of the IS/OS junction line during follow-up (Pearson r = 0.775; p < 0.001). The IS/OS junction restoration cannot be detected immediately after fluid resolution in the majority of cases. It became evident 6-12 months later and was completed 24 months after fluid absorption. Improvement in BCVA was noticed only during the first 2 years of follow-up. No significant changes were noticed in BCVA or the IS/OS line after 2 years. Among the studied variables, the final photoreceptor layer condition and BCVA immediately after fluid absorption are the main factors predicting final BCVA after successful surgical treatment of ODP maculopathy.

Log-Linear Models for Gene Association

PubMed Central

Hu, Jianhua; Joshi, Adarsh; Johnson, Valen E.

2009-01-01

We describe a class of log-linear models for the detection of interactions in high-dimensional genomic data. This class of models leads to a Bayesian model selection algorithm that can be applied to data that have been reduced to contingency tables using ranks of observations within subjects, and discretization of these ranks within gene/network components. Many normalization issues associated with the analysis of genomic data are thereby avoided. A prior density based on Ewens’ sampling distribution is used to restrict the number of interacting components assigned high posterior probability, and the calculation of posterior model probabilities is expedited by approximations based on the likelihood ratio statistic. Simulation studies are used to evaluate the efficiency of the resulting algorithm for known interaction structures. Finally, the algorithm is validated in a microarray study for which it was possible to obtain biological confirmation of detected interactions. PMID:19655032

A new concept for stainless steels ranking upon the resistance to cavitation erosion

NASA Astrophysics Data System (ADS)

Bordeasu, I.; Popoviciu, M. O.; Salcianu, L. C.; Ghera, C.; Micu, L. M.; Badarau, R.; Iosif, A.; Pirvulescu, L. D.; Podoleanu, C. E.

2017-01-01

In present, the ranking of materials as their resistance to cavitation erosion is obtained by using laboratory tests finalized with the characteristic curves mean depth erosion against time MDE(t) and mean depth erosion rate against time MDER(t). In some previous papers, Bordeasu and co-workers give procedures to establish exponential equation representing the curves, with minimum scatter of the experimental obtained results. For a given material, both exponential equations MDE(t) and MDER(t) have the same values for the parameters of scale and for the shape one. For the ranking of materials is sometimes important to establish single figure. Till now in Timisoara Polytechnic University Cavitation Laboratory were used three such numbers: the stable value of the curve MDER(t), the resistance to cavitation erosion (Rcav ≡ 1/MDERstable) and the normalized cavitation resistance Rns which is the rate between vs = MDERstable for the analyzed material and vse= MDERse the mean depth erosion rate for the steel OH12NDL (Rns = vs/vse ). OH12NDL is a material used for manufacturing the blades of numerous Kaplan turbines in Romania for which both cavitation erosion laboratory tests and field measurements of cavitation erosions are available. In the present paper we recommend a new method for ranking the materials upon cavitation erosion resistance. This method uses the scale and shape parameters of the exponential equations which represents the characteristic cavitation erosion curves. Till now the method was applied only for stainless steels. The experimental results show that the scale parameter represents an excellent method for ranking the stainless steels. In the future this kind of ranking will be tested also for other materials especially for bronzes used for manufacturing ship propellers.

Impact of Forest Management on Species Richness: Global Meta-Analysis and Economic Trade-Offs

NASA Astrophysics Data System (ADS)

Chaudhary, Abhishek; Burivalova, Zuzana; Koh, Lian Pin; Hellweg, Stefanie

2016-04-01

Forests managed for timber have an important role to play in conserving global biodiversity. We evaluated the most common timber production systems worldwide in terms of their impact on local species richness by conducting a categorical meta-analysis. We reviewed 287 published studies containing 1008 comparisons of species richness in managed and unmanaged forests and derived management, taxon, and continent specific effect sizes. We show that in terms of local species richness loss, forest management types can be ranked, from best to worse, as follows: selection and retention systems, reduced impact logging, conventional selective logging, clear-cutting, agroforestry, timber plantations, fuelwood plantations. Next, we calculated the economic profitability in terms of the net present value of timber harvesting from 10 hypothetical wood-producing Forest Management Units (FMU) from around the globe. The ranking of management types is altered when the species loss per unit profit generated from the FMU is considered. This is due to differences in yield, timber species prices, rotation cycle length and production costs. We thus conclude that it would be erroneous to dismiss or prioritize timber production regimes, based solely on their ranking of alpha diversity impacts.

Impact of Forest Management on Species Richness: Global Meta-Analysis and Economic Trade-Offs

PubMed Central

Chaudhary, Abhishek; Burivalova, Zuzana; Koh, Lian Pin; Hellweg, Stefanie

2016-01-01

Forests managed for timber have an important role to play in conserving global biodiversity. We evaluated the most common timber production systems worldwide in terms of their impact on local species richness by conducting a categorical meta-analysis. We reviewed 287 published studies containing 1008 comparisons of species richness in managed and unmanaged forests and derived management, taxon, and continent specific effect sizes. We show that in terms of local species richness loss, forest management types can be ranked, from best to worse, as follows: selection and retention systems, reduced impact logging, conventional selective logging, clear-cutting, agroforestry, timber plantations, fuelwood plantations. Next, we calculated the economic profitability in terms of the net present value of timber harvesting from 10 hypothetical wood-producing Forest Management Units (FMU) from around the globe. The ranking of management types is altered when the species loss per unit profit generated from the FMU is considered. This is due to differences in yield, timber species prices, rotation cycle length and production costs. We thus conclude that it would be erroneous to dismiss or prioritize timber production regimes, based solely on their ranking of alpha diversity impacts. PMID:27040604

Impact of Forest Management on Species Richness: Global Meta-Analysis and Economic Trade-Offs.

PubMed

Chaudhary, Abhishek; Burivalova, Zuzana; Koh, Lian Pin; Hellweg, Stefanie

2016-04-04

Forests managed for timber have an important role to play in conserving global biodiversity. We evaluated the most common timber production systems worldwide in terms of their impact on local species richness by conducting a categorical meta-analysis. We reviewed 287 published studies containing 1008 comparisons of species richness in managed and unmanaged forests and derived management, taxon, and continent specific effect sizes. We show that in terms of local species richness loss, forest management types can be ranked, from best to worse, as follows: selection and retention systems, reduced impact logging, conventional selective logging, clear-cutting, agroforestry, timber plantations, fuelwood plantations. Next, we calculated the economic profitability in terms of the net present value of timber harvesting from 10 hypothetical wood-producing Forest Management Units (FMU) from around the globe. The ranking of management types is altered when the species loss per unit profit generated from the FMU is considered. This is due to differences in yield, timber species prices, rotation cycle length and production costs. We thus conclude that it would be erroneous to dismiss or prioritize timber production regimes, based solely on their ranking of alpha diversity impacts.

High-throughput determination of octanol/water partition coefficients using a shake-flask method and novel two-phase solvent system.

PubMed

Morikawa, Go; Suzuka, Chihiro; Shoji, Atsushi; Shibusawa, Yoichi; Yanagida, Akio

2016-01-05

A high-throughput method for determining the octanol/water partition coefficient (P(o/w)) of a large variety of compounds exhibiting a wide range in hydrophobicity was established. The method combines a simple shake-flask method with a novel two-phase solvent system comprising an acetonitrile-phosphate buffer (0.1 M, pH 7.4)-1-octanol (25:25:4, v/v/v; AN system). The AN system partition coefficients (K(AN)) of 51 standard compounds for which log P(o/w) (at pH 7.4; log D) values had been reported were determined by single two-phase partitioning in test tubes, followed by measurement of the solute concentration in both phases using an automatic flow injection-ultraviolet detection system. The log K(AN) values were closely related to reported log D values, and the relationship could be expressed by the following linear regression equation: log D=2.8630 log K(AN) -0.1497(n=51). The relationship reveals that log D values (+8 to -8) for a large variety of highly hydrophobic and/or hydrophilic compounds can be estimated indirectly from the narrow range of log K(AN) values (+3 to -3) determined using the present method. Furthermore, log K(AN) values for highly polar compounds for which no log D values have been reported, such as amino acids, peptides, proteins, nucleosides, and nucleotides, can be estimated using the present method. The wide-ranging log D values (+5.9 to -7.5) of these molecules were estimated for the first time from their log K(AN) values and the above regression equation. Copyright © 2015 Elsevier B.V. All rights reserved.

E2F3a gene expression has prognostic significance in childhood acute lymphoblastic leukemia.

PubMed

Wang, Kai-Ling; Mei, Yan-Yan; Cui, Lei; Zhao, Xiao-Xi; Li, Wei-Jing; Gao, Chao; Liu, Shu-Guang; Jiao, Ying; Liu, Fei-Fei; Wu, Min-Yuan; Ding, Wei; Li, Zhi-Gang

2014-10-01

To study E2F3a expression and its clinical significance in children with acute lymphoblastic leukemia (ALL). We quantified E2F3a expression at diagnosis in 148 children with ALL by real-time PCR. In the test cohort (n = 48), receiver operating characteristic (ROC) curve was used to find the best cut-off point to divide the patients into E2F3a low- and high-expression groups. The prognostic significance of E2F3a expression was investigated in the test cohort and confirmed in the validation cohort (n = 100). The correlations of E2F3a expression with the clinical features and treatment outcome of these patients were analyzed. ROC curve analysis indicated that the best cut-off point of E2F3a expression was 0.3780. In the test cohort, leukemia-free survival (LFS) and event-free survival (EFS) of the low-expression group were lower than those of the high-expression group (log rank: P = 0.026 for both). This finding was verified in the validation cohort. LFS, EFS, and overall survival were also lower in the low-expression group than in the high-expression group (log rank, P = 0.015, 0.008, and 0.002 respectively). E2F3a low expression was correlated with the existence of BCR-ABL fusion. An algorithm composed of E2F3a expression and minimal residual disease (MRD) could predict relapse or induction failure more precisely than current risk stratification. These results were still significant in the ALL patients without BCR-ABL fusion. Low expression of E2F3a was associated with inferior prognosis in childhood ALL. An algorithm composed of E2F3a expression and MRD could predict relapse or induction failure more precisely than that of the current risk stratification. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Clinical outcome in women with HER2-positive de novo or recurring stage IV breast cancer receiving trastuzumab-based therapy.

PubMed

Rossi, Valentina; Nolè, Franco; Redana, Stefania; Adamoli, Laura; Martinello, Rossella; Aurilio, Gaetano; Verri, Elena; Sapino, Anna; Viale, Giuseppe; Aglietta, Massimo; Montemurro, Filippo

2014-02-01

Five to 10% of women with newly diagnosed breast cancer have synchronous metastases (de novo stage IV). A further 20% will develop metastases during follow-up (recurring stage IV). We compared the clinical outcomes of women with HER2-positive metastatic breast cancer (MBC) receiving first-line trastuzumab-based therapy according to type of metastatic presentation. Retrospective analysis of 331 MBC patients receiving first-line trastuzumab-based treatment. Response rates (RR) were compared by the chi-square test. Time-to progression (TTP) and overall survival (OS) curves were compared by the log-rank test. Cox-proportional hazards models were used to study predictors of PFS and OS, including the type of metastatic presentation. Seventy-seven patients (23%) had de novo stage IV disease. Forty-six of these patients underwent surgery of the primary ("de novo/surgery"). Response rates to first-line trastuzumab-based therapy and median progression-free survival did not differ in patients with "recurring", "de novo/surgery" and "de novo" without surgery ("de novo/no surgery) stage IV breast cancer. However, women with "de novo/surgery" stage IV breast cancer had the longest median OS (60 months), and those with "de novo/no surgery" stage IV breast cancer the shortest (26 months). For women with recurring metastatic breast cancer median OS was 40 months (overall log-rank test, p < 0.01). Multivariate analysis confirmed these findings. Our analysis shows that response rates and PFS to first-line trastuzumab-based therapy do not differ significantly between de novo and recurring stage IV, HER2 positive breast cancer. The observed difference in OS favoring women with de novo stage IV disease submitted to surgery of the primary tumor could be the result of a selection bias. Copyright © 2013 Elsevier Ltd. All rights reserved.

Histological grading of ovarian clear cell adenocarcinoma: proposal for a simple and reproducible grouping system based on tumor growth architecture.

PubMed

Yamamoto, Sohei; Tsuda, Hitoshi; Shimazaki, Hideyuki; Takano, Masashi; Yoshikawa, Tomoyuki; Kuzuya, Kazuo; Tsuda, Hiroshi; Kurachi, Hirohisa; Kigawa, Junzo; Kikuchi, Yoshihiro; Sugiyama, Toru; Matsubara, Osamu

2012-03-01

In this study, we aimed to develop a histological grading system for ovarian clear cell adenocarcinoma (CCA), based on the tumor growth architectures. Cases were defined as Group A if ≥90% of a tumor examined was composed of well-differentiated tubulocystic and/or papillary architectures; Group C if at least 10% of the tumor was composed of very poorly differentiated histology (i.e. solid masses or individual infiltrating tumor cells with no or little glandular/papillary differentiation); and tumors not corresponding to the first 2 descriptions were defined as Group B. The interobserver reproducibility and prognostic value of the assigned groups were analyzed for 159 CCAs from 5 institutions. The level of agreement in assigning the groups between 2 pathologists was 88.7% (=0.82). After consensus was reached, 46 (29%), 79 (50%), and 34 (21%) tumors were classified in Groups A, B, and C, respectively. In early-stage cases [International Federation of Gynecology and Obstetrics (FIGO) stage I-II], Group A tumors had significantly better outcomes (100% 5-yr survival) than Group B tumors (82% 5-yr survival, P=0.024 by log-rank test) or Group C tumors (56% 5-yr survival, P=0.00054 by log-rank test). Moreover, early-stage Group B tumors had significantly better outcomes than Group C tumors (P<0.001 by a generalized Wilcoxon test). In advanced cases (FIGO stage III-IV), Group A tumors had significantly better outcomes than Group C tumors (52% vs. 16% 5-yr survival, respectively, P=0.043). Group A and C tumors defined with our system were identified to have favorable and unfavorable prognostic factors, respectively, independent of the clinical stage of the disease and presence of residual tumors after the initial surgery. The proposed grouping system could divide patients with CCA into 3 subgroups with distinct prognostic indications, providing a 3-tier histological grading system for ovarian CCA.

Severity of OSAS, CPAP and cardiovascular events: A follow-up study.

PubMed

Baratta, Francesco; Pastori, Daniele; Fabiani, Mario; Fabiani, Valerio; Ceci, Fabrizio; Lillo, Rossella; Lolli, Valeria; Brunori, Marco; Pannitteri, Gaetano; Cravotto, Elena; De Vito, Corrado; Angelico, Francesco; Del Ben, Maria

2018-05-01

Previous studies suggested obstructive sleep apnoea syndrome (OSAS) as a major risk factor for incident cardiovascular events. However, the relationship between OSAS severity, the use of continuous positive airway pressure (CPAP) treatment and the development of cardiovascular disease is still matter of debate. The aim was to test the association between OSAS and cardiovascular events in patients with concomitant cardio-metabolic diseases and the potential impact of CPAP therapy on cardiovascular outcomes. Prospective observational cohort study of consecutive outpatients with suspected metabolic disorders who had complete clinical and biochemical workup including polysomnography because of heavy snoring and possible OSAS. The primary endpoint was a composite of major adverse cardiovascular and cerebrovascular events (MACCE). Median follow-up was 81.3 months, including 434 patients (2701.2 person/years); 83 had a primary snoring, 84 had mild, 93 moderate and 174 severe OSAS, respectively. The incidence of MACCE was 0.8% per year (95% confidence interval [CI] 0.2-2.1) in primary snorers and 2.1% per year (95% CI 1.5-2.8) for those with OSAS. A positive association was observed between event-free survival and OSAS severity (log-rank test; P = .041). A multivariable Cox regression analysis showed obesity (HR = 8.011, 95% CI 1.071-59.922, P = .043), moderate OSAS (vs non-OSAS HR = 3.853, 95% CI 1.069-13.879, P = .039) and severe OSAS (vs non-OSAS HR = 3.540, 95% CI 1.026-12.217, P = .045) as predictors of MACCE. No significant association was observed between CPAP treatment and MACCE (log-rank test; P = .227). Our findings support the role of moderate/severe OSAS as a risk factor for incident MACCE. CPAP treatment was not associated with a lower rate of MACCE. © 2018 Stichting European Society for Clinical Investigation Journal Foundation.

Phenotyping Chronic Lung Allograft Dysfunction Using Body Plethysmography and Computed Tomography.

PubMed

Suhling, H; Dettmer, S; Greer, M; Fuehner, T; Avsar, M; Haverich, A; Welte, T; Gottlieb, J

2016-11-01

Restrictive subtype of chronic lung allograft dysfunction (CLAD) was recently described after lung transplantation. This study compares different definitions of a restrictive phenotype in CLAD patients and impact on survival. Eighty-nine CLAD patients out of 1191 screened patients (September 1987 to July 2012) were included as complete longitudinal lung volume measurements and chest computed tomography (CT) after CLAD onset was available. CT findings and lung volumes were quantified and survival was calculated for distinctive groups and predictive factors for worse survival were investigated. Graft survival in patients with total lung capacity (TLC) between 90% and 81% of baseline (BL) (n = 13, 15%) in CLAD course was similar to those with TLC >90% BL (n = 64, 56%; log-rank test p = 0.9). Twelve patients (13%) developed a TLC ≤80% BL and 10 (11%) had significant parenchymal changes on CT, of whom 6 (46%) also had TLC ≤80% BL. CT changes correlated with TLC ≤80% BL (Φ-coefficient = 0.48, p = 0.001). Patients with either TLC ≤80% or significant CT changes (n = 16, 18%) had a significantly reduced survival (log-rank p < 0.001). Forced vital capacity loss at CLAD onset was associated with poorer survival but did not correlate with the TLC or CT changes. A restrictive subtype of CLAD may be defined by either TLC ≤80% BL or severe parenchymal changes on chest CT. © Copyright 2016 The American Society of Transplantation and the American Society of Transplant Surgeons.

Changes in stereoacuity following implantable Collamer lens implantation in patients with myopia

PubMed Central

Khokhar, Sudarshan; Gupta, Shikha; Gogia, Varun; Tewari, Ruchir; Agarwal, Tushar

2015-01-01

The study evaluated the impact of implantable Collamer lens (ICL) implantation on stereoacuity in myopes in a retrospective case series. Ninety-five eyes of 48 patients were recruited. Distance and near stereoacuity were measured using distance Randot stereotest and TNO test, respectively, before surgery and at 4 weeks postoperatively. Mean age of the patients was 23.67 ± 3.7 years. Mean uncorrected distance visual acuity (UDVA) was 1.28 ± 0.37 logarithm of the minimum angle of resolution (logMAR) (median: 1.3; range: 0.3–1.8), and median best-corrected distance visual acuity (BDVA) was 0.18 logMAR (range: 0–0.6). There was a significant improvement in both UDVA and BDVA postsurgery (P < 0.001; Wilcoxon signed rank test). The overall improvement in stereopsis was observed in 15/48 (31.25%) and 13/48 (27.10%) subjects for near and distance, respectively, with no significant difference between the two (P = 0.82; Fisher's exact test). Among stereoblind individuals, the odd's ratio for near stereoacuity to improve in comparison to distance stereoacuity was 8.85 (95% confidence interval: 1.68–46.70; P = 0.01). ICL implantation for refractive correction aided stereoacuity improvement in myopes more so for near. PMID:26655005

MiRNA-TF-gene network analysis through ranking of biomolecules for multi-informative uterine leiomyoma dataset.

PubMed

Mallik, Saurav; Maulik, Ujjwal

2015-10-01

Gene ranking is an important problem in bioinformatics. Here, we propose a new framework for ranking biomolecules (viz., miRNAs, transcription-factors/TFs and genes) in a multi-informative uterine leiomyoma dataset having both gene expression and methylation data using (statistical) eigenvector centrality based approach. At first, genes that are both differentially expressed and methylated, are identified using Limma statistical test. A network, comprising these genes, corresponding TFs from TRANSFAC and ITFP databases, and targeter miRNAs from miRWalk database, is then built. The biomolecules are then ranked based on eigenvector centrality. Our proposed method provides better average accuracy in hub gene and non-hub gene classifications than other methods. Furthermore, pre-ranked Gene set enrichment analysis is applied on the pathway database as well as GO-term databases of Molecular Signatures Database with providing a pre-ranked gene-list based on different centrality values for comparing among the ranking methods. Finally, top novel potential gene-markers for the uterine leiomyoma are provided. Copyright © 2015 Elsevier Inc. All rights reserved.

Requirements-Driven Log Analysis Extended Abstract

NASA Technical Reports Server (NTRS)

Havelund, Klaus

2012-01-01

Imagine that you are tasked to help a project improve their testing effort. In a realistic scenario it will quickly become clear, that having an impact is diffcult. First of all, it will likely be a challenge to suggest an alternative approach which is significantly more automated and/or more effective than current practice. The reality is that an average software system has a complex input/output behavior. An automated testing approach will have to auto-generate test cases, each being a pair (i; o) consisting of a test input i and an oracle o. The test input i has to be somewhat meaningful, and the oracle o can be very complicated to compute. Second, even in case where some testing technology has been developed that might improve current practice, it is then likely difficult to completely change the current behavior of the testing team unless the technique is obviously superior and does everything already done by existing technology. So is there an easier way to incorporate formal methods-based approaches than the full edged test revolution? Fortunately the answer is affirmative. A relatively simple approach is to benefit from possibly already existing logging infrastructure, which after all is part of most systems put in production. A log is a sequence of events, generated by special log recording statements, most often manually inserted in the code by the programmers. An event can be considered as a data record: a mapping from field names to values. We can analyze such a log using formal methods, for example checking it against a formal specification. This separates running the system for analyzing its behavior. It is not meant as an alternative to testing since it does not address the important in- put generation problem. However, it offers a solution which testing teams might accept since it has low impact on the existing process. A single person might be assigned to perform such log analysis, compared to the entire testing team changing behavior.

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies

NASA Astrophysics Data System (ADS)

Gaieb, Zied; Liu, Shuai; Gathiaka, Symon; Chiu, Michael; Yang, Huanwang; Shao, Chenghua; Feher, Victoria A.; Walters, W. Patrick; Kuhn, Bernd; Rudolph, Markus G.; Burley, Stephen K.; Gilson, Michael K.; Amaro, Rommie E.

2018-01-01

The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank (http://www.pdb.org), and in affinity ranking and scoring of bound ligands.

Prognostic Impact of the Combination of Recurrence Score and Quantitative Estrogen Receptor Expression (ESR1) on Predicting Late Distant Recurrence Risk in Estrogen Receptor-Positive Breast Cancer After 5 Years of Tamoxifen: Results From NRG Oncology/National Surgical Adjuvant Breast and Bowel Project B-28 and B-14.

PubMed

Wolmark, Norman; Mamounas, Eleftherios P; Baehner, Frederick L; Butler, Steven M; Tang, Gong; Jamshidian, Farid; Sing, Amy P; Shak, Steven; Paik, Soonmyung

2016-07-10

We determined the utility of the 21-Gene Recurrence Score (RS) in predicting late (> 5 years) distant recurrence (LDR) in stage I and II breast cancer within high and low-ESR1-expressing groups. RS was assessed in chemotherapy/tamoxifen-treated, estrogen receptor (ER) -positive, node-positive National Surgical Adjuvant Breast and Bowel Project B-28 patients and tamoxifen-treated, ER-positive, node-negative B-14 patients. The association of the RS with risk of distant recurrence (DR) 0 to 5 years and those at risk > 5 years was assessed. An ESR1 expression cut point was optimized in B-28 and tested in B-14. Median follow-up was 11.2 years for B-28 and 13.9 years for B-14. Of 1,065 B-28 patients, 36% had low (< 18), 34% intermediate (18 to 30), and 30% high (≥ 31) RS. Of 668 B-14 patients, 51% had low, 22% intermediate, and 27% high RS. Median ESR1 expression by reverse transcriptase polymerase chain reaction was: B-28, 9.7 normalized expression cycle threshold units (CT) and B-14, 10.7 CT. In B-28, RS was associated with DR 0 to 5 years (log-rank P < .001) and > 5 to 10 years (log-rank P = .02) regardless of ESR1 expression. An ESR1 expression cut point of 9.1 CT was identified in B-28. It was validated in B-14 patients for whom the RS was associated with DR in years 5 to 15: 6.8% (95% CI, 4.4% to 10.6%) versus 11.2% (95% CI, 6.2% to 19.9%) versus 16.4% (95% CI, 10.2% to 25.7%) for RS < 18, RS 18 to 30, and RS ≥ 31, respectively (log-rank P = .01). For LDR, RS is strongly prognostic in patients with higher quantitative ESR1. Risk of LDR is relatively low for patients with low RS. These results suggest the value of extended tamoxifen therapy merits evaluation in patients with intermediate and high RS with higher ESR1 expression at initial diagnosis. © 2016 by American Society of Clinical Oncology.

An improved evaluation method for measuring TOC of the Longmaxi Formation shale in the Sichuan Basin, south China

NASA Astrophysics Data System (ADS)

Zhang, Y.; Hu, C.; Wang, M.

2017-12-01

The evaluation of total organic carbon (TOC) in shale using logging data is one of the most crucial steps in shale gas exploration. However, it didn't achieve the ideal effect for the application of `ΔlogR' method in the Longmaxi Formation shale of Sichuan Basin.The reason may be the organic matter carbonization in Longmaxi Formation. An improved evaluation method, using the classification by lithology and sedimentary structure: 1) silty mudstone (wellsite logging data show silty); 2) calcareous mudstone (calcareous content > 25%); 3) laminated mudstone (laminations are recognized by core and imaging logging technology); 4) massive mudstone (massive textures are recognized by core and imaging logging technology, was proposed. This study compares two logging evaluation methods for measuring TOC in shale: the △logR method and the new proposed method. The results showed that the correlation coefficient between the calculated TOC and the tested TOC, based on the △logR method, was only 0.17. The correlation coefficient obtained according to the new method reached 0.80. The calculation results illustrated that, because of the good correlation between lithologies and sedimentary structure zones and TOC of different types of shale, the shale reservoirs could be graded according to four shale types. The new proposed method is more efficient, faster, and has higher vertical resolution than the △logR method. In addition, a new software had been completed. It was found to be especially effective under conditions of insufficient data during the early stages of shale gas exploration in the Silurian Longmaxi Formation, Muai Syncline Belt, south of the Sichuan Basin.

Detecting well casing leaks in Bangladesh using a salt spiking method

USGS Publications Warehouse

Stahl, M.O.; Ong, J.B.; Harvey, C.F.; Johnson, C.D.; Badruzzaman, A.B.M.; Tarek, M.H.; VanGeen, A.; Anderson, J.A.; Lane, J.W.

2014-01-01

We apply fluid-replacement logging in arsenic-contaminated regions of Bangladesh using a low-cost, down-well fluid conductivity logging tool to detect leaks in the cased section of wells. The fluid-conductivity tool is designed for the developing world: it is lightweight and easily transportable, operable by one person, and can be built for minimal cost. The fluid-replacement test identifies leaking casing by comparison of fluid conductivity logs collected before and after spiking the wellbore with a sodium chloride tracer. Here, we present results of fluid-replacement logging tests from both leaking and non-leaking casing from wells in Araihazar and Munshiganj, Bangladesh, and demonstrate that the low-cost tool produces measurements comparable to those obtained with a standard geophysical logging tool. Finally, we suggest well testing procedures and approaches for preventing casing leaks in Bangladesh and other developing countries.

Detecting well casing leaks in Bangladesh using a salt spiking method.

PubMed

Stahl, M O; Ong, J B; Harvey, C F; Johnson, C D; Badruzzaman, A B M; Tarek, M H; van Geen, A; Anderson, J A; Lane, J W

2014-09-01

We apply fluid-replacement logging in arsenic-contaminated regions of Bangladesh using a low-cost, down-well fluid conductivity logging tool to detect leaks in the cased section of wells. The fluid-conductivity tool is designed for the developing world: it is lightweight and easily transportable, operable by one person, and can be built for minimal cost. The fluid-replacement test identifies leaking casing by comparison of fluid conductivity logs collected before and after spiking the wellbore with a sodium chloride tracer. Here, we present results of fluid-replacement logging tests from both leaking and non-leaking casing from wells in Araihazar and Munshiganj, Bangladesh, and demonstrate that the low-cost tool produces measurements comparable to those obtained with a standard geophysical logging tool. Finally, we suggest well testing procedures and approaches for preventing casing leaks in Bangladesh and other developing countries. © 2014, National Ground Water Association.

Optimal ranking regime analysis of U.S. climate variablility. Part II: Precipitation and streamflow

USDA-ARS?s Scientific Manuscript database

In a preceding companion paper the Optimal Ranking Regime (ORR) method was used to identify intra- to multi-decadal (IMD) regimes in U.S. climate division temperature data during 1896-2012. Here, the method is used to test for annual and seasonal precipitation regimes during that same period. In add...

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization.

PubMed

Jia, Zhilong; Zhang, Xiang; Guan, Naiyang; Bo, Xiaochen; Barnes, Michael R; Luo, Zhigang

2015-01-01

RNA-sequencing is rapidly becoming the method of choice for studying the full complexity of transcriptomes, however with increasing dimensionality, accurate gene ranking is becoming increasingly challenging. This paper proposes an accurate and sensitive gene ranking method that implements discriminant non-negative matrix factorization (DNMF) for RNA-seq data. To the best of our knowledge, this is the first work to explore the utility of DNMF for gene ranking. When incorporating Fisher's discriminant criteria and setting the reduced dimension as two, DNMF learns two factors to approximate the original gene expression data, abstracting the up-regulated or down-regulated metagene by using the sample label information. The first factor denotes all the genes' weights of two metagenes as the additive combination of all genes, while the second learned factor represents the expression values of two metagenes. In the gene ranking stage, all the genes are ranked as a descending sequence according to the differential values of the metagene weights. Leveraging the nature of NMF and Fisher's criterion, DNMF can robustly boost the gene ranking performance. The Area Under the Curve analysis of differential expression analysis on two benchmarking tests of four RNA-seq data sets with similar phenotypes showed that our proposed DNMF-based gene ranking method outperforms other widely used methods. Moreover, the Gene Set Enrichment Analysis also showed DNMF outweighs others. DNMF is also computationally efficient, substantially outperforming all other benchmarked methods. Consequently, we suggest DNMF is an effective method for the analysis of differential gene expression and gene ranking for RNA-seq data.

Social ranking effects on tooth-brushing behaviour.

PubMed

Maltby, John; Paterson, Kevin; Day, Liz; Jones, Ceri; Kinnear, Hayley; Buchanan, Heather

2016-05-01

A tooth-brushing social rank hypothesis is tested suggesting tooth-brushing duration is influenced when individuals position their behaviour in a rank when comparing their behaviour with other individuals. Study 1 used a correlation design, Study 2 used a semi-experimental design, and Study 3 used a randomized intervention design to examine the tooth-brushing social rank hypothesis in terms of self-reported attitudes, cognitions, and behaviour towards tooth-brushing duration. Study 1 surveyed participants to examine whether the perceived health benefits of tooth-brushing duration could be predicted from the ranking of each person's tooth-brushing duration. Study 2 tested whether manipulating the rank position of the tooth-brushing duration influenced participant-perceived health benefits of tooth-brushing duration. Study 3 used a longitudinal intervention method to examine whether messages relating to the rank positions of tooth-brushing durations causally influenced the self-report tooth-brushing duration. Study 1 demonstrates that perceptions of the health benefits from tooth-brushing duration are predicted by the perceptions of how that behaviour ranks in comparison to other people's behaviour. Study 2 demonstrates that the perceptions of the health benefits of tooth-brushing duration can be manipulated experimentally by changing the ranked position of a person's tooth-brushing duration. Study 3 experimentally demonstrates the possibility of increasing the length of time for which individuals clean their teeth by focusing on how they rank among their peers in terms of tooth-brushing duration. The effectiveness of interventions using social-ranking methods relative to those that emphasize comparisons made against group averages or normative guidelines are discussed. What is already known on this subject? Individual make judgements based on social rank information. Social rank information has been shown to influence positive health behaviours such as exercise. What does this study add? The health benefits of tooth-brushing are predicted by how tooth-brushing duration ranks within a distribution. Focussing on how teeth-cleaning duration ranks among others produces longer teeth-cleaning durations. © 2015 The British Psychological Society.

Long-term prognosis in patients continuing taking antithrombotics after peptic ulcer bleeding

PubMed Central

Wang, Xi-Xu; Dong, Bo; Hong, Biao; Gong, Yi-Qun; Wang, Wei; Wang, Jue; Zhou, Zhen-Yu; Jiang, Wei-Jun

2017-01-01

AIM To investigate the long-term prognosis in peptic ulcer patients continuing taking antithrombotics after ulcer bleeding, and to determine the risk factors that influence the prognosis. METHODS All clinical data of peptic ulcer patients treated from January 1, 2009 to January 1, 2014 were retrospectively collected and analyzed. Patients were divided into either a continuing group to continue taking antithrombotic drugs after ulcer bleeding or a discontinuing group to discontinue antithrombotic drugs. The primary outcome of follow-up in peptic ulcer bleeding patients was recurrent bleeding, and secondary outcome was death or acute cardiovascular disease occurrence. The final date of follow-up was December 31, 2014. Basic demographic data, complications, and disease classifications were analyzed and compared by t- or χ2-test. The number of patients that achieved various outcomes was counted and analyzed statistically. A survival curve was drawn using the Kaplan-Meier method, and the difference was compared using the log-rank test. COX regression multivariate analysis was applied to analyze risk factors for the prognosis of peptic ulcer patients. RESULTS A total of 167 patients were enrolled into this study. As for the baseline information, differences in age, smoking, alcohol abuse, and acute cardiovascular diseases were statistically significant between the continuing and discontinuing groups (70.8 ± 11.4 vs 62.4 ± 12.0, P < 0.001; 8 (8.2%) vs 15 (21.7%), P < 0.05; 65 (66.3%) vs 13 (18.8%), P < 0.001). At the end of the study, 18 patients had recurrent bleeding and three patients died or had acute cardiovascular disease in the continuing group, while four patients had recurrent bleeding and 15 patients died or had acute cardiovascular disease in the discontinuing group. The differences in these results were statistically significant (P = 0.022, P = 0.000). The Kaplan-Meier survival curve indicated that the incidence of recurrent bleeding was higher in patients in the continuing group, and the risk of death and developing acute cardiovascular disease was higher in patients in the discontinuing group (log-rank test, P = 0.000 for both). Furthermore, COX regression multivariate analysis revealed that the hazard ratio (HR) for recurrent bleeding was 2.986 (95%CI: 067-8.356, P = 0.015) in the continuing group, while HR for death or acute cardiovascular disease was 5.216 (95%CI: 1.035-26.278, P = 0.028). CONCLUSION After the occurrence of peptic ulcer bleeding, continuing antithrombotics increases the risk of recurrent bleeding events, while discontinuing antithrombotics would increase the risk of death and developing cardiovascular disease. This suggests that clinicians should comprehensively consider the use of antithrombotics after peptic ulcer bleeding. PMID:28216980

Ranking of Prokaryotic Genomes Based on Maximization of Sortedness of Gene Lengths

PubMed Central

Bolshoy, A; Salih, B; Cohen, I; Tatarinova, T

2014-01-01

How variations of gene lengths (some genes become longer than their predecessors, while other genes become shorter and the sizes of these factions are randomly different from organism to organism) depend on organismal evolution and adaptation is still an open question. We propose to rank the genomes according to lengths of their genes, and then find association between the genome rank and variousproperties, such as growth temperature, nucleotide composition, and pathogenicity. This approach reveals evolutionary driving factors. The main purpose of this study is to test effectiveness and robustness of several ranking methods. The selected method of evaluation is measuring of overall sortedness of the data. We have demonstrated that all considered methods give consistent results and Bubble Sort and Simulated Annealing achieve the highest sortedness. Also, Bubble Sort is considerably faster than the Simulated Annealing method. PMID:26146586

Ranking of Prokaryotic Genomes Based on Maximization of Sortedness of Gene Lengths.

PubMed

Bolshoy, A; Salih, B; Cohen, I; Tatarinova, T

How variations of gene lengths (some genes become longer than their predecessors, while other genes become shorter and the sizes of these factions are randomly different from organism to organism) depend on organismal evolution and adaptation is still an open question. We propose to rank the genomes according to lengths of their genes, and then find association between the genome rank and variousproperties, such as growth temperature, nucleotide composition, and pathogenicity. This approach reveals evolutionary driving factors. The main purpose of this study is to test effectiveness and robustness of several ranking methods. The selected method of evaluation is measuring of overall sortedness of the data. We have demonstrated that all considered methods give consistent results and Bubble Sort and Simulated Annealing achieve the highest sortedness. Also, Bubble Sort is considerably faster than the Simulated Annealing method.

Age at diagnosis and prognosis of oral cancer in relation to the patient's residential area: experience from a medical center in Taiwan.

PubMed

Su, Che-Chun; Chung, Jian-An; Hsu, Yun-Ying; Huang, Su-Ju; Lian, Ie-Bin

2008-11-01

Smoking and betel quid chewing are established risk factors for oral cancer in Taiwan. The prevalence of these risk factors in the central county of Changhua falls within the middle range nationally, yet the county has the highest incidence of oral cancer in Taiwan. The purpose of this study, therefore, was to identify if patients' ages and prognoses at diagnosis were related to their place of residence and, if so, to explore environmental and geographical factors which might explain local variance in the incidence of oral cancers within Changhua and their prevalence in the county as a whole. The paper contains results from a retrospective review of medical records for patients diagnosed with oral cancer in Changhua County who were treated at the Changhua Christian Hospital (CCH) between 1994 and 2005. The Wilcoxon signed rank test, ANOVA, t-test, Kaplan-Meier curve and log-rank tests were carried out to examine the association between patients' places of residence, their ages at diagnosis, and their overall prognoses. A total of 1363 oral cancer cases were diagnosed in the study period. These consisted of 1272 males and 91 females. A steady increase in the number of patients diagnosed with oral cancer annually was noted. The tongue and buccal mucosa were the two most frequently affected sites constituting 56% of cases, while squamous cell carcinoma was diagnosed in nearly 80% of the study population. The mean ages at diagnosis were 53.1 and 52.8 years for patients living in the northern and central areas of Changhua, and 55.1 years for those living in the south. Patients living in the northern and central areas of Changhua had poorer long-term prognoses as indicated by Kaplan-Meier survival curves and the log-rank test, and it appears that differences in the level, type and distribution of industry in these areas distinguish these patients from those living in the south of the county. In particular, the density of electroplating factories in northern and central Changhua is significantly higher than in the south. Patients living in northern and central areas of Changhua have their oral cancers diagnosed at a younger age and have poorer long-term prognoses than those living in the south of the county in spite of their being treated at the same hospital. We conclude that factors explaining local differences in the prognosis of oral cancer patients in this part of Taiwan require further investigation, as does Changhua's high overall incidence for these cancers.

Recurrence risk model for esophageal cancer after radical surgery

PubMed Central

Tao, Hua; Song, Dan; Chen, Cheng

2013-01-01

Objective The aim of the present study was to construct a risk assessment model which was tested by disease-free survival (DFS) of esophageal cancer after radical surgery. Methods A total of 164 consecutive esophageal cancer patients who had undergone radical surgery between January 2005 and December 2006 were retrospectively analyzed. The cutpoint of value at risk (VaR) was inferred by stem-and-leaf plot, as well as by independent-samples t-test for recurrence-free time, further confirmed by crosstab chi-square test, univariate analysis and Cox regression analysis for DFS. Results The cutpoint of VaR was 0.3 on the basis of our model. The rate of recurrence was 30.3% (30/99) and 52.3% (34/65) in VaR <0.3 and VaR ≥0.3 (chi-square test, χ2 =7.984, P=0.005), respectively. The 1-, 3-, and 5-year DFS of esophageal cancer after radical surgery was 70.4%, 48.7%, and 45.3%, respectively in VaR ≥0.3, whereas 91.5%, 75.8%, and 67.3%, respectively in VaR <0.3 (Log-rank test, χ2 =9.59, P=0.0020), and further confirmed by Cox regression analysis [hazard ratio =2.10, 95% confidence interval (CI): 1.2649-3.4751; P=0.0041]. Conclusions The model could be applied for integrated assessment of recurrence risk after radical surgery for esophageal cancer. PMID:24255579

Comparison and ranking of superelasticity of different austenite active nickel-titanium orthodontic archwires using mechanical tensile testing and correlating with its electrical resistivity

PubMed Central

Nagarajan, D.; Baskaranarayanan, Balashanmugam; Usha, K.; Jayanthi, M. S.; Vijjaykanth, M.

2016-01-01

Introduction: The application of light and continuous forces for optimum physiological response and the least damage to the tooth supporting structures should be the primary aim of an orthodontist. Nickel-titanium (NiTi) alloys with their desirable properties are one of the natural choices of the clinicians. Aim: This study was aimed to compare and rank them based on its tensile strength and electrical resistivity. Materials and Methods: The sample consisted of eight groups of 0.017 inch × 0.025 inch rectangular archwires from eight different manufacturers, and five samples from each group for tensile testing and nine samples for electrical resistivity tests were used. Data for stress at 10% strain and the initial slope were statistically analyzed with an analysis of variance and Scheffe tests with P < 0.05. The stress/strain plots of each product were ranked for superelastic behavior. The rankings of the wires tested were based primarily on the unloading curve's slope which is indicative of the magnitude of the deactivation force and secondarily on the length of the horizontal segment which is indicative of continuous forces during deactivation. For calculating the electric resistivity, the change in resistance after inducing strain in the wires was taken into account for the calculation of degree of martensite transformation and for ranking. Results: In tensile testing Ortho Organizers wires ranked first and GAC Lowland NiTi wires ranked last. For resistivity tests Ormco A wires were found superior and Morelli remained last. Conclusion: these rankings should be correlated clinically and need further studies. PMID:27829751

Combined Estimation of Hydrogeologic Conceptual Model and Parameter Uncertainty

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyer, Philip D.; Ye, Ming; Neuman, Shlomo P.

2004-03-01

The objective of the research described in this report is the development and application of a methodology for comprehensively assessing the hydrogeologic uncertainties involved in dose assessment, including uncertainties associated with conceptual models, parameters, and scenarios. This report describes and applies a statistical method to quantitatively estimate the combined uncertainty in model predictions arising from conceptual model and parameter uncertainties. The method relies on model averaging to combine the predictions of a set of alternative models. Implementation is driven by the available data. When there is minimal site-specific data the method can be carried out with prior parameter estimates basedmore » on generic data and subjective prior model probabilities. For sites with observations of system behavior (and optionally data characterizing model parameters), the method uses model calibration to update the prior parameter estimates and model probabilities based on the correspondence between model predictions and site observations. The set of model alternatives can contain both simplified and complex models, with the requirement that all models be based on the same set of data. The method was applied to the geostatistical modeling of air permeability at a fractured rock site. Seven alternative variogram models of log air permeability were considered to represent data from single-hole pneumatic injection tests in six boreholes at the site. Unbiased maximum likelihood estimates of variogram and drift parameters were obtained for each model. Standard information criteria provided an ambiguous ranking of the models, which would not justify selecting one of them and discarding all others as is commonly done in practice. Instead, some of the models were eliminated based on their negligibly small updated probabilities and the rest were used to project the measured log permeabilities by kriging onto a rock volume containing the six boreholes. These four projections, and associated kriging variances, were averaged using the posterior model probabilities as weights. Finally, cross-validation was conducted by eliminating from consideration all data from one borehole at a time, repeating the above process, and comparing the predictive capability of the model-averaged result with that of each individual model. Using two quantitative measures of comparison, the model-averaged result was superior to any individual geostatistical model of log permeability considered.« less

High expression of Parkin predicts easier recurrence of patients with adjuvant transarterial chemoembolization.

PubMed

Zhang, Changlie; Song, Zhihong; Yu, Guangji

2017-10-01

To investigate the clinical significance of E3 ubiquitin ligase Parkin in patients with adjuvant transarterial chemoembolization after curative resection of hepatocellular carcinoma. Parkin expression of hepatocellular carcinomas was detected and its correlation with clinicopathological factors was analyzed with χ 2 test. The significance of Parkin in prognosis and recurrence was analyzed with log-rank test and the Cox-regression model. High expression of Parkin could result in lower recurrence-free survival rate instead of overall survival rate. Larger tumor size, positive tumor recurrence, advanced T, N, M and TNM stage were significantly associated with poorer prognosis. Larger tumor size, advanced T and TNM stage could lead to higher recurrence. High Parkin expression could predict easier recurrence to patients with adjuvant transarterial chemoembolization.

Sensitivity ranking for freshwater invertebrates towards hydrocarbon contaminants.

PubMed

Gerner, Nadine V; Cailleaud, Kevin; Bassères, Anne; Liess, Matthias; Beketov, Mikhail A

2017-11-01

Hydrocarbons have an utmost economical importance but may also cause substantial ecological impacts due to accidents or inadequate transportation and use. Currently, freshwater biomonitoring methods lack an indicator that can unequivocally reflect the impacts caused by hydrocarbons while being independent from effects of other stressors. The aim of the present study was to develop a sensitivity ranking for freshwater invertebrates towards hydrocarbon contaminants, which can be used in hydrocarbon-specific bioindicators. We employed the Relative Sensitivity method and developed the sensitivity ranking S hydrocarbons based on literature ecotoxicological data supplemented with rapid and mesocosm test results. A first validation of the sensitivity ranking based on an earlier field study has been conducted and revealed the S hydrocarbons ranking to be promising for application in sensitivity based indicators. Thus, the first results indicate that the ranking can serve as the core component of future hydrocarbon-specific and sensitivity trait based bioindicators.

Separate-channel analysis of two-channel microarrays: recovering inter-spot information.

PubMed

Smyth, Gordon K; Altman, Naomi S

2013-05-26

Two-channel (or two-color) microarrays are cost-effective platforms for comparative analysis of gene expression. They are traditionally analysed in terms of the log-ratios (M-values) of the two channel intensities at each spot, but this analysis does not use all the information available in the separate channel observations. Mixed models have been proposed to analyse intensities from the two channels as separate observations, but such models can be complex to use and the gain in efficiency over the log-ratio analysis is difficult to quantify. Mixed models yield test statistics for the null distributions can be specified only approximately, and some approaches do not borrow strength between genes. This article reformulates the mixed model to clarify the relationship with the traditional log-ratio analysis, to facilitate information borrowing between genes, and to obtain an exact distributional theory for the resulting test statistics. The mixed model is transformed to operate on the M-values and A-values (average log-expression for each spot) instead of on the log-expression values. The log-ratio analysis is shown to ignore information contained in the A-values. The relative efficiency of the log-ratio analysis is shown to depend on the size of the intraspot correlation. A new separate channel analysis method is proposed that assumes a constant intra-spot correlation coefficient across all genes. This approach permits the mixed model to be transformed into an ordinary linear model, allowing the data analysis to use a well-understood empirical Bayes analysis pipeline for linear modeling of microarray data. This yields statistically powerful test statistics that have an exact distributional theory. The log-ratio, mixed model and common correlation methods are compared using three case studies. The results show that separate channel analyses that borrow strength between genes are more powerful than log-ratio analyses. The common correlation analysis is the most powerful of all. The common correlation method proposed in this article for separate-channel analysis of two-channel microarray data is no more difficult to apply in practice than the traditional log-ratio analysis. It provides an intuitive and powerful means to conduct analyses and make comparisons that might otherwise not be possible.

Pre-treatment red blood cell distribution width provides prognostic information in multiple myeloma.

PubMed

Zhou, Di; Xu, Peipei; Peng, Miaoxin; Shao, Xiaoyan; Wang, Miao; Ouyang, Jian; Chen, Bing

2018-06-01

The red blood cell distribution width (RDW), a credible marker for abnormal erythropoiesis, has recently been studied as a prognostic factor in oncology, but its role in multiple myeloma (MM) hasn't been thoroughly investigated. We performed a retrospective study in 162 patients with multiple myeloma. Categorical parameters were analyzed using Pearson chi-squared test. The Mann-Whitney and Wilcoxon tests were used for group comparisons. Comparisons of repeated samples data were analyzed with the general linear model repeated-measures procedure. The Kaplan-Meier product-limit method was used to determine OS and PFS, and the differences were assessed by the log-rank test. High RDW baseline was significantly associated with indexes including haemoglobin, bone marrow plasma cell infiltration, and cytogenetics risk stratification. After chemotherapy, the overall response rate (ORR) decreased as RDW baseline increased. In 24 patients with high RDW baseline, it was revealed RDW value decreased when patients achieved complete remission (CR), but increased when the disease progressed. The normal-RDW baseline group showed both longer overall survival (OS) and progression-free survival (PFS) than the high-RDW baseline group. Our study suggests pre-treatment RDW level is a prognostic factor in MM and should be regarded as an important parameter for assessment of therapeutic efficiency. Copyright © 2018. Published by Elsevier B.V.

Expression and prognostic examination of heat shock proteins (HSP 27, HSP 70, and HSP 90) in medulloblastoma.

PubMed

Hauser, Péter; Hanzély, Zoltán; Jakab, Zsuzsanna; Oláh, Lászlóné; Szabó, Erika; Jeney, András; Schuler, Dezso; Fekete, Gyoörgy; Bognár, László; Garami, Miklós

2006-07-01

Expression of heat shock proteins (HSPs) is of prognostic significance in several tumor types. HSP expression levels were determined in medulloblastomas and tested whether HSPs expression was associated with prognostic parameters. Expression of antiapoptotic HSP 27, HSP 70, and HSP 90 was investigated by immunohistochemistry, on paraffin-embedded sections from 65 patients. Expression of HSPs was validated on internal vascular controls and by Western blotting analysis. Sample evaluation was based on the estimated percentage of HSP positive tumor cells. For survival analysis Kaplan-Meier method, for statistical analysis chi2 test, univariate analysis, and log rank test were applied. Expression of HSPs varied in medulloblastomas. On the basis of the average expression rate of HSPs, at HSP 27 and HSP 90 with a 10% cut off, and at HSP 70 with a 70% cut off 2 groups were created. The amount of expression of any of the HSP types was not significantly associated with known prognostic factors (age of patient, extent of resection, presence of metastasis) and histologic subtype. After an average follow-up period of 4.30 years, no significant difference was observed in survival depending on the expression of HSP 27 or HSP 70 or HSP 90. The high expression of HSPs indicates that these proteins are potential therapeutic targets.

AML outcome: role of nucleotide excision repair polymorphisms in intermediate risk patients

PubMed Central

Strom, Sara S; Estey, Elihu H; Outschoorn, Ubaldo Martinez; Guillermo, Garcia-Manero

2010-01-01

Purpose Acute Myeloid Leukemia (AML) is frequently associated with genetic abnormalities. Based on pre-treatment cytogenetics, patients are classified into favorable, intermediate and poor subgroups. Cytogenetics predicts treatment outcome for the favorable and poor subgroups but not for the intermediate subgroup. Polymorphisms within the nucleotide excision repair (NER) pathway may lead to inter-individual differences in DNA repair capacity (DRC) which could influence outcome. Methods We studied the role of 6 polymorphisms (ERCC1 Gln504Lys, XPD Lys751Gln, XPC Ala499Val, XPC Lys939Gln, XPG Asp1104His, and CCNH Val270Ala) within NER pathway on overall and disease-free survival among 170 adult de-novo AML patients with intermediate cytogenetics [diploid (n=117); non-diploid (n=53)], treated with induction chemotherapy. Kaplan-Meier methods and Cox proportional hazards models were performed. Results Diploid patients with the XPD AC/CC genotype survived shorter than those with the wild-type (AA) genotype (median survival 22 vs. 40 months, log-rank p = 0.03). Similarly diploid patients with XPC CT/TT genotype survived shorter than those with the wild-type (CC) genotype (median survival 15 vs. 30 months, log-rank p = 0.02). Among diploid patients, after adjusting for clinical and socio-demographic variables, patients carrying both XPD AC/CC and XPC CT/TT had a greater than two-fold increased risk of dying compared to those with the wild-type genotypes (HR=2.49; 95%CI: 1.06–5.85). No significant associations were observed for disease-free survival in AML patients. Conclusion By reduced DRC, this combined genotype may result in greater susceptibility to treatment effects decreasing overall survival. These findings could in the future help in selecting treatment strategies for patients with normal cytogenetics. PMID:20141440

GRP78 Protein Expression as Prognostic Values in Neoadjuvant Chemoradiotherapy and Laparoscopic Surgery for Locally Advanced Rectal Cancer.

PubMed

Lee, Hee Yeon; Jung, Ji-Han; Cho, Hyun-Min; Kim, Sung Hwan; Lee, Kang-Moon; Kim, Hyung-Jin; Lee, Jong Hoon; Shim, Byoung Yong

2015-10-01

We investigated the relationships between biomarkers related to endoplasmic reticulum stress proteins (glucose-regulated protein of molecular mass 78 [GRP78] and Cripto-1 [teratocarcinoma-derived growth factor 1 protein]), pathologic response, and prognosis in locally advanced rectal cancer. All clinical stage II and III rectal cancer patients received 50.4 Gy over 5.5 weeks, plus 5-fluorouracil (400 mg/m(2)/day) and leucovorin (20 mg/m(2)/day) bolus on days 1 to 5 and 29 to 33, and surgery was performed at 7 to 10 weeks after completion of all therapies. Expression of GRP78 and Cripto-1 proteins was determined by immunohistochemistry and was assessed in 101 patients with rectal cancer treated with neoadjuvant chemoradiotherapy (CRT). High expression of GRP78 and Cripto-1 proteins was observed in 86 patients (85.1%) and 49 patients (48.5%), respectively. Low expression of GRP78 protein was associated with a significantly high rate of down staging (80.0% vs. 52.3%, respectively; p=0.046) and a significantly low rate of recurrence (0% vs. 33.7%, respectively; p=0.008) compared with high expression of GRP78 protein. Mean recurrence-free survival according to GRP78 expression could not be estimated because the low expression group did not develop recurrence events but showed a significant correlation with time to recurrence, based on the log rank method (p=0.007). GRP78 also showed correlation with overall survival, based on the log rank method (p=0.045). GRP78 expression is a predictive and prognostic factor for down staging, recurrence, and survival in rectal cancer patients treated with 5-fluorouracil and leucovorin neoadjuvant CRT.

Campylobacter contamination in broiler carcasses and correlation with slaughterhouses operational hygiene inspection.

PubMed

Habib, Ihab; Berkvens, Dirk; De Zutter, Lieven; Dierick, Katelijne; Van Huffel, Xavier; Speybroeck, Niko; Geeraerd, Annemie H; Uyttendaele, Mieke

2012-02-01

This study investigates factors associated with Campylobacter contamination of broiler carcasses, using survey data collected from nine Belgian slaughterhouses in 2008 in accordance with a European Union baseline study. Campylobacter were detected in 51.9% (202/389) (95% confidence interval, 46.8%-56.9%) of broiler carcasses. Campylobacter concentration was <10 CFU/g in 49.6% of carcasses, while 20.6% were contaminated with ≥ 1000 CFU/g. The mean Campylobacter concentration, as calculated by maximum likelihood estimation for left-censored data, was 1.8 log(10) CFU/g, with a standard deviation of 1.9 log(10) CFU/g. There was statistically significant variation among slaughterhouses in prevalence and concentrations of Campylobacter in their sampled carcasses. Campylobacter prevalence (but not concentrations) was positively associated with increase in broilers age. Both Campylobacter prevalence and concentration were significantly higher in carcasses sampled during June and September (but not in July and August) than carcasses sampled in January. We also investigated the correlation (Spearman's rank correlation test) between the scores of official control inspections and Campylobacter prevalence for eight out of the nine slaughterhouses. The control inspections were routinely performed by the Belgian Federal Agency for the Safety of the Food Chain, and the concluded inspection scores were used as a general numerical indicator for the status of operational hygiene and quality of management in the slaughterhouses. Ranking of slaughterhouses based on their inspection scores was statistically correlated (Spearman's correlation coefficient = 0.857) with their ranking based on prevalence of Campylobacter. In the present study we demonstrate how the outcomes from a routine baseline survey could be coupled with other readily available data from national control authorities in order to enable a better insight over Campylobacter contamination status in broiler slaughterhouses. Findings from this work call for subsequent in-depth investigations on technical and hygiene management factors that could impact Campylobacter contamination across broiler slaughterhouses. Copyright © 2011 Elsevier Ltd. All rights reserved.

Risk of colorectal cancer among immigrants to Ontario, Canada.

PubMed

Paszat, Lawrence; Sutradhar, Rinku; Liu, Ying; Baxter, Nancy N; Tinmouth, Jill; Rabeneck, Linda

2017-07-06

The risk of colorectal cancer (CRC) varies around the world and between females and males. We aimed to compare the risk of CRC among immigrants to Ontario, Canada, to its general population. We used an exposure-control matched design. We identified persons in the Immigration, Refugees and Citizenship Canada Permanent Resident Database with first eligibility for the Ontario Health Insurance Plan between July 1, 1991 and June 30, 2008 at age 40 years or older, and matched five controls by year of birth and sex on the immigrant's first eligibility date. We identified CRC from the Ontario Cancer Registry between the index date and December 31, 2014. All analyses were stratified by sex. We calculated crude and relative rates of CRC. We estimated risk of CRC over time by the Kaplan-Meier method and compared immigrants to controls in age and sex stratified strata using log-rank tests. We modeled the hazard of CRC using Cox proportional hazards regression, accounting for within-cluster correlation by a robust sandwich variance estimation approach, and assessed an interaction with time since eligibility. Among females, 1877 cases of CRC were observed among 209,843 immigrants, and 16,517 cases among 1,049,215 controls; the crude relative rate among female immigrants was 0.623. Among males, 1956 cases of CRC were observed among 191,792 immigrants and 18,329 cases among 958,960 controls; the crude relative rate among male immigrants was 0.582.. Comparing immigrants to controls in all age and sex stratified strata, the log rank test p < 0.0001 except for females aged > = 75 years at index, where p = 0.01. The age-adjusted hazard ratio (HR) for CRC among female immigrants was 0.63 (95% CI 0.59, 0.67) during the first 10 years, and 0.66 (95% CI 0.59, 0.74) thereafter. Among male immigrants the age-adjusted HR = 0.55 (95% CI 0.52, 0.59) during the first 10 years and increased to 0.63 (95% CI 0.57, 0.71) thereafter. The adjusted HR > = 1 only among immigrants born in Europe and Central Asia. The risk of CRC among immigrants to Ontario relative to controls varies by origin and over time since immigration.

Iliac artery stenting in patients with poor distal runoff: Influence of concomitant infrainguinal arterial reconstruction.

PubMed

Timaran, Carlos H; Ohki, Takao; Gargiulo, Nicholas J; Veith, Frank J; Stevens, Scott L; Freeman, Michael B; Goldman, Mitchell H

2003-09-01

Inadequate infrainguinal runoff is considered an important risk factor for iliac stent failure. However, the influence of concomitant infrainguinal arterial reconstruction (CIAR) on iliac stent patency is unknown. This study evaluated the influence of CIAR on outcome of iliac angioplasty and stenting (IAS) in patients with poor distal runoff. Over 5 years (1996 to 2001), 68 IAS procedures (78 stents) were performed in 62 patients with poor distal runoff (angiographic runoff score >or=5). The SVS/AAVS reporting standards were followed to define outcome variables and risk factors. Data were analyzed with both univariate analysis (Kaplan-Meier method [K-M]) and regression analysis (Cox proportional hazards model). Indications for iliac artery stenting were disabling claudication (59%) and limb salvage (41%). Of the 68 procedures, IAS with CIAR was performed in 31 patients (46%), and IAS alone was performed in 37 patients (54%). Patients undergoing IAS with CIAR were older (P =.03) and had more extensive and multifocal iliac artery occlusive disease, with more TASC (TransAtlantic Inter-Society Consensus) type C lesions (P =.03), compared with patients undergoing IAS alone. No other significant differences in risk factors were noted. Runoff scores between patients undergoing IAS with CIAR and those undergoing IAS alone were not significantly different (median runoff scores, 6 [range, 5-8] and 7 [range, 5-9], respectively; P =.77). Primary stent patency rate at 1, 3, and 5 years was 87%, 54%, and 42%, respectively, for patients undergoing IAS with CIAR, and was 76%, 66%, and 55%, respectively, for patients undergoing IAS. Univariate analysis revealed that primary stent patency rate was not significantly different between the 2 groups (K-M, log-rank test, P =.81). Primary graft patency rate for CIAR was 81%, 52%, and 46% at 1, 3, and 5 years, respectively. Performing CIAR did not affect primary iliac stent patency (relative risk, 1.1; 95% confidence interval, 0.49-2.47; P =.81). Overall, there was a trend toward improved limb salvage in patients undergoing IAS with CIAR, compared with those undergoing IAS alone (K-M, log rank test, P =.07). In patients undergoing IAS with poor distal runoff, CIAR does not improve iliac artery stent patency. Infrainguinal bypass procedures should therefore be reserved for patients who do not demonstrate clinical improvement and possibly for those with limb-threatening ischemia.

Geophysical, stratigraphic, and flow-zone logs of selected test, monitor, and water-supply wells in Cayuga County, New York

USGS Publications Warehouse

Anderson, J. Alton; Williams, John H.; Eckhardt, David A.V.; Miller, Todd S.

2003-01-01

Volatile-organic compounds have been detected in water sampled from more than 50 supply wells between the City of Auburn and Village of Union Springs in Cayuga County, New York, and the area was declared a Superfund site in 2002. In 2001-04, geophysical logs were collected from 37 test, monitor, and water-supply wells as a preliminary part of the investigation of volatile-organic compound contamination in the carbonate-bedrock aquifer system. The geophysical logs included gamma, induction, caliper, wellbore image, deviation, fluid resistivity and temperature, and flowmeter. The geophysical logs were analyzed along with core samples and outcrops of the bedrock to define the stratigraphic units and flow zones penetrated by the wells. This report describes the logging methods used in the study and presents the geophysical, stratigraphic, and flow-zone logs.

Speaker-sensitive emotion recognition via ranking: Studies on acted and spontaneous speech☆

PubMed Central

Cao, Houwei; Verma, Ragini; Nenkova, Ani

2014-01-01

We introduce a ranking approach for emotion recognition which naturally incorporates information about the general expressivity of speakers. We demonstrate that our approach leads to substantial gains in accuracy compared to conventional approaches. We train ranking SVMs for individual emotions, treating the data from each speaker as a separate query, and combine the predictions from all rankers to perform multi-class prediction. The ranking method provides two natural benefits. It captures speaker specific information even in speaker-independent training/testing conditions. It also incorporates the intuition that each utterance can express a mix of possible emotion and that considering the degree to which each emotion is expressed can be productively exploited to identify the dominant emotion. We compare the performance of the rankers and their combination to standard SVM classification approaches on two publicly available datasets of acted emotional speech, Berlin and LDC, as well as on spontaneous emotional data from the FAU Aibo dataset. On acted data, ranking approaches exhibit significantly better performance compared to SVM classification both in distinguishing a specific emotion from all others and in multi-class prediction. On the spontaneous data, which contains mostly neutral utterances with a relatively small portion of less intense emotional utterances, ranking-based classifiers again achieve much higher precision in identifying emotional utterances than conventional SVM classifiers. In addition, we discuss the complementarity of conventional SVM and ranking-based classifiers. On all three datasets we find dramatically higher accuracy for the test items on whose prediction the two methods agree compared to the accuracy of individual methods. Furthermore on the spontaneous data the ranking and standard classification are complementary and we obtain marked improvement when we combine the two classifiers by late-stage fusion. PMID:25422534

Speaker-sensitive emotion recognition via ranking: Studies on acted and spontaneous speech☆

PubMed

Cao, Houwei; Verma, Ragini; Nenkova, Ani

2015-01-01

We introduce a ranking approach for emotion recognition which naturally incorporates information about the general expressivity of speakers. We demonstrate that our approach leads to substantial gains in accuracy compared to conventional approaches. We train ranking SVMs for individual emotions, treating the data from each speaker as a separate query, and combine the predictions from all rankers to perform multi-class prediction. The ranking method provides two natural benefits. It captures speaker specific information even in speaker-independent training/testing conditions. It also incorporates the intuition that each utterance can express a mix of possible emotion and that considering the degree to which each emotion is expressed can be productively exploited to identify the dominant emotion. We compare the performance of the rankers and their combination to standard SVM classification approaches on two publicly available datasets of acted emotional speech, Berlin and LDC, as well as on spontaneous emotional data from the FAU Aibo dataset. On acted data, ranking approaches exhibit significantly better performance compared to SVM classification both in distinguishing a specific emotion from all others and in multi-class prediction. On the spontaneous data, which contains mostly neutral utterances with a relatively small portion of less intense emotional utterances, ranking-based classifiers again achieve much higher precision in identifying emotional utterances than conventional SVM classifiers. In addition, we discuss the complementarity of conventional SVM and ranking-based classifiers. On all three datasets we find dramatically higher accuracy for the test items on whose prediction the two methods agree compared to the accuracy of individual methods. Furthermore on the spontaneous data the ranking and standard classification are complementary and we obtain marked improvement when we combine the two classifiers by late-stage fusion.

Acoustic evaluation of wood quality in standing trees. Part I, Acoustic wave behavior

Treesearch

Xiping Wang; Robert J. Ross; Peter Carter

2007-01-01

Acoustic wave velocities in standing trees or live softwood species were measured by the time-of-flight (TOF) method. Tree velocities were compared with acoustic velocities measured in corresponding butt logs through a resonance acoustic method. The experimental data showed a skewed relationship between tree and log acoustic measurements. For most trees tested,...

Regeneration alternatives for upland white spruce after buring and logging in interior Alaska

Treesearch

R. V. Densmore; G. P. Juday; John C. Zasada

1999-01-01

Site-preparation and regeneration methods for white spruce (Picea glaucu (Meench) Voss) were tested near Fairbanks Alaska, on two upland sites which had been burned in a wildfire and salvage logged. After 5 and 10 years, white spruce regeneration did not differ among the four scarification methods but tended to be lower without scarification....

Atrophic gastritis and enlarged gastric folds diagnosed by double-contrast upper gastrointestinal barium X-ray radiography are useful to predict future gastric cancer development based on the 3-year prospective observation.

PubMed

Yamamichi, Nobutake; Hirano, Chigaya; Ichinose, Masao; Takahashi, Yu; Minatsuki, Chihiro; Matsuda, Rie; Nakayama, Chiemi; Shimamoto, Takeshi; Kodashima, Shinya; Ono, Satoshi; Tsuji, Yosuke; Niimi, Keiko; Sakaguchi, Yoshiki; Kataoka, Yosuke; Saito, Itaru; Asada-Hirayama, Itsuko; Takeuchi, Chihiro; Yakabi, Seiichi; Kaikimoto, Hikaru; Matsumoto, Yuta; Yamaguchi, Daisuke; Kageyama-Yahara, Natsuko; Fujishiro, Mitsuhiro; Wada, Ryoichi; Mitsushima, Toru; Koike, Kazuhiko

2016-07-01

Double-contrast upper gastrointestinal barium X-ray radiography (UGI-XR) is the standard gastric cancer screening method in Japan. Atrophic gastritis and enlarged gastric folds are considered the two major features of Helicobacter pylori-induced chronic gastritis, but the clinical meaning of evaluating them by UGI-XR has not been elucidated. We analyzed healthy UGI-XR examinees without a history of gastrectomy, previous Helicobacter pylori eradication and usage of gastric acid suppressants. Of the 6433 subjects, 1936 (30.1 %) had atrophic gastritis and 1253 (19.5 %) had enlarged gastric folds. During the 3-year prospective observational follow-up, gastric cancer developed in seven subjects, six of whom (85.7 %) had atrophic gastritis with H. pylori infection and five of whom (71.4 %) had enlarged gastric folds with H. pylori infection. The Kaplan-Meier method with log-rank testing revealed that both UGI-XR-based atrophic gastritis (p = 0.0011) and enlarged gastric folds (p = 0.0003) are significant predictors for future gastric cancer incidence.

TOKYO criteria 2014 for transpapillary biliary stenting.

PubMed

Isayama, Hiroyuki; Hamada, Tsuyoshi; Yasuda, Ichiro; Itoi, Takao; Ryozawa, Shomei; Nakai, Yousuke; Kogure, Hirofumi; Koike, Kazuhiko

2015-01-01

It is difficult to carry out meta-analyses or to compare the results of different studies of biliary stents because there is no uniform evaluation method. Therefore, a standardized reporting system is required. We propose a new standardized system for reporting on biliary stents, the 'TOKYO criteria 2014', based on a consensus among Japanese pancreatobiliary endoscopists. Instead of stent occlusion, we use recurrent biliary obstruction, which includes occlusion and migration. The time to recurrent biliary obstruction was estimated using Kaplan-Meier analysis with the log-rank test. We can evaluate both plastic and self-expandable metallic stents (uncovered and covered). We also propose specification of the cause of recurrent biliary obstruction, identification of complications other than recurrent biliary obstruction, indication of severity, measures of technical and clinical success, and a standard for clinical care. Most importantly, the TOKYO criteria 2014 allow comparison of biliary stent quality across studies. Because blocked stents can be drained not only using transpapillary techniques but also by an endoscopic ultrasonography-guided transmural procedure, we should devise an evaluation method that includes transmural stenting in the near future. © 2014 The Authors. Digestive Endoscopy © 2014 Japan Gastroenterological Endoscopy Society.

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

PubMed

Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

2009-12-24

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

Relative toxicity of products of pyrolysis and combustion of polymeric materials using various test conditions

NASA Technical Reports Server (NTRS)

Hilado, C. J.

1976-01-01

Relative toxicity data for a large number of natural and synthetic polymeric materials are presented which were obtained by 11 pyrolysis and three flaming-combustion test methods. The materials tested include flexible and rigid polyurethane foams, different kinds of fabrics and woods, and a variety of commodity polymers such as polyethylene. Animal exposure chambers of different volumes containing mice, rats, or rabbits were used in the tests, which were performed over the temperature range from ambient to 800 C with and without air flow or recirculation. The test results are found to be sensitive to such variables as exposure mode, temperature, air flow and dilution, material concentration, and animal species, but relative toxicity rankings appear to be similar for many methods and materials. It is concluded that times to incapacitance and to death provide a more suitable basis for relative toxicity rankings than percent mortality alone, that temperature is the most important variable in the tests reported, and that variables such as chamber volume and animal species may not significantly affect the rankings.

Effect of tooth whitening strips on fatigue resistance and flexural strength of bovine dentin in vitro

PubMed Central

Kim, Namhee; De Souza, Grace M.

2017-01-01

Objective To determine the effects of whitening strips on bovine dentin fatigue resistance and flexural strength in vitro. Materials and methods A total of eighty bovine dentin specimens (2x2x17mm) were treated with either: control glycerine gel on plastic film wrap or whitening strips containing 9.5% hydrogen peroxide. Treatment was applied for 30 minutes, twice a day, for 1- or 4-weeks. After the last treatment, ten specimens per group were randomly selected to undergo fatigue testing (106 cycles, 3Hz, 20N) while the other ten were subjected to flexural strength testing after ten days of storage in artificial saliva. Kaplan-Meier method with a log rank test, Wilcoxon test and Cox regression were used to assess fatigue test results (p<0.05). One-way ANOVA and Tukey’s tests were used to compare the flexural strength results (p<0.05). Results There were significant differences in survival during the fatigue test among the groups (p<0.001). Treatment (control or bleach) was a significant factor for specimen survival (p<0.001, Exp(B) = 33.45). There were significant differences in mean flexural strength (p<0.001). No significant difference was found between “1-wk control” and “4-wk control”. The mean flexural strength and fatigue resistance of the “4-wk bleach” were significantly lower than all the other groups. Conclusions The use of whitening strips reduced the fatigue resistance and flexural strength of bovine dentin in vitro. Until the effect of whitening strips on mechanical properties of human dentin is fully elucidated, it remains prudent to advise patients to avoid excessive direct use of whitening strips on dentin. PMID:28278191

Impact of Shocks on Mortality in Patients with Ischemic or Dilated Cardiomyopathy and Defibrillators Implanted for Primary Prevention

PubMed Central

Streitner, Florian; Herrmann, Thomas; Kuschyk, Juergen; Lang, Siegfried; Doesch, Christina; Papavassiliu, Theano; Streitner, Ines; Veltmann, Christian; Haghi, Dariusch; Borggrefe, Martin

2013-01-01

Background Emerging interest is seen in the paradox of defibrillator shocks for ventricular tachyarrhythmia and increased mortality risk. Particularly in patients with dilated cardiomyopathy (DCM), the prognostic importance of shocks is unclear. The purpose of this study was to compare the outcome after shocks in patients with ischemic cardiomyopathy (ICM) or DCM and defibrillators (ICD) implanted for primary prevention. Methods and Results Data of 561 patients were analyzed (mean age 68.6±10.6 years, mean left ventricular ejection fraction 28.6±7.3%). During a median follow-up of 49.3 months, occurrence of device therapies and all-cause mortality were recorded. 74 out of 561 patients (13.2%) experienced ≥1 appropriate and 51 out of 561 patients (9.1%) ≥1 inappropriate shock. All-cause mortality was 24.2% (136 out of 561 subjects). Appropriate shock was associated with a trend to higher mortality in the overall patient population (HR 1.48, 95% CI 0.96–2.28, log rank p = 0.072). The effect was significant in ICM patients (HR 1.61, 95% CI 1.00–2.59, log rank p = 0.049) but not in DCM patients (HR 1.03, 95% CI 0.36–2.96, log rank p = 0.96). Appropriate shocks occurring before the median follow-up revealed a much stronger impact on mortality (HR for the overall patient population 2.12, 95% CI 1.24–3.63, p = 0.005). The effect was driven by ICM patients (HR 2.48, 95% CI 1.41–4.37, p = 0.001), as appropriate shocks again did not influence survival of DCM patients (HR 0.63, 95% CI 0.083–4.75, p = 0.65). Appropriate shocks occurring after the median follow-up and inappropriate shocks occurring at any time revealed no impact on survival in any of the groups (p = ns). Conclusion Appropriate shocks are associated with reduced survival in patients with ICM but not in patients with DCM and ICDs implanted for primary prevention. Furthermore, the negative effect of appropriate shocks on survival in ICM patients is only evident within the first 4 years after device implantation. PMID:23675514

Behavioral economic analysis of drug preference using multiple choice procedure data.

PubMed

Greenwald, Mark K

2008-01-11

The multiple choice procedure has been used to evaluate preference for psychoactive drugs, relative to money amounts (price), in human subjects. The present re-analysis shows that MCP data are compatible with behavioral economic analysis of drug choices. Demand curves were constructed from studies with intravenous fentanyl, intramuscular hydromorphone and oral methadone in opioid-dependent individuals; oral d-amphetamine, oral MDMA alone and during fluoxetine treatment, and smoked marijuana alone or following naltrexone pretreatment in recreational drug users. For each participant and dose, the MCP crossover point was converted into unit price (UP) by dividing the money value ($) by the drug dose (mg/70kg). At the crossover value, the dose ceases to function as a reinforcer, so "0" was entered for this and higher UPs to reflect lack of drug choice. At lower UPs, the dose functions as a reinforcer and "1" was entered to reflect drug choice. Data for UP vs. average percent choice were plotted in log-log space to generate demand functions. Rank of order of opioid inelasticity (slope of non-linear regression) was: fentanyl>hydromorphone (continuing heroin users)>methadone>hydromorphone (heroin abstainers). Rank order of psychostimulant inelasticity was d-amphetamine>MDMA>MDMA+fluoxetine. Smoked marijuana was more inelastic with high-dose naltrexone. These findings show this method translates individuals' drug preferences into estimates of population demand, which has the potential to yield insights into pharmacotherapy efficacy, abuse liability assessment, and individual differences in susceptibility to drug abuse.

Behavioral Economic Analysis of Drug Preference Using Multiple Choice Procedure Data

PubMed Central

Greenwald, Mark K.

2008-01-01

The Multiple Choice Procedure has been used to evaluate preference for psychoactive drugs, relative to money amounts (price), in human subjects. The present re-analysis shows that MCP data are compatible with behavioral economic analysis of drug choices. Demand curves were constructed from studies with intravenous fentanyl, intramuscular hydromorphone and oral methadone in opioid-dependent individuals; oral d-amphetamine, oral MDMA alone and during fluoxetine treatment, and smoked marijuana alone or following naltrexone pretreatment in recreational drug users. For each participant and dose, the MCP crossover point was converted into unit price (UP) by dividing the money value ($) by the drug dose (mg/70 kg). At the crossover value, the dose ceases to function as a reinforcer, so “0” was entered for this and higher UPs to reflect lack of drug choice. At lower UPs, the dose functions as a reinforcer and “1” was entered to reflect drug choice. Data for UP vs. average percent choice were plotted in log-log space to generate demand functions. Rank of order of opioid inelasticity (slope of non-linear regression) was: fentanyl > hydromorphone (continuing heroin users) > methadone > hydromorphone (heroin abstainers). Rank order of psychostimulant inelasticity was d-amphetamine > MDMA > MDMA + fluoxetine. Smoked marijuana was more inelastic with high-dose naltrexone. These findings show this method translates individuals’ drug preferences into estimates of population demand, which has the potential to yield insights into pharmacotherapy efficacy, abuse liability assessment, and individual differences in susceptibility to drug abuse. PMID:17949924

Differential p16/INK4A cyclin-dependent kinase inhibitor expression correlates with chemotherapy efficacy in a cohort of 88 malignant pleural mesothelioma patients

PubMed Central

Jennings, C J; Murer, B; O'Grady, A; Hearn, L M; Harvey, B J; Kay, E W; Thomas, W

2015-01-01

Background: Malignant pleural mesothelioma (MPM) is a rare and essentially incurable malignancy most often linked with occupational exposure to asbestos fibres. In common with other malignancies, the development and progression of MPM is associated with extensive dysregulation of cell cycle checkpoint proteins that modulate cell proliferation, apoptosis, DNA repair and senescence. Methods: The expression of cyclin-dependent kinase inhibitor p16/INK4A was evaluated by immunohistochemistry using tumour biopsy specimens from 88 MPM cases and a semi-quantitative score for p16/INK4A expression was obtained. Post-diagnosis survival and the survival benefit of chemotherapeutic intervention was correlated with p16/INK4A expression. Results: A low, intermediate and high score for p16/INK4A expression was observed for 45 (51.1%), 28 (31.8%) and 15 (17.1%) of the MPM cases, respectively. Those cases with intermediate or high p16/INK4A tumour expression had a significantly better post-diagnosis survival than those cases whose tumours lost p16 expression (log-rank P<0.001). Those patients with sustained p16/INK4A expression who received chemotherapy also had a better survival than those treated patients whose tumours had lost p16/INK4A expression (log-rank P<0.001). Conclusions: Sustained p16/INK4A expression predicts better post-diagnosis survival in MPM and also better survival following chemotherapeutic intervention. PMID:26057448

Influence of different methods of cleaning custom bases on the shear bond strength of indirectly bonded brackets.

PubMed

Kanashiro, Lylian K; Robles-Ruíz, Julissa J; Ciamponi, Ana L; Medeiros, Igor S; Tortamano, André; Paiva, João B

2014-09-01

To determine the influence on shear bond strength and bond failure location of four cleaning methods for orthodontic bracket custom bases. In vitro laboratory study. Eighty bovine teeth were divided at random into four groups. The bracket custom bases were cleaned with different methods: group 1 with methyl methacrylate monomer, group 2 with acetone, group 3 with 50 μm aluminium oxide particles and group 4 with detergent. The brackets were indirectly bonded onto the teeth with the Sondhi Rapid-Set self-curing adhesive. The maximum required shear bond strength to debond the brackets was recorded. The bond failure location was evaluated using the Adhesive Remnant Index (ARI). One-way analysis of variance (ANOVA) analysis (P<0·05) was used to detect significant differences in the bond strength. Kaplan-Meier survival plots and log-rank test were done to compare the survival distribution between the groups. The Kruskal-Wallis test (P<0·05) was used to evaluate the differences in the ARI scores. The mean bond strengths in groups 1, 2, 3 and 4 were 23·7±5·0, 25·3±5·1, 25·6±3·7 and 25·7±4·2 MPa, respectively. There were no significant statistically differences in either the bond strength or the ARI score between the groups. The four custom base-cleaning methods presented the same efficiencies on indirect bond of the brackets; thus, practitioners can choose the method that works best for them. © 2014 British Orthodontic Society.

A robust semi-parametric warping estimator of the survivor function with an application to two-group comparisons

PubMed Central

Hutson, Alan D

2018-01-01

In this note, we develop a new and novel semi-parametric estimator of the survival curve that is comparable to the product-limit estimator under very relaxed assumptions. The estimator is based on a beta parametrization that warps the empirical distribution of the observed censored and uncensored data. The parameters are obtained using a pseudo-maximum likelihood approach adjusting the survival curve accounting for the censored observations. In the univariate setting, the new estimator tends to better extend the range of the survival estimation given a high degree of censoring. However, the key feature of this paper is that we develop a new two-group semi-parametric exact permutation test for comparing survival curves that is generally superior to the classic log-rank and Wilcoxon tests and provides the best global power across a variety of alternatives. The new test is readily extended to the k group setting. PMID:26988931

A New Direction of Cancer Classification: Positive Effect of Low-Ranking MicroRNAs.

PubMed

Li, Feifei; Piao, Minghao; Piao, Yongjun; Li, Meijing; Ryu, Keun Ho

2014-10-01

Many studies based on microRNA (miRNA) expression profiles showed a new aspect of cancer classification. Because one characteristic of miRNA expression data is the high dimensionality, feature selection methods have been used to facilitate dimensionality reduction. The feature selection methods have one shortcoming thus far: they just consider the problem of where feature to class is 1:1 or n:1. However, because one miRNA may influence more than one type of cancer, human miRNA is considered to be ranked low in traditional feature selection methods and are removed most of the time. In view of the limitation of the miRNA number, low-ranking miRNAs are also important to cancer classification. We considered both high- and low-ranking features to cover all problems (1:1, n:1, 1:n, and m:n) in cancer classification. First, we used the correlation-based feature selection method to select the high-ranking miRNAs, and chose the support vector machine, Bayes network, decision tree, k-nearest-neighbor, and logistic classifier to construct cancer classification. Then, we chose Chi-square test, information gain, gain ratio, and Pearson's correlation feature selection methods to build the m:n feature subset, and used the selected miRNAs to determine cancer classification. The low-ranking miRNA expression profiles achieved higher classification accuracy compared with just using high-ranking miRNAs in traditional feature selection methods. Our results demonstrate that the m:n feature subset made a positive impression of low-ranking miRNAs in cancer classification.

Adaptive linear rank tests for eQTL studies

PubMed Central

Szymczak, Silke; Scheinhardt, Markus O.; Zeller, Tanja; Wild, Philipp S.; Blankenberg, Stefan; Ziegler, Andreas

2013-01-01

Expression quantitative trait loci (eQTL) studies are performed to identify single-nucleotide polymorphisms that modify average expression values of genes, proteins, or metabolites, depending on the genotype. As expression values are often not normally distributed, statistical methods for eQTL studies should be valid and powerful in these situations. Adaptive tests are promising alternatives to standard approaches, such as the analysis of variance or the Kruskal–Wallis test. In a two-stage procedure, skewness and tail length of the distributions are estimated and used to select one of several linear rank tests. In this study, we compare two adaptive tests that were proposed in the literature using extensive Monte Carlo simulations of a wide range of different symmetric and skewed distributions. We derive a new adaptive test that combines the advantages of both literature-based approaches. The new test does not require the user to specify a distribution. It is slightly less powerful than the locally most powerful rank test for the correct distribution and at least as powerful as the maximin efficiency robust rank test. We illustrate the application of all tests using two examples from different eQTL studies. PMID:22933317

Adaptive linear rank tests for eQTL studies.

PubMed

Szymczak, Silke; Scheinhardt, Markus O; Zeller, Tanja; Wild, Philipp S; Blankenberg, Stefan; Ziegler, Andreas

2013-02-10

Expression quantitative trait loci (eQTL) studies are performed to identify single-nucleotide polymorphisms that modify average expression values of genes, proteins, or metabolites, depending on the genotype. As expression values are often not normally distributed, statistical methods for eQTL studies should be valid and powerful in these situations. Adaptive tests are promising alternatives to standard approaches, such as the analysis of variance or the Kruskal-Wallis test. In a two-stage procedure, skewness and tail length of the distributions are estimated and used to select one of several linear rank tests. In this study, we compare two adaptive tests that were proposed in the literature using extensive Monte Carlo simulations of a wide range of different symmetric and skewed distributions. We derive a new adaptive test that combines the advantages of both literature-based approaches. The new test does not require the user to specify a distribution. It is slightly less powerful than the locally most powerful rank test for the correct distribution and at least as powerful as the maximin efficiency robust rank test. We illustrate the application of all tests using two examples from different eQTL studies. Copyright © 2012 John Wiley & Sons, Ltd.

Effects of Chinese herbal medicine on hyperlipidemia and the risk of cardiovascular disease in HIV-infected patients in Taiwan.

PubMed

Tsai, Fuu-Jen; Li, Te-Mao; Cheng, Chi-Fung; Wu, Yang-Chang; Lai, Chih-Ho; Ho, Tsung-Jung; Liu, Xiang; Tsang, Hsinyi; Lin, Ting-Hsu; Liao, Chiu-Chu; Huang, Shao-Mei; Li, Ju-Pi; Lin, Jung-Chun; Lin, Chih-Chien; Liang, Wen-Miin; Lin, Ying-Ju

2018-06-12

Due to the development of antiretroviral therapy (ART), HIV/AIDS is now regarded as a treatable chronic disease. Chinese herbal medicine (CHM) is a type of complementary and alternative medicine (CAM) that has been widely applied in the healthcare system in Taiwan. The aim of this study was to investigate the frequency of use and patterns of prescription for the CHM-based treatment of HIV-infected patients and to assess the long-term effects of CHM on hyperlipidemia and cardiovascular disease events in these patients. We identified 21,846 HIV-infected patients (ICD-9-CM: 042-044, 079, and V08 codes). Of these, 1083 and 2166 patients who used CHM and were non-users, respectively, were matched for age, gender, and ART use before CHM. The chi-squared test, Cox proportional hazard model, Kaplan-Meier method, and the log-rank test were used for comparisons between these two groups. CHM users had a lower risk of hyperlipidemia compared with non-users after adjusting for comorbidities by using a multivariate Cox proportional hazard model (P = 0.0011; HR: 0.66, 95% CI: 0.52-0.85). In addition, the CHM users had a lower risk of cardiovascular disease compared with non-users after adjusting for comorbidities (P = 0.0004; HR: 0.67, 95% CI: 0.53-0.83). The 10-year cumulative incidences of hyperlipidemia and cardiovascular disease were lower in the CHM group (P < 0.0001 for both, log rank test). Among the 12 most commonly used CHMs in these patients, Jia-Wei-Xiao-Yao-San (JWXYS) (46.1%), Ge-Gen-Tang (GGT) (40.6%), and Yin-Qiao-San (YQS) (38.0%) were the most common herbal formulas used. Huang-Qin (HQin) (44.6%), Yan-Hu-Suo (YHS) (40.5%), and Jie-Geng (JG) (39.5%) were the most commonly used single herbs. A CHM network analysis showed that JG was the core CHM in one cluster, and BM, MXSGT, and HQin were important CHMs in that cluster. In the other cluster, YHS was the core CHM, and SYGCT and JWXYS were important CHMs. CHM as adjunctive therapy may reduce hyperlipidemia and the risk for cardiovascular disease in HIV-infected patients. The list of the comprehensive herbal medicines that the patients used might be useful in further scientific investigations or therapeutic interventions for preventing atherosclerosis among HIV-infected patients. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of a two-body wet abrasion test method with attention to the effects of reused abradant

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blau, Peter Julian; Dehoff, Ryan R

2012-01-01

Abrasive wear is among the most common and costliest causes for material wastage, and it occurs in many forms. A simple method has been developed to quantify the response of metals and alloys to two-body wet abrasion. A metallographic polishing machine was modified to create a disk-on-flat sliding test rig. Adhesive-backed SiC grinding papers were used under fixed load and speed to rank the abrasive wear of seven alloy steels, some of which are candidates for drill cones for geothermal drilling. Standardized two-body abrasion tests, like those described in ASTM G132, feed unused abrasive into the contact; however, the currentmore » work investigated whether useful rankings could still be obtained with a simpler testing configuration in which specimens repeatedly slide on the same wear path under water-lubricated conditions. Tests using abrasive grit sizes of 120 and 180 resulted in the same relative ranking of the alloys although the coarser grit produced more total wear. Wear decreased when the same abrasive disk was re-used for up to five runs, but the relative rankings of the steels remained the same. This procedure was presented to ASTM Committee G2 on Wear and Erosion as a potential standard test for wet two-body abrasive wear.« less

Association of single nucleotide polymorphisms in promoter of matrix metalloproteinase-2, 8 genes with bladder cancer risk in Northern India.

PubMed

Srivastava, Priyanka; Kapoor, Rakesh; Mittal, Rama D

2013-02-01

Matrix metalloproteinases (MMPs) are expressed in melanocytes and their overexpression has been linked to tumor development, progression, and metastasis. At the genetic level, following functional promoter polymorphisms are known to modify the gene transcription: -1306 C > T, -735 C > T in MMP2, and 799 C > T in MMP8 gene. Hence we hypothesize that functional polymorphisms in the 2 MMP SNPs in promoter region may modulate the risk for bladder cancer (BC) progression in North Indian population. Genotyping for these polymorphisms were done in a group of 200 BC and 200 age matched, similar ethnicity unrelated healthy controls using PCR-based methods. Two-sided χ(2), Cox-regression was utilized to evaluate the associations between genotype and various clinical and epidemiologic factors. Multivariate analyses were conducted using logistic regression, adjusting for known BC confounders such as age and gender. Survival analysis was done using the Kaplan-Meier method and differences in survival were assessed using the log rank test. Individuals with MMP2 (-1306) TT genotype as well as T allele were at higher risk of BC (P, 0.042; OR, 2.85; P, 0.001; OR, 1.76). This effect was even more apparent in case of CT+TT (P < 0.001; OR, 2.61). In MMP2 (735), CT+TT demonstrated significant risk (P, 0.034; OR, 1.66). In MMP8 (799), reduced risk was observed with TT genotype (P, 0.006; OR, 0.27). Haplotype analysis showed that individuals with haplotype 735C-1306T and 735T-1306C were at 1.9- and 1.5-fold higher risk. MMP2 -1306CC in combination with MMP8 799CT genotype showed protective effect. The genotype CT and CT+TT of MMP2 1306C > T were associated with high risk of recurrence in BCG treated patients (HR, 4.32; P, 0.006 and HR, 2.06; P, 0.047) thus showing reduced recurrence free survival (CT+TT/CC = 34/45 months; log rank P, 0.039). Our data suggested that variant allele of MMP2 1306C > T was associated with high risk of tumor recurrence and reduced recurrence free survival in superficial BC patients. Copyright © 2013 Elsevier Inc. All rights reserved.

Effect of PR interval prolongation on long-term outcomes in patients with left bundle branch block vs non-left bundle branch block morphologies undergoing cardiac resynchronization therapy.

PubMed

Rickard, John; Karim, Mohammad; Baranowski, Bryan; Cantillon, Daniel; Spragg, David; Tang, W H Wilson; Niebauer, Mark; Grimm, Richard; Trulock, Kevin; Wilkoff, Bruce; Varma, Niraj

2017-10-01

Although the influence of QRS duration (QRSd) and/or bundle branch block morphology on outcomes of cardiac resynchronization therapy (CRT) have been well studied, the effect of PR interval remains uncertain. The purpose of this study was to evaluate the impact of PR prolongation (PRp) before CRT on long-term outcomes, specifically taking into account bundle branch block morphology and QRSd. We extracted clinical data on consecutive patients undergoing CRT. Multivariate models were constructed to analyze the effect of PRp (≥200 ms) on the combined endpoint of death, heart transplant, or left ventricular assist device. Kaplan-Meier curves were constructed stratifying patients based on bundle branch block and QRSd (dichotomized by 150 ms). Of the 472 patients who met inclusion criteria, 197 (41.7%) had PR interval ≥200 ms. During follow-up (mean 5.1 ± 2.6 years) there were 214 endpoints, of which 109 (23.1%) occurred in patients with PRp. In multivariate analysis, PRp was independently associated with worsened outcomes (hazard ratio 1.34, 95% confidence interval 1.01-1.77, P = .04). When stratified by bundle branch block morphology, PRp was significantly associated with worsened outcomes (log-rank P <.001) in patients with LBBB but not in those with non-LBBB (log-rank P = .55). Among patients with LBBB, stratified by QRSd, patients without PRp had improved outcomes compared to those with PRp independent of QRSd (log-rank P <.001). PRp is an independent predictor of impaired long-term outcome after CRT among patients with LBBB but not in non-LBBB patients. Notably, among LBBB patients, PRp is a more important predictor than QRSd in assessing long-term outcomes. Copyright © 2017. Published by Elsevier Inc.

Improved survival of patients with hepatocellular carcinoma and compensated hepatitis C virus-related cirrhosis who attained sustained virological response.

PubMed

Bruno, Savino; Di Marco, Vito; Iavarone, Massimo; Roffi, Luigi; Boccaccio, Vincenzo; Crosignani, Andrea; Cabibbo, Giuseppe; Rossi, Sonia; Calvaruso, Vincenza; Aghemo, Alessio; Giacomelli, Luca; Craxì, Antonio; Colombo, Massimo; Maisonneuve, Patrick

2017-10-01

Few studies examined the outcome of patients with hepatitis C virus (HCV)-related cirrhosis who developed hepatocellular carcinoma (HCC). The relative weight as determinant of death for cancer vs end-stage liver disease (ESLD) and the benefit of HCV eradication remain undefined. This multicentre, retrospective analysis evaluates overall survival (OS), rate of decompensation and tumour recurrence in compensated HCC patients treated with interferon (IFN) according to HCV status since HCC diagnosis. Two groups of patients with HCV-related cirrhosis and HCC were followed since HCC diagnosis: (i) compensated cirrhotics with prior sustained virological response (SVR) on IFN-based regimens (N=19); (ii) compensated cirrhotics without SVR (viraemic) (N=156). Over a median follow-up of 3.0 years since the onset of HCC, OS was longer for HCC patients with SVR than for viraemic patients (log-rank P=.004). The 5-year OS rate was 65.9% in patients with SVR vs 31.9% in viraemic patients. Similar trends were reported for hepatic decompensation (log-rank P=.01) and tumour recurrence (log-rank P=.01). These findings were confirmed at multivariable and propensity score analysis. At propensity analysis, 0/19 compensated patients with SVR died for ESLD vs 7/19 (37%) viraemic patients (P=.004). HCC mortality was similar in the two groups. Hepatocellular carcinoma patients with prior SVR and compensated cirrhosis at the time of tumour diagnosis have prolonged OS than viraemic patients. Given the lack of cirrhosis progression, no SVR patient ultimately died for ESLD while this condition appears the main cause of death among viraemic patients. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

EGFR and AKT1 overexpression are mutually exclusive and associated with a poor survival in resected gastric adenocarcinomas.

PubMed

Petrini, Iacopo; Lencioni, Monica; Vasile, Enrico; Fornaro, Lorenzo; Belluomini, Lorenzo; Pasquini, Giulia; Ginocchi, Laura; Caparello, Chiara; Musettini, Gianna; Vivaldi, Caterina; Caponi, Sara; Ricci, Sergio; Proietti, Agenese; Fontanini, Gabriella; Naccarato, Antonio Giuseppe; Nardini, Vincenzo; Santi, Stefano; Falcone, Alfredo

2018-02-14

The evaluation of molecular targets in gastric cancer has demonstrated the predictive role of HER2 amplification for trastuzumab treatment in metastatic gastric cancer. Besides HER2, other molecular targets are under evaluation in metastatic gastric tumors. However, very little is known about their role in resected tumors. We evaluated the expression of HER2, EGFR, MET, AKT1 and phospho-mTOR in resected stage II-III adenocarcinomas. Ninety-two patients with resected stomach (63%) or gastro-esophageal adenocarcinomas (27%) were evaluated. Antibodies anti-HER2, EGFR, MET, AKT1 and phospho-mTOR were used for immunostaining of formalin-fixed paraffin-embedded slides. Using FISH, HER2 amplification was evaluated in cases with an intermediate (+2) staining. EGFR overexpression (11%) was a poor prognostic factor for overall survival (3-year OS: 47% vs 77%; Log-Rank p= 0.033). MET overexpression (36%) was associated with a trend for a worse survival (3-year OS: 65% vs 77%; Log-Rank p= 0.084). HER2 amplification/overexpression and mTOR hyper-phosphorylation were observed in 13% and 48% of tumors, respectively. AKT1 overexpression (8%) was not a prognostic factor by itself (p= 0.234). AKT1 and EGFR overexpression was mutually exclusive and patients with EGFR or AKT1 overexpression experienced a poor prognosis (3-year OS: 52% vs. 79%, Log-Rank p= 0.005). EGFR is confirmed a poor prognostic factor in resected gastric cancers. We firstly describe a mutually exclusive overexpression of EGFR and AKT1 with potential prognostic implications, suggesting the relevance of this pathway for the growth of gastric cancers.

Determination of real-time polymerase chain reaction uncertainty of measurement using replicate analysis and a graphical user interface with Fieller’s theorem

PubMed Central

Stuart, James Ian; Delport, Johan; Lannigan, Robert; Zahariadis, George

2014-01-01

BACKGROUND: Disease monitoring of viruses using real-time polymerase chain reaction (PCR) requires knowledge of the precision of the test to determine what constitutes a significant change. Calculation of quantitative PCR confidence limits requires bivariate statistical methods. OBJECTIVE: To develop a simple-to-use graphical user interface to determine the uncertainty of measurement (UOM) of BK virus, cytomegalovirus (CMV) and Epstein-Barr virus (EBV) real-time PCR assays. METHODS: Thirty positive clinical samples for each of the three viral assays were repeated once. A graphical user interface was developed using a spreadsheet (Excel, Microsoft Corporation, USA) to enable data entry and calculation of the UOM (according to Fieller’s theorem) and PCR efficiency. RESULTS: The confidence limits for the BK virus, CMV and EBV tests were ∼0.5 log, 0.5 log to 1.0 log, and 0.5 log to 1.0 log, respectively. The efficiencies of these assays, in the same order were 105%, 119% and 90%. The confidence limits remained stable over the linear range of all three tests. DISCUSSION: A >5 fold (0.7 log) and a >3-fold (0.5 log) change in viral load were significant for CMV and EBV when the results were ≤1000 copies/mL and >1000 copies/mL, respectively. A >3-fold (0.5 log) change in viral load was significant for BK virus over its entire linear range. PCR efficiency was ideal for BK virus and EBV but not CMV. Standardized international reference materials and shared reporting of UOM among laboratories are required for the development of treatment guidelines for BK virus, CMV and EBV in the context of changes in viral load. PMID:25285125

The relation of functional visual acuity measurement methodology to tear functions and ocular surface status.

PubMed

Kaido, Minako; Ishida, Reiko; Dogru, Murat; Tsubota, Kazuo

2011-09-01

To investigate the relation of functional visual acuity (FVA) measurements with dry eye test parameters and to compare the testing methods with and without blink suppression and anesthetic instillation. A prospective comparative case series. Thirty right eyes of 30 dry eye patients and 25 right eyes of 25 normal subjects seen at Keio University School of Medicine, Department of Ophthalmology were studied. FVA testing was performed using a FVA measurement system with two different approaches, one in which measurements were made under natural blinking conditions without topical anesthesia (FVA-N) and the other in which the measurements were made under the blink suppression condition with topical anesthetic eye drops (FVA-BS). Tear function examinations, such as the Schirmer test, tear film break-up time, and fluorescein and Rose Bengal vital staining as ocular surface evaluation, were performed. The mean logMAR FVA-N scores and logMAR Landolt visual acuity scores were significantly lower in the dry eye subjects than in the healthy controls (p < 0.05), while there were no statistical differences between the logMAR FVA-BS scores of the dry eye subjects and those of the healthy controls. There was a significant correlation between the logMAR Landolt visual acuities and the logMAR FVA-N and logMAR FVA-BS scores. The FVA-N scores correlated significantly with tear quantities, tear stability and, especially, the ocular surface vital staining scores. FVA measurements performed under natural blinking significantly reflected the tear functions and ocular surface status of the eye and would appear to be a reliable method of FVA testing. FVA measurement is also an accurate predictor of dry eye status.

A new formulation of Gamma Delta Tocotrienol has superior bioavailability compared to existing Tocotrienol-Rich Fraction in healthy human subjects.

PubMed

Meganathan, Puvaneswari; Jabir, Rafid Salim; Fuang, Ho Gwo; Bhoo-Pathy, Nirmala; Choudhury, Roma Basu; Taib, Nur Aishah; Nesaretnam, Kalanithi; Chik, Zamri

2015-09-01

Gamma and delta tocotrienols are isomers of Vitamin E with established potency in pre-clinical anti-cancer research. This single-dose, randomized, crossover study aimed to compare the safety and bioavailability of a new formulation of Gamma Delta Tocotrienol (GDT) in comparison with the existing Tocotrienol-rich Fraction (TRF) in terms of gamma and delta isomers in healthy volunteers. Subjects were given either two 300 mg GDT (450 mg γ-T3 and 150 mg δ-T3) capsules or four 200 mg TRF (451.2 mg γ-T3 &102.72 mg δ-T3) capsules and blood samples were taken at several time points over 24 hours. Plasma tocotrienol concentrations were determined using HPLC method. The 90% CI for gamma and delta tocotrienols for the ratio of log-transformation of GDT/TRF for Cmax and AUC0-∞ (values were anti-logged and expressed as a percentage) were beyond the bioequivalence limits (106.21-195.46, 154.11-195.93 and 52.35-99.66, 74.82-89.44 respectively). The Wilcoxon Signed Rank Test for Tmax did not show any significant difference between GDT and TRF for both isomers (p > 0.05). No adverse events were reported during the entire period of study. GDT was found not bioequivalent to TRF, in terms of AUC and Cmax. Gamma tocotrienol in GDT showed superior bioavailability whilst delta tocotrienol showed less bioavailability compared to TRF.

Analysis of the Hessian for Inverse Scattering Problems. Part 3. Inverse Medium Scattering of Electromagnetic Waves in Three Dimensions

DTIC Science & Technology

2012-08-01

small data noise and model error, the discrete Hessian can be approximated by a low-rank matrix. This in turn enables fast solution of an appropriately...implication of the compactness of the Hessian is that for small data noise and model error, the discrete Hessian can be approximated by a low-rank matrix. This...probability distribution is given by the inverse of the Hessian of the negative log likelihood function. For Gaussian data noise and model error, this

Type I error rates of rare single nucleotide variants are inflated in tests of association with non-normally distributed traits using simple linear regression methods.

PubMed

Schwantes-An, Tae-Hwi; Sung, Heejong; Sabourin, Jeremy A; Justice, Cristina M; Sorant, Alexa J M; Wilson, Alexander F

2016-01-01

In this study, the effects of (a) the minor allele frequency of the single nucleotide variant (SNV), (b) the degree of departure from normality of the trait, and (c) the position of the SNVs on type I error rates were investigated in the Genetic Analysis Workshop (GAW) 19 whole exome sequence data. To test the distribution of the type I error rate, 5 simulated traits were considered: standard normal and gamma distributed traits; 2 transformed versions of the gamma trait (log 10 and rank-based inverse normal transformations); and trait Q1 provided by GAW 19. Each trait was tested with 313,340 SNVs. Tests of association were performed with simple linear regression and average type I error rates were determined for minor allele frequency classes. Rare SNVs (minor allele frequency < 0.05) showed inflated type I error rates for non-normally distributed traits that increased as the minor allele frequency decreased. The inflation of average type I error rates increased as the significance threshold decreased. Normally distributed traits did not show inflated type I error rates with respect to the minor allele frequency for rare SNVs. There was no consistent effect of transformation on the uniformity of the distribution of the location of SNVs with a type I error.

Effectiveness of combined macular buckle under direct vision and vitrectomy with ILM peeling in refractory macular hole retinal detachment with extreme high axial myopia: a 24-month comparative study

PubMed Central

Ma, Jin; Li, Honghui; Ding, Xiaohu; Tanumiharjo, Silvia; Lu, Lin

2017-01-01

Purpose To evaluate the efficacy of a combined macular buckle under direct vision and 23-gauge pars plana vitrectomy (PPV) with internal limiting membrane (ILM) peeling in refractory macular hole retinal detachment (MHRD) with extreme high axial myopia. Design Prospective, randomised controlled study. Participants The study included 98 eyes of 98 patients of MHRD with extreme high axial (>30 mm) myopia. Intervention Patients were randomly assigned to undergo PPV with ILM peeling (group 1, n=52) or PPV with ILM peeling combined with macular buckle under direct vision (group 2, n=46). Main outcome measures Complete ocular examination included best-corrected visual acuity (BCVA) (LogMAR), applanation tonometry, optical biometry, slit-lamp biomicroscopy, colour fundus photography, ultrasound examination and optical coherence tomography at baseline and every follow-up visit. Results Initial retinal reattachment rate was significantly higher in group 2 than in group 1 at 12-month postoperatively (χ2 test, p=0.020). Macular hole closure rate in group 2 was significantly higher than that in group 1 at 3, 12, 18 and 24 months postoperatively (Fisher's exact test, p<0.05). In initial retinal reattachment cases, the mean BCVA decreased significantly in group 2 than in group 1 at 3 months postoperatively (Wilcoxon matched pairs signed rank test, p=0.036), and had increased significantly in group 2 than in group 1 since 6 months postoperatively (Wilcoxon matched pairs signed rank test, p<0.05). Mean axial lengths in group 2 were significantly shorter than that of group 1 at each follow-up time point (Wilcoxon matched pairs signed rank test, p<0.05). Conclusions Combined macular buckle under direct vision and PPV with ILM peeling is more effective in treatment of MHRD with extreme high axial (>30 mm) myopia. PMID:28292775

Evaluation of resveratrol, green tea extract, curcumin, oxaloacetic acid, and medium-chain triglyceride oil on life span of genetically heterogeneous mice.

PubMed

Strong, Randy; Miller, Richard A; Astle, Clinton M; Baur, Joseph A; de Cabo, Rafael; Fernandez, Elizabeth; Guo, Wen; Javors, Martin; Kirkland, James L; Nelson, James F; Sinclair, David A; Teter, Bruce; Williams, David; Zaveri, Nurulain; Nadon, Nancy L; Harrison, David E

2013-01-01

The National Institute on Aging Interventions Testing Program (ITP) was established to evaluate agents that are hypothesized to increase life span and/or health span in genetically heterogeneous mice. Each compound is tested in parallel at three test sites. It is the goal of the ITP to publish all results, negative or positive. We report here on the results of lifelong treatment of mice, beginning at 4 months of age, with each of five agents, that is, green tea extract (GTE), curcumin, oxaloacetic acid, medium-chain triglyceride oil, and resveratrol, on the life span of genetically heterogeneous mice. Each agent was administered beginning at 4 months of age. None of these five agents had a statistically significant effect on life span of male or female mice, by log-rank test, at the concentrations tested, although a secondary analysis suggested that GTE might diminish the risk of midlife deaths in females only.

Evaluation of Resveratrol, Green Tea Extract, Curcumin, Oxaloacetic Acid, and Medium-Chain Triglyceride Oil on Life Span of Genetically Heterogeneous Mice

PubMed Central

Miller, Richard A.; Astle, Clinton M.; Baur, Joseph A.; de Cabo, Rafael; Fernandez, Elizabeth; Guo, Wen; Javors, Martin; Kirkland, James L.; Nelson, James F.; Sinclair, David A.; Teter, Bruce; Williams, David; Zaveri, Nurulain; Nadon, Nancy L.; Harrison, David E.

2013-01-01

The National Institute on Aging Interventions Testing Program (ITP) was established to evaluate agents that are hypothesized to increase life span and/or health span in genetically heterogeneous mice. Each compound is tested in parallel at three test sites. It is the goal of the ITP to publish all results, negative or positive. We report here on the results of lifelong treatment of mice, beginning at 4 months of age, with each of five agents, that is, green tea extract (GTE), curcumin, oxaloacetic acid, medium-chain triglyceride oil, and resveratrol, on the life span of genetically heterogeneous mice. Each agent was administered beginning at 4 months of age. None of these five agents had a statistically significant effect on life span of male or female mice, by log-rank test, at the concentrations tested, although a secondary analysis suggested that GTE might diminish the risk of midlife deaths in females only. PMID:22451473

Monte Carlo simulations guided by imaging to predict the in vitro ranking of radiosensitizing nanoparticles

PubMed Central

Retif, Paul; Reinhard, Aurélie; Paquot, Héna; Jouan-Hureaux, Valérie; Chateau, Alicia; Sancey, Lucie; Barberi-Heyob, Muriel; Pinel, Sophie; Bastogne, Thierry

2016-01-01

This article addresses the in silico–in vitro prediction issue of organometallic nanoparticles (NPs)-based radiosensitization enhancement. The goal was to carry out computational experiments to quickly identify efficient nanostructures and then to preferentially select the most promising ones for the subsequent in vivo studies. To this aim, this interdisciplinary article introduces a new theoretical Monte Carlo computational ranking method and tests it using 3 different organometallic NPs in terms of size and composition. While the ranking predicted in a classical theoretical scenario did not fit the reference results at all, in contrast, we showed for the first time how our accelerated in silico virtual screening method, based on basic in vitro experimental data (which takes into account the NPs cell biodistribution), was able to predict a relevant ranking in accordance with in vitro clonogenic efficiency. This corroborates the pertinence of such a prior ranking method that could speed up the preclinical development of NPs in radiation therapy. PMID:27920524

Monte Carlo simulations guided by imaging to predict the in vitro ranking of radiosensitizing nanoparticles.

PubMed

Retif, Paul; Reinhard, Aurélie; Paquot, Héna; Jouan-Hureaux, Valérie; Chateau, Alicia; Sancey, Lucie; Barberi-Heyob, Muriel; Pinel, Sophie; Bastogne, Thierry

This article addresses the in silico-in vitro prediction issue of organometallic nanoparticles (NPs)-based radiosensitization enhancement. The goal was to carry out computational experiments to quickly identify efficient nanostructures and then to preferentially select the most promising ones for the subsequent in vivo studies. To this aim, this interdisciplinary article introduces a new theoretical Monte Carlo computational ranking method and tests it using 3 different organometallic NPs in terms of size and composition. While the ranking predicted in a classical theoretical scenario did not fit the reference results at all, in contrast, we showed for the first time how our accelerated in silico virtual screening method, based on basic in vitro experimental data (which takes into account the NPs cell biodistribution), was able to predict a relevant ranking in accordance with in vitro clonogenic efficiency. This corroborates the pertinence of such a prior ranking method that could speed up the preclinical development of NPs in radiation therapy.

Psychophysical assessment of low visual function in patients with retinal degenerative diseases (RDDs) with the Diagnosys full-field stimulus threshold (D-FST).

PubMed

Klein, M; Birch, D G

2009-12-01

To determine whether the Diagnosys full-field stimulus threshold (D-FST) is a valid, sensitive and repeatable psychophysical method of measuring and following visual function in low-vision subjects. Fifty-three affected eyes of 42 subjects with severe retinal degenerative diseases (RDDs) were tested with achromatic stimuli on the D-FST. Included were subjects who were either unable to perform a static perimetric field or had non-detectable or sub-microvolt electroretinograms (ERGs). A subset of 21 eyes of 17 subjects was tested on both the D-FST and the FST2, a previous established full-field threshold test. Seven eyes of 7 normal control subjects were tested on both the D-FST and the FST2. Results for the two methods were compared with the Bland-Altman test. On the D-FST, a threshold could successfully be determined for 13 of 14 eyes with light perception (LP) only (median 0.9 +/- 1.4 log cd/m2), and all eyes determined to be counting fingers (CF; median 0.3 +/- 1.8 log cd/m2). The median full-field threshold for the normal controls was -4.3 +/- 0.6 log cd/m2 on the D-FST and -4.8 +/- 0.9 log cd/m2 on the FST2. The D-FST offers a commercially available method with a robust psychophysical algorithm and is a useful tool for following visual function in low vision subjects.

The Integral Method, a new approach to quantify bactericidal activity.

PubMed

Gottardi, Waldemar; Pfleiderer, Jörg; Nagl, Markus

2015-08-01

The bactericidal activity (BA) of antimicrobial agents is generally derived from the results of killing assays. A reliable quantitative characterization and particularly a comparison of these substances, however, are impossible with this information. We here propose a new method that takes into account the course of the complete killing curve for assaying BA and that allows a clear-cut quantitative comparison of antimicrobial agents with only one number. The new Integral Method, based on the reciprocal area below the killing curve, reliably calculates an average BA [log10 CFU/min] and, by implementation of the agent's concentration C, the average specific bactericidal activity SBA=BA/C [log10 CFU/min/mM]. Based on experimental killing data, the pertaining BA and SBA values of exemplary active halogen compounds were established, allowing quantitative assertions. N-chlorotaurine (NCT), chloramine T (CAT), monochloramine (NH2Cl), and iodine (I2) showed extremely diverging SBA values of 0.0020±0.0005, 1.11±0.15, 3.49±0.22, and 291±137log10 CFU/min/mM, respectively, against Staphylococcus aureus. This immediately demonstrates an approximately 550-fold stronger activity of CAT, 1730-fold of NH2Cl, and 150,000-fold of I2 compared to NCT. The inferred quantitative assertions and conclusions prove the new method suitable for characterizing bactericidal activity. Its application comprises the effect of defined agents on various bacteria, the consequence of temperature shifts, the influence of varying drug structure, dose-effect relationships, ranking of isosteric agents, comparison of competing commercial antimicrobial formulations, and the effect of additives. Copyright © 2015 Elsevier B.V. All rights reserved.

Epileptic Seizure Detection with Log-Euclidean Gaussian Kernel-Based Sparse Representation.

PubMed

Yuan, Shasha; Zhou, Weidong; Wu, Qi; Zhang, Yanli

2016-05-01

Epileptic seizure detection plays an important role in the diagnosis of epilepsy and reducing the massive workload of reviewing electroencephalography (EEG) recordings. In this work, a novel algorithm is developed to detect seizures employing log-Euclidean Gaussian kernel-based sparse representation (SR) in long-term EEG recordings. Unlike the traditional SR for vector data in Euclidean space, the log-Euclidean Gaussian kernel-based SR framework is proposed for seizure detection in the space of the symmetric positive definite (SPD) matrices, which form a Riemannian manifold. Since the Riemannian manifold is nonlinear, the log-Euclidean Gaussian kernel function is applied to embed it into a reproducing kernel Hilbert space (RKHS) for performing SR. The EEG signals of all channels are divided into epochs and the SPD matrices representing EEG epochs are generated by covariance descriptors. Then, the testing samples are sparsely coded over the dictionary composed by training samples utilizing log-Euclidean Gaussian kernel-based SR. The classification of testing samples is achieved by computing the minimal reconstructed residuals. The proposed method is evaluated on the Freiburg EEG dataset of 21 patients and shows its notable performance on both epoch-based and event-based assessments. Moreover, this method handles multiple channels of EEG recordings synchronously which is more speedy and efficient than traditional seizure detection methods.

Time of default in tuberculosis patients on directly observed treatment.

PubMed

Pardeshi, Geeta S

2010-09-01

Default remains an important challenge for the Revised National Tuberculosis Control Programme, which has achieved improved cure rates. This study describes the pattern of time of default in patients on DOTS. Tuberculosis Unit in District Tuberculosis Centre, Yavatmal, India; Retrospective cohort study. This analysis was done among the cohort of patients of registered at the Tuberculosis Unit during the year 2004. The time of default was assessed from the tuberculosis register. The sputum smear conversion and treatment outcome were also assessed. Kaplan-Meier plots and log rank tests. Overall, the default rate amongst the 716 patients registered at the Tuberculosis Unit was 10.33%. There was a significant difference in the default rate over time between the three DOTS categories (log rank statistic= 15.49, P=0.0004). Amongst the 331 smear-positive patients, the cumulative default rates at the end of intensive phase were 4% and 16%; while by end of treatment period, the default rates were 6% and 31% in category I and category II, respectively. A majority of the smear-positive patients in category II belonged to the group 'treatment after default' (56/95), and 30% of them defaulted during re-treatment. The sputum smear conversion rate at the end of intensive phase was 84%. Amongst 36 patients without smear conversion at the end of intensive phase, 55% had treatment failure. Patients defaulting in intensive phase of treatment and without smear conversion at the end of intensive phase should be retrieved on a priority basis. Default constitutes not only a major reason for patients needing re-treatment but also a risk for repeated default.

Comparison of five-year outcome in African Americans versus Caucasians following percutaneous coronary intervention.

PubMed

Pradhan, Jyotiranjan; Schreiber, Theodore L; Niraj, Ashutosh; Veeranna, Vikas; Ramesh, Krithi; Saigh, Lisa; Afonso, Luis

2008-07-01

Studies regarding short-term outcomes after percutaneous coronary intervention (PCI) have reported no ethnic differences and data on long-term follow-up is conflicting and sparse. 730 consecutive patients (67% African American) undergoing PCI from January 1999 to December 2000 at a tertiary care center in Detroit, MI, were followed up. End points studied included either all cause mortality collected from Social Security Death Index or first hospital admission after the index procedure due to myocardial infarction(MI), congestive heart failure(CHF), and revascularization (PCI or coronary artery bypass graft surgery). African-Americans undergoing PCI had significant differences in baseline cardiovascular co-morbidity and were more likely to present with acute myocardial infarction than Caucasians. On Kaplan Meier survival analysis and log rank test, each ethnic group had equivalent survival for cumulative end points upto 6-month follow-up, however longer follow-up to 5 year was characterized by lower survival rate in African Americans compared to Caucasians (41% vs. 54%, log rank P 0.01). After adjustment for potential confounders, AA ethnicity (Adjusted HR 1.62, 95% CI 1.01-1.28, P 0.04) remained a predictor of adverse cardiac outcome (Death/MI/CHF) at five-year follow-up (Cox regression propensity adjusted hazard analysis). African American patients undergoing PCI had unfavorable baseline cardiovascular characteristics but comparable short-term outcome compared to whites. However, at 5-year follow-up, African Americans had worse clinical outcome, higher incidence of acute myocardial infarction, congestive heart failure and significantly lower long-term survival.

Simulated-use validation of a sponge ATP method for determining the adequacy of manual cleaning of endoscope channels.

PubMed

Alfa, Michelle J; Olson, Nancy

2016-05-04

The objective of this study was to validate the relative light unit (RLU) cut-off of adequate cleaning of flexible colonoscopes for an ATP (adenosine tri-phosphate) test kit that used a sponge channel collection method. This was a simulated-use study. The instrument channel segment of a flexible colonoscope was soiled with ATS (artificial test soil) containing approximately 8 Log10 Enterococcus faecalis and Pseudomonas aeruginosa/mL. Full cleaning, partial cleaning and no cleaning were evaluated for ATP, protein and bacterial residuals. Channel samples were collected using a sponge device to assess residual RLUs. Parallel colonoscopes inoculated and cleaned in the same manner were sampled using the flush method to quantitatively assess protein and bacterial residuals. The protein and viable count benchmarks for adequate cleaning were <6.4 ug/cm(2) and <4 Log10 cfu/cm(2). The negative controls for the instrument channel, over the course of the study remained low with on average 14 RLUs, 0.04 ug/cm(2) protein and 0.025 Log10 cfu/cm(2). Partial cleaning resulted in an average of 6601 RLUs, 3.99 ug/cm(2), 5.25 Log10 cfu/cm(2) E. faecalis and 4.48 Log10 cfu/cm(2) P. aeruginosa. After full cleaning, the average RLU was 29 (range 7-71 RLUs) and the average protein, E. faecalis and P. aeruginosa residuals were 0.23 ug/cm(2), 0.79 and 1.61 Log10 cfu/cm(2), respectively. The validated cut-off for acceptable manual cleaning was set at ≤100 RLUs for the sponge collected channel ATP test kit.

Petrophysical approach for S-wave velocity prediction based on brittleness index and total organic carbon of shale gas reservoir: A case study from Horn River Basin, Canada

NASA Astrophysics Data System (ADS)

Kim, Taeyoun; Hwang, Seho; Jang, Seonghyung

2017-01-01

When finding the "sweet spot" of a shale gas reservoir, it is essential to estimate the brittleness index (BI) and total organic carbon (TOC) of the formation. Particularly, the BI is one of the key factors in determining the crack propagation and crushing efficiency for hydraulic fracturing. There are several methods for estimating the BI of a formation, but most of them are empirical equations that are specific to particular rock types. We estimated the mineralogical BI based on elemental capture spectroscopy (ECS) log and elastic BI based on well log data, and we propose a new method for predicting S-wave velocity (VS) using mineralogical BI and elastic BI. The TOC is related to the gas content of shale gas reservoirs. Since it is difficult to perform core analysis for all intervals of shale gas reservoirs, we make empirical equations for the Horn River Basin, Canada, as well as TOC log using a linear relation between core-tested TOC and well log data. In addition, two empirical equations have been suggested for VS prediction based on density and gamma ray log used for TOC analysis. By applying the empirical equations proposed from the perspective of BI and TOC to another well log data and then comparing predicted VS log with real VS log, the validity of empirical equations suggested in this paper has been tested.

Implementation of preference ranking organization method for enrichment evaluation (Promethee) on selection system of student’s achievement

NASA Astrophysics Data System (ADS)

Karlitasari, L.; Suhartini, D.; Nurrosikawati, L.

2018-03-01

Selection of Student Achievement is conducted every year, starting from the level of Study Program, Faculty, to University, which then rank one will be sent to Kopertis level. The criteria made for the selection are Academic and Rich Scientific, Organizational, Personality, and English. In order for the selection of Student Achievement is Objective, then in addition to the presence of the jury is expected to use methods that support the decision to be more optimal in determining the Student Achievement. One method used is the Promethee Method. Preference Ranking Organization Method for Enrichment Evaluation (Promethee) is a method of ranking in Multi Criteria Decision Making (MCDM). PROMETHEE has the advantage that there is a preference type against the criteria that can take into account alternatives with other alternatives on the same criteria. The conjecture of alternate dominance over a criterion used in PROMETHEE is the use of values in the relationships between alternative ranking values. Based on the calculation result, from 7 applicants between Manual and Promethee Matrices, rank 1, 2, and 3, did not change, only 4 to 7 positions were changed. However, after the sensitivity test, almost all criteria experience a high level of sensitivity. Although it does not affect the students who will be sent to the next level, but can bring psychological impact on prospective student’s achievement

A denoising algorithm for CT image using low-rank sparse coding

NASA Astrophysics Data System (ADS)

Lei, Yang; Xu, Dong; Zhou, Zhengyang; Wang, Tonghe; Dong, Xue; Liu, Tian; Dhabaan, Anees; Curran, Walter J.; Yang, Xiaofeng

2018-03-01

We propose a denoising method of CT image based on low-rank sparse coding. The proposed method constructs an adaptive dictionary of image patches and estimates the sparse coding regularization parameters using the Bayesian interpretation. A low-rank approximation approach is used to simultaneously construct the dictionary and achieve sparse representation through clustering similar image patches. A variable-splitting scheme and a quadratic optimization are used to reconstruct CT image based on achieved sparse coefficients. We tested this denoising technology using phantom, brain and abdominal CT images. The experimental results showed that the proposed method delivers state-of-art denoising performance, both in terms of objective criteria and visual quality.

Predictive value of CHFR and MLH1 methylation in human gastric cancer.

PubMed

Li, Yazhuo; Yang, Yunsheng; Lu, Youyong; Herman, James G; Brock, Malcolm V; Zhao, Po; Guo, Mingzhou

2015-04-01

Gastric carcinoma (GC) has one of the highest mortality rates of cancer diseases and has a high incidence rate in China. Palliative chemotherapy is the main treatment for advanced gastric cancer. It is necessary to compare the effectiveness and toxicities of different regimens. This study explores the possibility of methylation of DNA damage repair genes serving as a prognostic and chemo-sensitive marker in human gastric cancer. The methylation status of five DNA damage repair genes (CHFR, FANCF, MGMT, MLH1, and RASSF1A) was detected by nested methylation-specific PCR in 102 paraffin-embedded gastric cancer samples. Chi-square or Fisher's exact tests were used to evaluate the association of methylation status and clinic-pathological factors. The Kaplan-Meier method and Cox proportional hazards models were employed to analyze the association of methylation status and chemo-sensitivity. The results indicate that CHFR, MLH1, RASSF1A, MGMT, and FANCF were methylated in 34.3% (35/102), 21.6% (22/102), 12.7% (13/102), 9.8% (10/102), and 0% (0/102) of samples, respectively. No association was found between methylation of CHFR, MLH1, RASSF1A, MGMT, or FANCF with gender, age, tumor size, tumor differentiation, lymph node metastasis, and TNM stage. In docetaxel-treated gastric cancer patients, resistance to docetaxel was found in CHFR unmethylated patients by Cox proportional hazards model (HR 0.243, 95% CI, 0.069-0.859, p = 0.028), and overall survival is longer in the CHFR methylated group compared with the CHFR unmethylated group (log-rank, p = 0.036). In oxaliplatin-treated gastric cancer patients, resistance to oxaliplatin was found in MLH1 methylated patients (HR 2.988, 95% CI, 1.064-8.394, p = 0.038), and overall survival was longer in the MLH1 unmethylated group compared with the MLH1 methylated group (log-rank, p = 0.046). CHFR is frequently methylated in human gastric cancer, and CHFR methylation may serve as a docetaxel-sensitive marker. MLH1 methylation was related to oxaliplatin resistance in gastric cancer patients.

Impact of heart rate in atrial fibrillation versus sinus rhythm on mortality in octogenarian patients with acute coronary syndrome

PubMed Central

Li, Shijun; Barywani, Salim; Fu, Michael

2017-01-01

Introduction Association of heart rate (HR) with mortality in patients with acute coronary syndrome (ACS) and aged ≥ 80 years are underrepresented in clinical trials. We therefore aimed to investigate the association of HR in atrial fibrillation (AF) versus sinus rhythm (SR) with all-cause mortality in octogenarian patients with ACS. Methods A total of 336 patients with ACS patients and aged ≥ 80 years were enrolled into the current study. The end point of interest was death from any cause. Association of HR in AF versus SR with mortality was analyzed by Kaplan-Meier curve following log-rank test and multivariable Cox regression analysis. Results In total, 63 (87.5%) of patients with AF were dead and 147 (59.8%) of patients with SR were dead during the follow-up period. The best cut-off was 80 bpm, with a sensitivity of 62% and specificity of 66%. HR ≤ 80 bpm in SR but not in AF was associated with better outcome as compared with HR > 80 bpm (Chi-Square = 26.55, Log rank P < 0.001). In SR subgroup, the hazard ratios of HR ≤ 80 bpm were 0.51(95% CI 0.37-0.70, P < 0.001) adjusted for age, 0.46 (95%CI 0.33-0.63, P < 0.001) adjusted for gender, 0.62 (95%CI 0.42- 0.93, P = 0.020) adjusted for multivariables respectively. In AF subgroup, the hazard ratios of HR ≤ 80 bpm were 0.83(95% CI 0.49-1.38, P = 0.464) adjusted for age, 0.96 (95%CI 0.59-1.58, P = 0.882) adjusted for gender, 0.72(95% CI 0.41-1.26, P = 0.249) adjusted for multivariables respectively. Conclusion The current study demonstrates that heart rate is an independent prognostic predictor for all-cause mortality, and HR ≤ 80 bpm is associated with improved outcome in SR but not in AF in octogenarian patients with ACS. PMID:29255559

Prognostic Role of Pre–Radiation Therapy {sup 18}F-Fluorodeoxyglucose Positron Emission Tomography for Primary Mediastinal B-Cell Lymphomas Treated with R-CHOP or R-CHOP-Like Chemotherapy Plus Radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Filippi, Andrea Riccardo, E-mail: andreariccardo.filippi@unito.it; Piva, Cristina; Levis, Mario

Purpose: To validate, in a monoinstitutional cohort with extended follow-up, that post–rituximab chemotherapy (R-CT) {sup 18}F-fluorodeoxyglucose positron emission tomography ({sup 18}FDG-PET) is a prognostic factor allowing discrimination of primary mediastinal B-cell lymphoma (PMBCL) patients at higher risk for progression after radiation therapy. Methods and Materials: We analyzed 51 patients, and {sup 18}FDG-PET scans were re-examined evaluating both the Deauville 5-point scale (D5PS) score and the standardized uptake value (SUV) of residual activity, if present. These parameters were then tested by univariate analysis for a potential correlation with progression-free survival (PFS) as the primary study endpoint. Results: Median follow-up time was 51 monthsmore » (range, 9-153 months). After R-CT, D5PS score was 1 in 10 (19.6%), 2 in 11 (21.6%), 3 in 7 (13.8%), 4 in 17 (33.3%), and 5 in 6 patients (11.7%). Forty-three out of 51 patients (84.3%) had an SUV{sub max} ≤5, and 8 out of 51 (15.7%) had an SUV{sub max} ≥5. Overall, 6 patients experienced progression or relapse: 1 had a D5PS score 2 (with SUV{sub max} ≤5), and 5 had a D5PS score 5 (and SUV{sub max} ≥5). Patients with a D5PS score 5 showed significantly lower PFS rates versus all other scores (log-rank P<.001), as did patients with SUV{sub max} ≥5 when compared with those with SUV{sub max} ≤5 (log-rank P<.001). Conclusions: The present study confirmed the prognostic role of {sup 18}FDG-PET after R-CT, with patients with a D5PS score of 5 and/or an SUV{sub max} ≥5 being at high risk of progression/relapse after RT.« less

Pretreatment 18F-FDG PET Textural Features in Locally Advanced Non-Small Cell Lung Cancer: Secondary Analysis of ACRIN 6668/RTOG 0235.

PubMed

Ohri, Nitin; Duan, Fenghai; Snyder, Bradley S; Wei, Bo; Machtay, Mitchell; Alavi, Abass; Siegel, Barry A; Johnson, Douglas W; Bradley, Jeffrey D; DeNittis, Albert; Werner-Wasik, Maria; El Naqa, Issam

2016-06-01

In a secondary analysis of American College of Radiology Imaging Network (ACRIN) 6668/RTOG 0235, high pretreatment metabolic tumor volume (MTV) on (18)F-FDG PET was found to be a poor prognostic factor for patients treated with chemoradiotherapy for locally advanced non-small cell lung cancer (NSCLC). Here we utilize the same dataset to explore whether heterogeneity metrics based on PET textural features can provide additional prognostic information. Patients with locally advanced NSCLC underwent (18)F-FDG PET prior to treatment. A gradient-based segmentation tool was used to contour each patient's primary tumor. MTV, maximum SUV, and 43 textural features were extracted for each tumor. To address overfitting and high collinearity among PET features, the least absolute shrinkage and selection operator (LASSO) method was applied to identify features that were independent predictors of overall survival (OS) after adjusting for MTV. Recursive binary partitioning in a conditional inference framework was utilized to identify optimal thresholds. Kaplan-Meier curves and log-rank testing were used to compare outcomes among patient groups. Two hundred one patients met inclusion criteria. The LASSO procedure identified 1 textural feature (SumMean) as an independent predictor of OS. The optimal cutpoint for MTV was 93.3 cm(3), and the optimal SumMean cutpoint for tumors above 93.3 cm(3) was 0.018. This grouped patients into three categories: low tumor MTV (n = 155; median OS, 22.6 mo), high tumor MTV and high SumMean (n = 23; median OS, 20.0 mo), and high tumor MTV and low SumMean (n = 23; median OS, 6.2 mo; log-rank P < 0.001). We have described an appropriate methodology to evaluate the prognostic value of textural PET features in the context of established prognostic factors. We have also identified a promising feature that may have prognostic value in locally advanced NSCLC patients with large tumors who are treated with chemoradiotherapy. Validation studies are warranted. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Effectiveness of automated ultraviolet-C light for decontamination of textiles inoculated with Enterococcus faecium.

PubMed

Smolle, C; Huss, F; Lindblad, M; Reischies, F; Tano, E

2018-01-01

Healthcare textiles are increasingly recognized as potential vehicles for transmission of hospital-acquired infections. This study tested the ability of an automated ultraviolet-C (UV-C) room disinfection device (Tru-D Smart UV-C) to decontaminate textiles inoculated with Enterococcus faecium in a clinical setting. Contaminated polycotton (50/50 polyester/cotton) swatches were distributed to predefined locations in a ward room and exposed to UV-C light. UV-C decontamination reduced E. faecium counts by a mean log 10 reduction factor of 1.37 (all P = 0.005, Wilcoxon signed rank test). UV-C decontamination may be a feasible adjunctive measure to conventional laundering to preserve the cleanliness of healthcare textiles in ward rooms. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma

PubMed Central

Liu, Li; Dinu, Valentin

2018-01-01

Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway’s topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher’s exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC) and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several significant pathways in subtypes of HCC are HCC subtype-associated specifically. In conclusion, PoTRA is a new approach to explore and discover pathways involved in cancer. PoTRA can be used as a complement to other existing methods to broaden our understanding of the biological mechanisms behind cancer at the system-level. PMID:29666752

Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma.

PubMed

Li, Chaoxing; Liu, Li; Dinu, Valentin

2018-01-01

Complex diseases such as cancer are usually the result of a combination of environmental factors and one or several biological pathways consisting of sets of genes. Each biological pathway exerts its function by delivering signaling through the gene network. Theoretically, a pathway is supposed to have a robust topological structure under normal physiological conditions. However, the pathway's topological structure could be altered under some pathological condition. It is well known that a normal biological network includes a small number of well-connected hub nodes and a large number of nodes that are non-hubs. In addition, it is reported that the loss of connectivity is a common topological trait of cancer networks, which is an assumption of our method. Hence, from normal to cancer, the process of the network losing connectivity might be the process of disrupting the structure of the network, namely, the number of hub genes might be altered in cancer compared to that in normal or the distribution of topological ranks of genes might be altered. Based on this, we propose a new PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) to detect pathways involved in cancer. We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fisher's exact test to test if the number of hub genes in each pathway is altered from normal to cancer. Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer. Hence, we use the Kolmogorov-Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes. We apply PoTRA to study hepatocellular carcinoma (HCC) and several subtypes of HCC. Very interestingly, we discover that all significant pathways in HCC are cancer-associated generally, while several significant pathways in subtypes of HCC are HCC subtype-associated specifically. In conclusion, PoTRA is a new approach to explore and discover pathways involved in cancer. PoTRA can be used as a complement to other existing methods to broaden our understanding of the biological mechanisms behind cancer at the system-level.

The prediction of airborne and structure-borne noise potential for a tire

NASA Astrophysics Data System (ADS)

Sakamoto, Nicholas Y.

Tire/pavement interaction noise is a major component of both exterior pass-by noise and vehicle interior noise. The current testing methods for ranking tires from loud to quiet require expensive equipment, multiple tires, and/or long experimental set-up and run times. If a laboratory based off-vehicle test could be used to identify the airborne and structure-borne potential of a tire from its dynamic characteristics, a relative ranking of a large group of tires could be performed at relatively modest expense. This would provide a smaller sample set of tires for follow-up testing and thus save expense for automobile OEMs. The focus of this research was identifying key noise features from a tire/pavement experiment. These results were compared against a stationary tire test in which the natural response of the tire to a forced input was measured. Since speed was identified as having some effect on the noise, an input function was also developed to allow the tires to be ranked at an appropriate speed. A relative noise model was used on a second sample set of tires to verify if the ranking could be used against interior vehicle measurements. While overall level analysis of the specified spectrum had mixed success, important noise generating features were identified, and the methods used could be improved to develop a standard off-vehicle test to predict a tire's noise potential.

A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments.

PubMed

Heskes, Tom; Eisinga, Rob; Breitling, Rainer

2014-11-21

The rank product method is a powerful statistical technique for identifying differentially expressed molecules in replicated experiments. A critical issue in molecule selection is accurate calculation of the p-value of the rank product statistic to adequately address multiple testing. Both exact calculation and permutation and gamma approximations have been proposed to determine molecule-level significance. These current approaches have serious drawbacks as they are either computationally burdensome or provide inaccurate estimates in the tail of the p-value distribution. We derive strict lower and upper bounds to the exact p-value along with an accurate approximation that can be used to assess the significance of the rank product statistic in a computationally fast manner. The bounds and the proposed approximation are shown to provide far better accuracy over existing approximate methods in determining tail probabilities, with the slightly conservative upper bound protecting against false positives. We illustrate the proposed method in the context of a recently published analysis on transcriptomic profiling performed in blood. We provide a method to determine upper bounds and accurate approximate p-values of the rank product statistic. The proposed algorithm provides an order of magnitude increase in throughput as compared with current approaches and offers the opportunity to explore new application domains with even larger multiple testing issue. The R code is published in one of the Additional files and is available at http://www.ru.nl/publish/pages/726696/rankprodbounds.zip .

An ensemble rank learning approach for gene prioritization.

PubMed

Lee, Po-Feng; Soo, Von-Wun

2013-01-01

Several different computational approaches have been developed to solve the gene prioritization problem. We intend to use the ensemble boosting learning techniques to combine variant computational approaches for gene prioritization in order to improve the overall performance. In particular we add a heuristic weighting function to the Rankboost algorithm according to: 1) the absolute ranks generated by the adopted methods for a certain gene, and 2) the ranking relationship between all gene-pairs from each prioritization result. We select 13 known prostate cancer genes in OMIM database as training set and protein coding gene data in HGNC database as test set. We adopt the leave-one-out strategy for the ensemble rank boosting learning. The experimental results show that our ensemble learning approach outperforms the four gene-prioritization methods in ToppGene suite in the ranking results of the 13 known genes in terms of mean average precision, ROC and AUC measures.

Evaluation of a web-based ECG-interpretation programme for undergraduate medical students.

PubMed

Nilsson, Mikael; Bolinder, Gunilla; Held, Claes; Johansson, Bo-Lennart; Fors, Uno; Ostergren, Jan

2008-04-23

Most clinicians and teachers agree that knowledge about ECG is of importance in the medical curriculum. Students at Karolinska Institute have asked for more training in ECG-interpretation during their undergraduate studies. Clinical tutors, however, have difficulties in meeting these demands due to shortage of time. Thus, alternative ways to learn and practice ECG-interpretation are needed. Education offered via the Internet is readily available, geographically independent and flexible. Furthermore, the quality of education may increase and become more effective through a superior educational approach, improved visualization and interactivity. A Web-based comprehensive ECG-interpretation programme has been evaluated. Medical students from the sixth semester were given an optional opportunity to access the programme from the start of their course. Usage logs and an initial evaluation survey were obtained from each student. A diagnostic test was performed in order to assess the effect on skills in ECG interpretation. Students from the corresponding course, at another teaching hospital and without access to the ECG-programme but with conventional teaching of ECG served as a control group. 20 of the 32 students in the intervention group had tested the programme after 2 months. On a five-graded scale (1- bad to 5 - very good) they ranked the utility of a web-based programme for this purpose as 4.1 and the quality of the programme software as 3.9. At the diagnostic test (maximal points 16) by the end of the 5-month course at the 6th semester the mean result for the students in the intervention group was 9.7 compared with 8.1 for the control group (p = 0.03). Students ranked the Web-based ECG-interpretation programme as a useful instrument to learn ECG. Furthermore, Internet-delivered education may be more effective than traditional teaching methods due to greater immediacy, improved visualisation and interactivity.

Clinicopathological parameters associated with histological background and recurrence after surgical intervention of vocal cord leukoplakia.

PubMed

Cui, Weixin; Xu, Wen; Yang, Qingwen; Hu, Rong

2017-06-01

Histological examination of biopsy shows usefulness in the diagnosis of vocal cord leukoplakia; however, in considerable amount of cases, the examination cannot provide definitive diagnosis of malignancy from benign conditions such as hyperplasia and dysplasia. The present work therefore was aimed to identify clinicopathological factors and molecular markers predictive of recurrence and malignant transformation of vocal cord leukoplakia.Clinical data of 555 cases of vocal cord leukoplakia enrolled from July 1999 to June 2014 were analyzed. The cohort consisted of keratosis (n = 137), hyperplasia (n = 139), dysplasia (n = 177), and primary (n = 10) and invasive (n = 46) carcinoma. Correlations between patients' backgrounds, clinicopathological factors, molecular markers (p53, p16, Ki67, cytokeratin, and proliferating cell nuclear antigen), and histology backgrounds were examined using by Pearson Chi-squared or Fisher exact test. Reflux symptom index (RSI) and reflux finding score (RFS) before and after treatment were compared using Wilcoxon signed-rank test. Risk factors for disease recurrence were identified using Cox proportional hazards models of multivariate analysis. Time to recurrence was analyzed using log-rank test of Kaplan-Meier method.In the present cohort, alcohol drinking was found associated with GRBAS grade (P = .0258) and the site (P = .0298) of leukoplakia. For the different disease types, chief complaint (P = .0179), GRBAS grade (P = .0101), mucosal wave (P < .0001), and molecular markers p53 (P < .0001) and Ki67 (P < .0001) were identified as correlates. RSI and RFS were significantly lowered by surgical intervention. A single side of leukoplakia was predictive of a lower risk of recurrence (odds ratio, 0.378; 95% confidence interval, 0.197-0.723; P = .0033). Absence of mucosal wave was associated with a shorter time-to-recurrence (P = .0357).The present work identified clinicopathological factors and molecular markers associated with the different histology of vocal cord leukoplakia, and also the prognostic factor for the low risk of recurrence after surgery.

Contrasting OLS and Quantile Regression Approaches to Student "Growth" Percentiles

ERIC Educational Resources Information Center

Castellano, Katherine Elizabeth; Ho, Andrew Dean

2013-01-01

Regression methods can locate student test scores in a conditional distribution, given past scores. This article contrasts and clarifies two approaches to describing these locations in terms of readily interpretable percentile ranks or "conditional status percentile ranks." The first is Betebenner's quantile regression approach that results in…

Propensity score-matching analysis of hybrid video-assisted thoracoscopic surgery and thoracoscopic lobectomy for clinical stage I lung cancer†.

PubMed

Iwata, Hisashi; Shirahashi, Koyo; Yamamoto, Hirotaka; Marui, Tsutomu; Matsumoto, Shinsuke; Mizuno, Yoshimasa; Matsumoto, Mitsuyoshi; Mitta, Shohei; Miyamoto, Yusaku; Komuro, Hiroyasu

2016-04-01

Video-assisted thoracoscopic surgery (VATS) lobectomy is classified into hybrid VATS (direct and video vision) and thoracoscopic VATS (video vision only). In this study, the outcomes of hybrid VATS and thoracoscopic VATS for clinical stage I lung cancer were compared using a propensity score-matching analysis. Hybrid and thoracoscopic VATS were performed in 178 and 76 patients, respectively. Propensity scores were calculated using logistic regression analysis and matched within a score of ±0.03 for age, sex, size of tumour, Charlson comorbidity index, preoperative therapy, percent vital capacity, forced expiratory volume in 1 s, clinical stage, pathological stage and histology. In the non-matched analysis, the results for hybrid and thoracoscopic VATS, respectively, were as follows: mean age, 69 ± 9 and 66 ± 10 years (P = 0.04); tumour size, 24 ± 10 and 20 ± 7 mm (P < 0.01); 2-deoxy-2 [F-18]fluorodeoxyglucose positron emission tomography SUV, 5.6 ± 4.4 and 3.6 ± 3.2 (P < 0.01); clinical stage (IA/IB), 130/48 and 69/7 (P < 0.01); pathological stage (IA/IB/IIA and IIB/IIIA and IIIB), 89/56/15/18 and 57/14/2/3 (P < 0.01); postoperative complications, 66 (37.1%) and 16 (21.1%; P = 0.01); respiratory complications, 32 (18.0%) and 6 (7.9%; P = 0.04); 5-year overall survival (OS), 77.0 and 88.8% (log-rank P = 0.045); and 5-year disease-free survival (DFS), 67.2 and 81.1% (log-rank P = 0.02). In 66 matched cases, the results for hybrid and thoracoscopic VATS, respectively, were as follows: mean operative time, 245 ± 96 and 285 ± 85 min (P = 0.01); blood loss, 95 ± 100 and 86 ± 123 ml (P = 0.67); mean duration of drainage, 3.6 ± 2.7 and 3.2 ± 2.2 days (P = 0.37); postoperative complications, 21 (31.8%) and 14 (21.2%; P = 0.17); respiratory complications, 11 (16.7%) and 5 (7.6%; P = 0.11); 5-year OS, 72.5 and 86.0% (log-rank P = 0.25); and 5-year DFS, 68.4 and 77.2% (log-rank P = 0.17). In this single-institution, propensity score-matched study, hybrid VATS showed a shorter operative time and similar outcomes compared with thoracoscopic lobectomy for clinical stage IA lung cancer. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Four decades of the kidney transplantation program at the Institute Nacional de Ciencias Médicas y Nutrición Salvador Zubirán in Mexico City.

PubMed

Morales-Buenrostro, Luis E; Marino-Vázquez, Lluvia A; Alberú, Josefina

2009-01-01

This is a retrospective study that includes four decades of kidney transplant program at our Institute, with a total of 923 kidney transplants in 872 recipients. In this report, the effect of variables in recipient, donor, and transplant on long-term graft survival was analyzed using the Kaplan Meier method with log-rank test for survival comparisons. Global graft survival at our center-analyzed by censoring for death-with-functioning-graft-for 1, 5 and 10 years was 93%, 83% and 74%, respectively, with median survival of 24.5 years. When analyzed for all-cause graft loss, 1, 5 and 10 year survival was 90%, 76% and 61%, with 12.8-year median survival. Variables associated with lower graft survival censored for death-with-functioning-graft were transplantation in an earlier decade, less histocompatibility, younger kidney transplant recipients, no induction therapy, and double drug initial immunosuppression. After Cox's regression multivariate analysis, the risk factors that remained associated with worse survival were younger recipient, earlier transplant decade, and deceased donor.

Histological changes associated with neoadjuvant chemotherapy are predictive of nodal metastases in high-risk prostate cancer patients

PubMed Central

O’Brien, Catherine; True, Lawrence D.; Higano, Celestia S.; Rademacher, Brooks L. S.; Garzotto, Mark; Beer, Tomasz M.

2011-01-01

Clinical trials are evaluating the effect of neoadjuvant chemotherapy on men with high risk prostate cancer. Little is known about the clinical significance of post-chemotherapy tumor histopathology. We assessed the prognostic and predictive value of histological features (intraductal carcinoma, vacuolated cell morphology, inconspicuous glands, cribriform architecture, and inconspicuous cancer cells) observed in 50 high-risk prostate cancers treated with pre-prostatectomy docetaxel and mitoxantrone. At a median follow-up of 65 months, the overall relapse-free survival (RFS) at 2 and 5 years was 65% and 49%, respectively. In univariate analyses (using Kaplan-Meier method and log-rank tests) intraductal (p=0.001) and cribriform (p=0.014) histologies were associated with shorter RFS. In multivariate analyses, using Cox’s proportional hazards regression, baseline PSA (p=0.004), lymph node metastases (p<0.001), and cribriform histology (p=0.007) were associated with shorter RFS. In multivariable logistic regression analysis, only intraductal pattern (p=0.007) predicted lymph node metastases. Intraductal and cribriform histologies apparently predict post-chemotherapy outcome. PMID:20231619

KRAS polymorphisms are associated with survival of CRC in Chinese population.

PubMed

Dai, Qiong; Wei, Hui Lian; Huang, Juan; Zhou, Tie Jun; Chai, Li; Yang, Zhi-Hui

2016-04-01

rs12245, rs12587, rs9266, rs1137282, rs61764370, and rs712 of KRAS oncogene are characterized in the 3'UTR. The study highlights the important role of these polymorphisms playing in the susceptibility, oxaliplatin-based chemotherapy sensitivity, progression, and prognosis of CRC. Improved multiplex ligation detection reaction (iMLDR) technique is used for genotyping. An unconditional logistic regression model was used to estimate the association of certain polymorphism and CRC risk. The Kaplan-Meier method, log-rank test, and Cox regression model were used to evaluate the effects of polymorphisms on survival analysis. Results demonstrated that TT genotype and T allele of rs712 were associated with the increased risk of CRC; the patients with GG genotype and G allele of rs61764370 had a shorter survival and a higher risk of relapse or metastasis of CRC. Our studies supported the conclusions that rs61764370 and rs712 polymorphisms of the KRAS are functional and it may play an important role in the development of CRC and oxaliplatin-based chemotherapy efficiency and prognosis of CRC.

Hazard Ranking Method for Populations Exposed to Arsenic in Private Water Supplies: Relation to Bedrock Geology

PubMed Central

Close, Rebecca; Watts, Michael J.; Ander, E. Louise; Smedley, Pauline L.; Verlander, Neville Q.; Gregory, Martin; Middleton, Daniel R. S.; Polya, David A.; Studden, Mike; Leonardi, Giovanni S.

2017-01-01

Approximately one million people in the UK are served by private water supplies (PWS) where main municipal water supply system connection is not practical or where PWS is the preferred option. Chronic exposure to contaminants in PWS may have adverse effects on health. South West England is an area with elevated arsenic concentrations in groundwater and over 9000 domestic dwellings here are supplied by PWS. There remains uncertainty as to the extent of the population exposed to arsenic (As), and the factors predicting such exposure. We describe a hazard assessment model based on simplified geology with the potential to predict exposure to As in PWS. Households with a recorded PWS in Cornwall were recruited to take part in a water sampling programme from 2011 to 2013. Bedrock geologies were aggregated and classified into nine Simplified Bedrock Geological Categories (SBGC), plus a cross-cutting “mineralized” area. PWS were sampled by random selection within SBGCs and some 508 households volunteered for the study. Transformations of the data were explored to estimate the distribution of As concentrations for PWS by SBGC. Using the distribution per SBGC, we predict the proportion of dwellings that would be affected by high concentrations and rank the geologies according to hazard. Within most SBGCs, As concentrations were found to have log-normal distributions. Across these areas, the proportion of dwellings predicted to have drinking water over the prescribed concentration value (PCV) for As ranged from 0% to 20%. From these results, a pilot predictive model was developed calculating the proportion of PWS above the PCV for As and hazard ranking supports local decision making and prioritization. With further development and testing, this can help local authorities predict the number of dwellings that might fail the PCV for As, based on bedrock geology. The model presented here for Cornwall could be applied in areas with similar geologies. Application of the method requires independent validation and further groundwater-derived PWS sampling on other geological formations. PMID:29194429

Suitability of the line intersect method for sampling hardwood logging residues

Treesearch

A. Jeff Martin

1976-01-01

The line intersect method of sampling logging residues was tested in Appalachian hardwoods and was found to provide unbiased estimates of the volume of residue in cubic feet per acre. Thirty-two chains of sample line were established on each of sixteen 1-acre plots on cutover areas in a variety of conditions. Estimates from these samples were then compared to actual...

[Influence of WeChat platform on the compliance of continuous treatment of scar in adult burn patients].

PubMed

Wang, F; Zhang, H L

2018-03-20

Objective: To explore influence of the WeChat platform on the compliance of continuous treatment of scar in adult burn patients. Methods: A total of 124 adult burn patients, conforming to the study criteria, admitted in the Department of Burns of our hospital from January 2015 to January 2016 were divided into WeChat group ( n =63) and control group ( n =61) according to the random number table. Patients in control group only received regular discharging rehabilitation guide, while patients in WeChat group received regular discharging rehabilitation guide and joined WeChat platform after being discharged from hospital. Through pushing rehabilitation plan and rehabilitation related knowledge, organizing support discussion of burn patients, answering the patients' questions, members of WeChat platform intervention group conducted continuous treatment for 6 months on patients of WeChat group. The compliance of functional exercise of patients in two groups in one week before discharge and 3 and 6 months after discharge was evaluated by using the self-made functional exercise compliance log sheet. The compliance of using anti-scar drug and appliance of patients in two groups in 3 and 6 months after discharge was evaluated by using self-made anti-scar drug and appliance usage log sheets. Data were processed with chi-square test, independent sample t test, non-parametric rank sum test of independent sample, and Wilcoxon rank sum test. Results: (1) The compliance ratio of functional exercise of patients in WeChat group (95.24%, 60/63) was close to 93.44% (57/61) in control group in one week before discharge ( χ (2)=0.188, P >0.05). The compliance ratios of functional exercise of patients in WeChat group were respectively 93.65% (59/63) and 87.30% (55/63) in 3 and 6 months after discharge, which were higher than 68.85% (42/61) and 65.57% (40/61) in control group ( χ (2)=12.615, 8.166, P <0.01). (2) The compliance of using anti-scar drug of patients in WeChat group was significantly better than that in control group in 3 and 6 months after discharge ( Z =-4.150, -4.563, P <0.01). (3) The compliance of using anti-scar appliance of patients in WeChat group in 3 and 6 months after discharge was obviously better than that in control group ( Z =-4.242, -4.301, P <0.01). Conclusions: By using WeChat platform to provide guide for scar rehabilitation continuous treatment, adult burn patients have better compliance to functional exercise and usage of anti-scar drug and appliance.

Multi-dimensional Rankings, Program Termination, and Complexity Bounds of Flowchart Programs

NASA Astrophysics Data System (ADS)

Alias, Christophe; Darte, Alain; Feautrier, Paul; Gonnord, Laure

Proving the termination of a flowchart program can be done by exhibiting a ranking function, i.e., a function from the program states to a well-founded set, which strictly decreases at each program step. A standard method to automatically generate such a function is to compute invariants for each program point and to search for a ranking in a restricted class of functions that can be handled with linear programming techniques. Previous algorithms based on affine rankings either are applicable only to simple loops (i.e., single-node flowcharts) and rely on enumeration, or are not complete in the sense that they are not guaranteed to find a ranking in the class of functions they consider, if one exists. Our first contribution is to propose an efficient algorithm to compute ranking functions: It can handle flowcharts of arbitrary structure, the class of candidate rankings it explores is larger, and our method, although greedy, is provably complete. Our second contribution is to show how to use the ranking functions we generate to get upper bounds for the computational complexity (number of transitions) of the source program. This estimate is a polynomial, which means that we can handle programs with more than linear complexity. We applied the method on a collection of test cases from the literature. We also show the links and differences with previous techniques based on the insertion of counters.

Correlation of chemical evaporation rate with vapor pressure.

PubMed

Mackay, Donald; van Wesenbeeck, Ian

2014-09-02

A new one-parameter correlation is developed for the evaporation rate (ER) of chemicals as a function of molar mass (M) and vapor pressure (P) that is simpler than existing correlations. It applies only to liquid surfaces that are unaffected by the underlying solid substrate as occurs in the standard ASTM evaporation rate test and to quiescent liquid pools. The relationship has a sounder theoretical basis than previous correlations because ER is correctly correlated with PM rather than P alone. The inclusion of M increases the slope of previous log ER versus log P regressions to a value close to 1.0 and yields a simpler one-parameter correlation, namely, ER (μg m(-1) h(-1)) = 1464P (Pa) × M (g mol(-1)). Applications are discussed for the screening level assessment and ranking of chemicals for evaporation rate, such as pesticides, fumigants, and hydrocarbon carrier fluids used in pesticide formulations, liquid consumer products used indoors, and accidental spills of liquids. The mechanistic significance of the single parameter as a mass-transfer coefficient or velocity is discussed.

Verification of learner’s differences by team-based learning in biochemistry classes

PubMed Central

2017-01-01

Purpose We tested the effect of team-based learning (TBL) on medical education through the second-year premedical students’ TBL scores in biochemistry classes over 5 years. Methods We analyzed the results based on test scores before and after the students’ debate. The groups of students for statistical analysis were divided as follows: group 1 comprised the top-ranked students, group 3 comprised the low-ranked students, and group 2 comprised the medium-ranked students. Therefore, group T comprised 382 students (the total number of students in group 1, 2, and 3). To calibrate the difficulty of the test, original scores were converted into standardized scores. We determined the differences of the tests using Student t-test, and the relationship between scores before, and after the TBL using linear regression tests. Results Although there was a decrease in the lowest score, group T and 3 showed a significant increase in both original and standardized scores; there was also an increase in the standardized score of group 3. There was a positive correlation between the pre- and the post-debate scores in group T, and 2. And the beta values of the pre-debate scores and “the changes between the pre- and post-debate scores” were statistically significant in both original and standardized scores. Conclusion TBL is one of the educational methods for helping students improve their grades, particularly those of low-ranked students. PMID:29207457

[The relationship between Ridit analysis and rank sum test for one-way ordinal contingency table in medical research].

PubMed

Wang, Ling; Xia, Jie-lai; Yu, Li-li; Li, Chan-juan; Wang, Su-zhen

2008-06-01

To explore several numerical methods of ordinal variable in one-way ordinal contingency table and their interrelationship, and to compare corresponding statistical analysis methods such as Ridit analysis and rank sum test. Formula deduction was based on five simplified grading approaches including rank_r(i), ridit_r(i), ridit_r(ci), ridit_r(mi), and table scores. Practical data set was verified by SAS8.2 in clinical practice (to test the effect of Shiwei solution in treatment for chronic tracheitis). Because of the linear relationship of rank_r(i) = N ridit_r(i) + 1/2 = N ridit_r(ci) = (N + 1) ridit_r(mi), the exact chi2 values in Ridit analysis based on ridit_r(i), ridit_r(ci), and ridit_r(mi), were completely the same, and they were equivalent to the Kruskal-Wallis H test. Traditional Ridit analysis was based on ridit_r(i), and its corresponding chi2 value calculated with an approximate variance (1/12) was conservative. The exact chi2 test of Ridit analysis should be used when comparing multiple groups in the clinical researches because of its special merits such as distribution of mean ridit value on (0,1) and clear graph expression. The exact chi2 test of Ridit analysis can be output directly by proc freq of SAS8.2 with ridit and modridit option (SCORES =). The exact chi2 test of Ridit analysis is equivalent to the Kruskal-Wallis H test, and should be used when comparing multiple groups in the clinical researches.

Handwashing and Ebola virus disease outbreaks: A randomized comparison of soap, hand sanitizer, and 0.05% chlorine solutions on the inactivation and removal of model organisms Phi6 and E. coli from hands and persistence in rinse water.

PubMed

Wolfe, Marlene K; Gallandat, Karin; Daniels, Kyle; Desmarais, Anne Marie; Scheinman, Pamela; Lantagne, Daniele

2017-01-01

To prevent Ebola transmission, frequent handwashing is recommended in Ebola Treatment Units and communities. However, little is known about which handwashing protocol is most efficacious. We evaluated six handwashing protocols (soap and water, alcohol-based hand sanitizer (ABHS), and 0.05% sodium dichloroisocyanurate, high-test hypochlorite, and stabilized and non-stabilized sodium hypochlorite solutions) for 1) efficacy of handwashing on the removal and inactivation of non-pathogenic model organisms and, 2) persistence of organisms in rinse water. Model organisms E. coli and bacteriophage Phi6 were used to evaluate handwashing with and without organic load added to simulate bodily fluids. Hands were inoculated with test organisms, washed, and rinsed using a glove juice method to retrieve remaining organisms. Impact was estimated by comparing the log reduction in organisms after handwashing to the log reduction without handwashing. Rinse water was collected to test for persistence of organisms. Handwashing resulted in a 1.94-3.01 log reduction in E. coli concentration without, and 2.18-3.34 with, soil load; and a 2.44-3.06 log reduction in Phi6 without, and 2.71-3.69 with, soil load. HTH performed most consistently well, with significantly greater log reductions than other handwashing protocols in three models. However, the magnitude of handwashing efficacy differences was small, suggesting protocols are similarly efficacious. Rinse water demonstrated a 0.28-4.77 log reduction in remaining E. coli without, and 0.21-4.49 with, soil load and a 1.26-2.02 log reduction in Phi6 without, and 1.30-2.20 with, soil load. Chlorine resulted in significantly less persistence of E. coli in both conditions and Phi6 without soil load in rinse water (p<0.001). Thus, chlorine-based methods may offer a benefit of reducing persistence in rinse water. We recommend responders use the most practical handwashing method to ensure hand hygiene in Ebola contexts, considering the potential benefit of chlorine-based methods in rinse water persistence.

Sawmill simulation: concepts and computer use

Treesearch

Hugh W. Reynolds; Charles J. Gatchell

1969-01-01

Product specifications were fed into a computer so that the yield of products from the same sample of logs could be determined for simulated sawing methods. Since different sawing patterns were tested on the same sample, variation among log samples was eliminated; hence, the statistical conclusions are very precise.

VEGF-A polymorphisms predict progression-free survival among advanced castration-resistant prostate cancer patients treated with metronomic cyclophosphamide

PubMed Central

Orlandi, P; Fontana, A; Fioravanti, A; Di Desidero, T; Galli, L; Derosa, L; Canu, B; Marconcini, R; Biasco, E; Solini, A; Francia, G; Danesi, R; Falcone, A; Bocci, G

2013-01-01

Background: No data are available on the pharmacogenetics of metronomic chemotherapy in prostate cancer. The aim of this study was to evaluate the association between VEGF-A sequence variants and prostate-specific antigen (PSA) progression, progression-free survival (PFS) and overall survival (OS), in advanced castration-resistant prostate cancer patients treated with metronomic cyclophosphamide (CTX), celecoxib and dexamethasone. Methods: Forty-three patients were enrolled, and genomic DNA was extracted. VEGF-A gene SNPs (−2578A/C, −634C/G, +936C/T) were analysed using TaqMan PCR assays. Hardy–Weinberg equilibrium was tested for each SNP, and genetic effects were evaluated by Fisher's exact test. PFS and OS were analysed with GraphPad Prism software, using the product limit method of Kaplan and Meier, and comparing survival curves using both the log-rank test and the Gehan–Wilcoxon test. We used Bonferroni correction to account for multiple testing, and a two-tailed P-value of <0.017 was considered statistically significant. Results: Overall, 20 patients (46%) experienced a reduction in PSA levels from baseline and, among them, 14 (32%) showed a confirmed PSA ≥50% decrease. In non-responders, the −2578CC genotype was more frequent (18.60% vs 2.33% in responders; P=0.0212) whereas the −634CC genotype frequency was 22.73% vs 0% in responders (P=0.0485). With regard to PFS, patients harbouring the −634CC genotype had a median PFS of 2.2 months whereas patients with the genotype −634CG/GG had a median PFS of 6.25 months (P=0.0042). Conclusion: The −634CC genotype is significantly associated with a shorter PFS in patients treated with a metronomic CTX schedule. PMID:23860526

An effective quarantine measure reduced the total incidence of influenza A H1N1 in the workplace: another way to control the H1N1 flu pandemic.

PubMed

Miyaki, Koichi; Sakurazawa, Hirofumi; Mikurube, Hajime; Nishizaka, Mika; Ando, Hidehiko; Song, Yixuan; Shimbo, Takuro

2011-01-01

To evaluate the effectiveness of a non-vaccine quarantine measure against pandemic influenza A H1N1 in workplaces. Design was quasi-cluster randomized controlled trial in two sibling companies (Cohort 1 n=6,634, Cohort 2 n=8,500). The follow-up period was from July 1st, 2009 to February 19th, 2010 (233 days). Intervention was voluntary waiting at home on full pay if the family became Influenza like Illness (ILI). The incidences of influenza A H1N1 and those of the subgroups whose families got ILI in both cohorts were compared by a Cox regression model and log-rank test. There were 189 and 270 workers who got H1N1 infection during the follow-up period in each cohort. In this period 317 workers in Cohort 1 were asked to wait at home for several days (100% obeyed). The intervention group (Cohort 1) showed a statistically significant lower risk (p for log-rank test=0.033) compared with the control (Cohort 2), and the hazard ratio of the intervention was 0.799 [0.658-0.970] after adjusting for age, sex, BMI and smoking status. The workers who were asked to wait at home showed H1N1 infection more frequently (49 out of 317) compared with the workers whose family got ILI but were not asked to wait and work regularly (77 out of 990, RR=2.17 [1.48-3.18]). The waiting on full pay policy in the workplace reduced the overall risk of influenza A H1N1 by about 20% in one flu season in Japan. This kind of non-vaccine measure will be a promising option in workplaces to control the next flu pandemic.

The newly proposed clinical and post-neoadjuvant treatment staging classifications for gastric adenocarcinoma for the American Joint Committee on Cancer (AJCC) staging.

PubMed

In, Haejin; Ravetch, Ethan; Langdon-Embry, Marisa; Palis, Bryan; Ajani, Jaffer A; Hofstetter, Wayne L; Kelsen, David P; Sano, Takeshi

2018-01-01

New stage grouping classifications for clinical (cStage) and post-neoadjuvant treatment (ypStage) stage for gastric adenocarcinoma have been proposed for the eighth edition of the AJCC manual. This article summarizes the analysis for these stages. Gastric adenocarcinoma patients diagnosed in 2004-2009 were identified from the National Cancer Database (NCDB). The cStage cohort included both surgical and nonsurgical cases, and the ypStage cohort included only patients who had chemotherapy or radiation therapy before surgery. Survival differences between the stage groups were determined by the log-rank test and prognostic accuracy was assessed by concordance index. Analysis was performed using SAS 9.4 (SAS, Cary, NC, USA). Five strata for cStage and four strata for ypStage were developed. The 5-year survival rates for cStages were 56.77%, 47.39%, 33.1%, 25.9%, and 5.0% for stages I, IIa, IIb, III, and IV, respectively, and the rates for ypStage were 74.2%, 46.3%, 19.2%, and 11.6% for stages I, II, III, and IV, respectively. The log-rank test showed that survival differences were well stratified and stage groupings were ordered and distinct (p < 0.0001). The proposed cStage and ypStage classification was sensitive and specific and had high prognostic accuracy (cStage: c index = 0.81, 95% CI, 0.79-0.83; ypStage: c index = 0.80, 95% CI, 0.73-0.87). The proposed eighth edition establishes two new staging schemata that provide essential prognostic data for patients before treatment and for patients who have undergone surgery following neoadjuvant therapy. These additions are a significant advance to the AJCC staging manual and will provide critical guidance to clinicians in making informed decisions throughout the treatment course.

Prevalence of Pulmonary Hypertension and its Influence on Survival in Patients With Advanced Chronic Obstructive Pulmonary Disease Prior to Lung Transplantation.

PubMed

Hayes, Don; Black, Sylvester M; Tobias, Joseph D; Mansour, Heidi M; Whitson, Bryan A

2016-01-01

Prevalence of pulmonary hypertension (PH) and its influence on survival in chronic obstructive pulmonary disease (COPD) are not well studied in the lung allocation score (LAS) era. The UNOS database was queried from 2005 to 2013 to identify first-time adult lung transplant candidates with COPD who were tracked from wait list entry date until death or censoring to determine both prevalence and influence of PH. Using right heart catheterization measurements, mild PH was defined as mean pulmonary artery pressure (mPAP) ≥ 25 mmHg and severe ≥ 35 mmHg. Of 1315 COPD candidates not transplanted, 1243 were used for survival analysis using Cox proportional hazards models, and 1010 (mild PH) and 244 (severe PH) were used for propensity score matching, respectively. A total of 52% (652) of subjects had PH mPAP ≥ 25 mmHg. Univariate analysis revealed significant differences in survival for mild PH (HR = 1.769; 95% CI: 1.331, 2.351; p < 0.001) and severe PH (HR = 3.271; 95% CI: 2.311, 4.630; p < 0.001). Kaplan-Meier survival function demonstrated significant disparities for mild PH (Log-rank test: Chi-square1: 15.87, p < 0.0001) and severe PH (Log-rank test: Chi-square1: 50.13, p < 0.0001). Multivariate Cox models identified significant risk for death for mild PH (HR = 1.987; 95% CI: 1.484, 2.662; p < 0.001) and severe PH (HR = 3.432; 95% CI: 2.410, 4.888; p < 0.001). Propensity score matching confirmed increased mortality hazard associated with mild PH (HR = 2.280; 95% CI: 1.425, 3.649; p = 0.001) and severe PH (HR = 7.000; 95% CI: 2.455, 19.957; p < 0.001). PH is highly prevalent in advanced COPD and associated with a significantly higher risk for mortality.

Sulfur hexafluoride (SF6) versus perfluoropropane (C3F8) tamponade and short term face-down position for macular hole repair: a randomized prospective study.

PubMed

Casini, Giamberto; Loiudice, Pasquale; De Cillà, Stefano; Radice, Paolo; Nardi, Marco

2016-01-01

To compare early visual and anatomical outcomes after either sulfur hexafluoride (SF 6 ) or perfluoropropane (C 3 F 8 ) tamponade for macular hole repair. 147 eyes affected by primary full-thickness macular hole underwent pars plana vitrectomy with dye assisted removal of the internal limiting membrane and gas tamponade. Prone position was prescribed for 48 h after surgery. All patients were divided into 3 groups depending on the size of the hole: small (<250 µm), medium (>250-<400 µm) or large (>400 µm). Eyes within the same group randomly received either SF 6 (70 eyes) or C 3 F 8 (77 eyes). A complete ophthalmic evaluation, including best corrected visual acuity and anatomic status of the macular holes, was conducted preoperatively, at 1 week and 1 month after surgery. Macular hole volume was calculated using optical coherence tomography scans. The Wilcoxon Signed Ranks Test, the Mann-Whitney Test, the Spearman's rank-order correlation coefficient and the study of variance for repeated measures were used for statistical analysis. Mean best-corrected visual acuity improved from 0.92 logMAR to 0.28 logMAR (P < 0.001). A reduction of the dimensions of macular holes was observed in all cases, with a total repair of 90 % (63/70 eyes) in the SF 6 group and 91 % in the C 3 F 8 group (70/77 eyes). There was a negative correlation between the initial minor diameter, the volume of the hole and the rate of anatomic success. Short-term anatomical and visual outcomes were similar in eyes treated with either SF 6 or C 3 F 8 , independently of the stage of the macular hole. The initial volume and the minor diameter of the hole may be considered as valid tools for predicting surgical success. Age and gender did not appear to have influenced the prognosis.

Normal serum protein electrophoresis and mutated IGHV genes detect very slowly evolving chronic lymphocytic leukemia patients.

PubMed

Chauzeix, Jasmine; Laforêt, Marie-Pierre; Deveza, Mélanie; Crowther, Liam; Marcellaud, Elodie; Derouault, Paco; Lia, Anne-Sophie; Boyer, François; Bargues, Nicolas; Olombel, Guillaume; Jaccard, Arnaud; Feuillard, Jean; Gachard, Nathalie; Rizzo, David

2018-05-09

More than 35 years after the Binet classification, there is still a need for simple prognostic markers in chronic lymphocytic leukemia (CLL). Here, we studied the treatment-free survival (TFS) impact of normal serum protein electrophoresis (SPE) at diagnosis. One hundred twelve patients with CLL were analyzed. The main prognostic factors (Binet stage; lymphocytosis; IGHV mutation status; TP53, SF3B1, NOTCH1, and BIRC3 mutations; and cytogenetic abnormalities) were studied. The frequencies of IGHV mutation status, cytogenetic abnormalities, and TP53, SF3B1, NOTCH1, and BIRC3 mutations were not significantly different between normal and abnormal SPE. Normal SPE was associated with Binet stage A, nonprogressive disease for 6 months, lymphocytosis below 30 G/L, and the absence of the IGHV3-21 gene rearrangement which is associated with poor prognosis. The TFS of patients with normal SPE was significantly longer than that of patients with abnormal SPE (log-rank test: P = 0.0015, with 51% untreated patients at 5.6 years and a perfect plateau afterward vs. a median TFS at 2.64 years for abnormal SPE with no plateau). Multivariate analysis using two different Cox models and bootstrapping showed that normal SPE was an independent good prognostic marker for either Binet stage, lymphocytosis, or IGHV mutation status. TFS was further increased when both normal SPE and mutated IGHV were present (log-rank test: P = 0.008, median not reached, plateau at 5.6 years and 66% untreated patients). A comparison with other prognostic markers suggested that normal SPE could reflect slowly advancing CLL disease. Altogether, our results show that a combination of normal SPE and mutated IGHV genes defines a subgroup of patients with CLL who evolve very slowly and who might never need treatment. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Stent patency in patients with distal malignant biliary obstruction receiving chemo(radio)therapy.

PubMed

Haal, Sylke; van Hooft, Jeanin E; Rauws, Erik A J; Fockens, Paul; Voermans, Rogier P

2017-11-01

 Recent literature suggests that chemo(radio)therapy might reduce the patency of plastic stents in patients with malignant biliary obstruction. Whether this might also be valid for other types of stents is unknown. The aim of this study was to determine the influence of chemo(radio)therapy on the patency of fully-covered self-expandable metal stents (FCSEMSs) and plastic stents.  We retrospectively reviewed the electronic medical records of patients with distal malignant biliary obstruction who underwent biliary stent placement between April 2001 and July 2015. Primary outcome was duration of stent patency. Secondary outcome was stent patency at 3 and 6 months. We used Kaplan-Meier survival analyses to compare stent patency rates between patients who received chemo(radio)therapy and patients who did not.  A total of 291 biliary stents (151 metal and 140 plastic) were identified. The median cumulative stent patency of FCSEMSs did not differ between patients receiving chemo(radio)therapy (n = 51) and those (n = 100) who did not ( P  = 0.70, log-rank test). The estimated cumulative stent patency of plastic stents was also comparable in 99 patients without and 41 patients with chemo(radio)therapy ( P  = 0.73, log-rank test). At 3 and 6 months, FCSEMS patency rates were 87 % and 83 % in patients without chemo(radio)therapy and 96 % and 83 % in patients with therapy, respectively. Plastic patency rates were 69 % and 55 % in patients without and 85 % and 39 % in patients with therapy, respectively. After 1 year, 78 % of the FCSEMSs were still patent in patients without chemo(radio)therapy and 69 % of the FCSEMSs were still patent in patients with therapy.  Our data indicate that chemo(radio)therapy does not reduce the patency of biliary fully-covered metal and plastic stents.

Prognostic significance of signal transducer and activator of transcription 5 and 5b expression in Epstein-Barr virus-positive patients with chronic lymphocytic leukemia.

PubMed

Diamantopoulos, Panagiotis T; Sofotasiou, Maria; Georgoussi, Zafiroula; Giannakopoulou, Nefeli; Papadopoulou, Vasiliki; Galanopoulos, Athanasios; Kontandreopoulou, Elina; Zervakis, Panagiotis; Pallaki, Paschalina; Kalala, Fani; Kyrtsonis, Marie-Christine; Dimitrakopoulou, Aglaia; Vassilakopoulos, Theodoros; Angelopoulou, Maria; Spanakis, Nikolaos; Viniou, Nora-Athina

2016-09-01

Signal transducer and activator of transcription (STAT) proteins have been intensively studied in hematologic malignancies, and the efficacy of agents against STATs in lymphomas is already under research. We investigated the expression of total STAT5 and STAT5b in peripheral blood samples of patients with chronic lymphocytic leukemia (CLL) in correlation with the presence of Epstein-Barr Virus (EBV) and its major oncoprotein (latent membrane protein 1, LMP1). The EBV load was measured in the peripheral blood by real-time PCR for the BXLF1 gene and the levels of LMP1 by PCR and ELISA. Western blotting was performed for total STAT5 and STAT5b in protein extracts. STAT5b was only expressed in patients (not in healthy subjects) and STAT5 but particularly STAT5b expression was correlated with the presence of the virus (77.3% vs. 51.2%, P = 0.006 for STAT5b) and to the expression of LMP1 (58.3% vs. 21.6%, P = 0.011 for STAT5b). Moreover, the expression of STAT5b and the presence of EBV and LMP1 were strongly negatively correlated with the overall survival of the patients (log-rank test P = 0.011, 0.015, 0.006, respectively). Double positive (for EBV and STAT5b) patients had the lowest overall survival (log-rank test P = 0.013). This is the first report of a survival disadvantage of EBV+ patients with CLL, and the first time that STAT5b expression is correlated with survival. The correlation of STAT5 expression with the presence of the virus, along with our survival correlations defines a subgroup of patients with CLL that may benefit from anti-STAT agents. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Metastasis in dedifferentiated liposarcoma: Predictors and outcome in 148 patients.

PubMed

Tirumani, S H; Tirumani, H; Jagannathan, J P; Shinagare, A B; Hornick, J L; Ramaiya, N H; Wagner, A J

2015-07-01

To describe the pattern of dedifferentiated liposarcoma (DDLPS) metastases and to analyze their predictors and outcome. In this retrospective study, we reviewed the imaging and clinical records of all consenting patients with histopathology-confirmed DDLPS seen from 2000 through 2012. The predictive value of clinical and histopathologic parameters for metastasis later in the disease course was analyzed using univariate and multivariate analyses. Survival of patients with and without metastasis was compared using Log-rank test. Records of 148 patients (57 women, 91 men; mean age 59 years, range 30-87 years) were reviewed. Distant metastases were observed in 44/148 patients (29.7%), 9/44 (20.5%) at presentation and 35/44 (79.5%) developing them later at a median interval of 8 months (IQR = 0.80-26 months). Median duration of follow-up was 38 months (IQR = 18-74 months) with 77/148 patients (31 with metastases) deceased at the time of analysis. Median survival was 28 months (IQR = 10-56 months) for patients with metastases and 38 months (IQR, 17-65 months) for patients without metastases (p = 0.0123, Log-Rank test; Hazard ratio 1.79 [95% confidence interval 1.11-2.84]). Lung was the most common site of metastases (33 patients, 22.3%). On univariate analysis, grade and local recurrence were associated with subsequent risk of metastasis where as age, tumor size, site, de novo dedifferentiation, number of previous surgical resections, margin positivity and chemoradiation were not. On multivariate analysis, high tumor grade (p-value = 0.0005, OR 5.05; 95% CI 2.01-13.48) and local recurrence (p-value = 0.0025, OR 4.46; 95% CI 1.67-13.40) predicted metastasis. Lung was most frequent site of DDLPS metastases. Risk of developing metastatic disease was statistically associated with tumor grade and local recurrence. Metastatic disease was associated with decreased survival. Copyright © 2015 Elsevier Ltd. All rights reserved.

IL1B and DEFB1 Polymorphisms Increase Susceptibility to Invasive Mold Infection After Solid-Organ Transplantation.

PubMed

Wójtowicz, Agnieszka; Gresnigt, Mark S; Lecompte, Thanh; Bibert, Stephanie; Manuel, Oriol; Joosten, Leo A B; Rüeger, Sina; Berger, Christoph; Boggian, Katia; Cusini, Alexia; Garzoni, Christian; Hirsch, Hans H; Weisser, Maja; Mueller, Nicolas J; Meylan, Pascal R; Steiger, Jürg; Kutalik, Zoltan; Pascual, Manuel; van Delden, Christian; van de Veerdonk, Frank L; Bochud, Pierre-Yves

2015-05-15

Single-nucleotide polymorphisms (SNPs) in immune genes have been associated with susceptibility to invasive mold infection (IMI) among hematopoietic stem cell but not solid-organ transplant (SOT) recipients. Twenty-four SNPs from systematically selected genes were genotyped among 1101 SOT recipients (715 kidney transplant recipients, 190 liver transplant recipients, 102 lung transplant recipients, 79 heart transplant recipients, and 15 recipients of other transplants) from the Swiss Transplant Cohort Study. Association between SNPs and the end point were assessed by log-rank test and Cox regression models. Cytokine production upon Aspergillus stimulation was measured by enzyme-linked immunosorbent assay in peripheral blood mononuclear cells (PBMCs) from healthy volunteers and correlated with relevant genotypes. Mold colonization (n = 45) and proven/probable IMI (n = 26) were associated with polymorphisms in the genes encoding interleukin 1β (IL1B; rs16944; recessive mode, P = .001 for colonization and P = .00005 for IMI, by the log-rank test), interleukin 1 receptor antagonist (IL1RN; rs419598; P = .01 and P = .02, respectively), and β-defensin 1 (DEFB1; rs1800972; P = .001 and P = .0002, respectively). The associations with IL1B and DEFB1 remained significant in a multivariate regression model (P = .002 for IL1B rs16944; P = .01 for DEFB1 rs1800972). The presence of 2 copies of the rare allele of rs16944 or rs419598 was associated with reduced Aspergillus-induced interleukin 1β and tumor necrosis factor α secretion by PBMCs. Functional polymorphisms in IL1B and DEFB1 influence susceptibility to mold infection in SOT recipients. This observation may contribute to individual risk stratification. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Double oral esomeprazole after a 3-day intravenous esomeprazole infusion reduces recurrent peptic ulcer bleeding in high-risk patients: a randomised controlled study.

PubMed

Cheng, Hsiu-Chi; Wu, Chung-Tai; Chang, Wei-Lun; Cheng, Wei-Chun; Chen, Wei-Ying; Sheu, Bor-Shyang

2014-12-01

Patients with high Rockall scores have increased risk of ulcer rebleeding after 3-day esomeprazole infusions. To investigate whether double oral esomeprazole given after a 3-day esomeprazole infusion decreases ulcer rebleeding for patients with high Rockall scores. We prospectively enrolled 293 patients with peptic ulcer bleeding who had achieved endoscopic haemostasis. After a 3-day esomeprazole infusion, patients with Rockall scores ≥6 were randomised into the oral double-dose group (n=93) or the oral standard-dose group (n=94) to receive 11 days of oral esomeprazole 40 mg twice daily or once daily, respectively. The patients with Rockall scores <6 served as controls (n=89); they received 11 days of oral esomeprazole 40 mg once daily. Thereafter, all patients received oral esomeprazole 40 mg once daily for two more weeks until the end of the 28-day study period. The primary end point was peptic ulcer rebleeding. Among patients with Rockall scores ≥6, the oral double-dose group had a higher cumulative rebleeding-free proportion than the oral standard-dose group (p=0.02, log-rank test). The proportion of patients free from recurrent bleeding during the 4th-28th day in the oral double-dose group remained lower than that of the group with Rockall scores <6 (p=0.03, log-rank test). Among patients with Rockall scores ≥6, the rebleeding rate was lower in the oral double-dose group than in the oral standard-dose group (4th-28th day: 10.8% vs 28.7%, p=0.002). Double oral esomeprazole at 40 mg twice daily after esomeprazole infusion reduced recurrent peptic ulcer bleeding in high-risk patients with Rockall scores ≥6. NCT01591083. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Automated lithology prediction from PGNAA and other geophysical logs.

PubMed

Borsaru, M; Zhou, B; Aizawa, T; Karashima, H; Hashimoto, T

2006-02-01

Different methods of lithology predictions from geophysical data have been developed in the last 15 years. The geophysical logs used for predicting lithology are the conventional logs: sonic, neutron-neutron, gamma (total natural-gamma) and density (backscattered gamma-gamma). The prompt gamma neutron activation analysis (PGNAA) is another established geophysical logging technique for in situ element analysis of rocks in boreholes. The work described in this paper was carried out to investigate the application of PGNAA to the lithology interpretation. The data interpretation was conducted using the automatic interpretation program LogTrans based on statistical analysis. Limited test suggests that PGNAA logging data can be used to predict the lithology. A success rate of 73% for lithology prediction was achieved from PGNAA logging data only. It can also be used in conjunction with the conventional geophysical logs to enhance the lithology prediction.

Woodstove Emission Sampling Methods Comparability Analysis and In-situ Evaluation of New Technology Woodstoves.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simons, Carl A.

1988-06-01

One major objective of this study was to compare several woodstove particulate emission sampling methods under laboratory and in-situ conditions. The laboratory work compared the EPA Method 5H, EPA Method 5G, and OMNI Automated Woodstove Emission Sampler (AWES)/Data LOG'r particulate emission sampling systems. A second major objective of the study was to evaluate the performance of two integral catalytic, two low emission non-catalytic, and two conventional technology woodstoves under in-situ conditions with AWES/Data LOG'r system. The AWES/Data LOG'r and EPA Method 5G sampling systems were also compared in an in-situ test on one of the integral catalytic woodstove models. 7more » figs., 12 tabs.« less

Improved Inactivation of Nonenveloped Enteric Viruses and Their Surrogates by a Novel Alcohol-Based Hand Sanitizer ▿

PubMed Central

Macinga, David R.; Sattar, Syed A.; Jaykus, Lee-Ann; Arbogast, James W.

2008-01-01

Norovirus is the leading cause of food-related illness in the United States, and contamination of ready-to-eat items by food handlers poses a high risk for disease. This study reports the in vitro (suspension test) and in vivo (fingerpad protocol) assessments of a new ethanol-based hand sanitizer containing a synergistic blend of polyquaternium polymer and organic acid, which is active against viruses of public health importance, including norovirus. When tested in suspension, the test product reduced the infectivity of the nonenveloped viruses human rotavirus (HRV), poliovirus type 1 (PV-1), and the human norovirus (HNV) surrogates feline calicivirus (FCV) F-9 and murine norovirus type 1 (MNV-1) by greater than 3 log10 after a 30-s exposure. In contrast, a benchmark alcohol-based hand sanitizer reduced only HRV by greater than 3 log10 and none of the additional viruses by greater than 1.2 log10 after the same exposure. In fingerpad experiments, the test product produced a 2.48 log10 reduction of MNV-1 after a 30-s exposure, whereas a 75% ethanol control produced a 0.91 log10 reduction. Additionally, the test product reduced the infectivity titers of adenovirus type 5 (ADV-5) and HRV by ≥3.16 log10 and ≥4.32 log10, respectively, by the fingerpad assay within 15 s; and PV-1 was reduced by 2.98 log10 in 30 s by the same method. Based on these results, we conclude that this new ethanol-based hand sanitizer is a promising option for reducing the transmission of enteric viruses, including norovirus, by food handlers and care providers. PMID:18586970

Improved inactivation of nonenveloped enteric viruses and their surrogates by a novel alcohol-based hand sanitizer.

PubMed

Macinga, David R; Sattar, Syed A; Jaykus, Lee-Ann; Arbogast, James W

2008-08-01

Norovirus is the leading cause of food-related illness in the United States, and contamination of ready-to-eat items by food handlers poses a high risk for disease. This study reports the in vitro (suspension test) and in vivo (fingerpad protocol) assessments of a new ethanol-based hand sanitizer containing a synergistic blend of polyquaternium polymer and organic acid, which is active against viruses of public health importance, including norovirus. When tested in suspension, the test product reduced the infectivity of the nonenveloped viruses human rotavirus (HRV), poliovirus type 1 (PV-1), and the human norovirus (HNV) surrogates feline calicivirus (FCV) F-9 and murine norovirus type 1 (MNV-1) by greater than 3 log(10) after a 30-s exposure. In contrast, a benchmark alcohol-based hand sanitizer reduced only HRV by greater than 3 log(10) and none of the additional viruses by greater than 1.2 log(10) after the same exposure. In fingerpad experiments, the test product produced a 2.48 log(10) reduction of MNV-1 after a 30-s exposure, whereas a 75% ethanol control produced a 0.91 log(10) reduction. Additionally, the test product reduced the infectivity titers of adenovirus type 5 (ADV-5) and HRV by > or =3.16 log(10) and > or =4.32 log(10), respectively, by the fingerpad assay within 15 s; and PV-1 was reduced by 2.98 log(10) in 30 s by the same method. Based on these results, we conclude that this new ethanol-based hand sanitizer is a promising option for reducing the transmission of enteric viruses, including norovirus, by food handlers and care providers.

Assessment of the prognostic and predictive utility of the Breast Cancer Index (BCI): an NCIC CTG MA.14 study.

PubMed

Sgroi, Dennis C; Chapman, Judy-Anne W; Badovinac-Crnjevic, T; Zarella, Elizabeth; Binns, Shemeica; Zhang, Yi; Schnabel, Catherine A; Erlander, Mark G; Pritchard, Kathleen I; Han, Lei; Shepherd, Lois E; Goss, Paul E; Pollak, Michael

2016-01-04

Biomarkers that can be used to accurately assess the residual risk of disease recurrence in women with hormone receptor-positive breast cancer are clinically valuable. We evaluated the prognostic value of the Breast Cancer Index (BCI), a continuous risk index based on a combination of HOXB13:IL17BR and molecular grade index, in women with early breast cancer treated with either tamoxifen alone or tamoxifen plus octreotide in the NCIC MA.14 phase III clinical trial (ClinicalTrials.gov Identifier NCT00002864; registered 1 November 1999). Gene expression analysis of BCI by real-time polymerase chain reaction was performed blinded to outcome on RNA extracted from archived formalin-fixed, paraffin-embedded tumor samples of 299 patients with both lymph node-negative (LN-) and lymph node-positive (LN+) disease enrolled in the MA.14 trial. Our primary objective was to determine the prognostic performance of BCI based on relapse-free survival (RFS). MA.14 patients experienced similar RFS on both treatment arms. Association of gene expression data with RFS was evaluated in univariate analysis with a stratified log-rank test statistic, depicted with a Kaplan-Meier plot and an adjusted Cox survivor plot. In the multivariate assessment, we used stratified Cox regression. The prognostic performance of an emerging, optimized linear BCI model was also assessed in a post hoc analysis. Of 299 samples, 292 were assessed successfully for BCI for 146 patients accrued in each MA.14 treatment arm. BCI risk groups had a significant univariate association with RFS (stratified log-rank p = 0.005, unstratified log-rank p = 0.007). Adjusted 10-year RFS in BCI low-, intermediate-, and high-risk groups was 87.5 %, 83.9 %, and 74.7 %, respectively. BCI had a significant prognostic effect [hazard ratio (HR) 2.34, 95 % confidence interval (CI) 1.33-4.11; p = 0.004], although not a predictive effect, on RFS in stratified multivariate analysis, adjusted for pathological tumor stage (HR 2.22, 95 % CI 1.22-4.07; p = 0.01). In the post hoc multivariate analysis, higher linear BCI was associated with shorter RFS (p = 0.002). BCI had a strong prognostic effect on RFS in patients with early-stage breast cancer treated with tamoxifen alone or with tamoxifen and octreotide. BCI was prognostic in both LN- and LN+ patients. This retrospective study is an independent validation of the prognostic performance of BCI in a prospective trial.

Simulation Testing for Selection of Critical Care Medicine Trainees. A Pilot Feasibility Study.

PubMed

Cocciante, Adriano G; Nguyen, Martin N; Marane, Candida F; Panayiotou, Anita E; Karahalios, Amalia; Beer, Janet A; Johal, Navroop; Morris, John; Turner, Stacy; Hessian, Elizabeth C

2016-04-01

Selection of physicians into anesthesiology, intensive care, and emergency medicine training has traditionally relied on evaluation of curriculum vitae, letters of recommendation, and interviews, despite these methods being poor predictors of subsequent workplace performance. In this study, we evaluated the feasibility and face validity of incorporating assessment of nontechnical skills in simulation and personality traits into an existing junior doctor selection framework. Candidates short-listed for a critical care residency position were invited to participate in the study. On the interview day, consenting candidates participated in a simulation scenario and debriefing and completed a personality test (16 Personality Factor Questionnaire) and a survey. Timing of participants' progression through the stations and faculty staff numbers were evaluated. Nontechnical skills were evaluated and candidates ranked using the Ottawa Crisis Resource Management Global Rating Scale (Ottawa GRS). Nontechnical skills ranking and traditional selection method ranking were compared using the concordance correlation coefficient. Interrater reliability was assessed using the concordance correlation coefficient. Thirteen of 20 eligible participants consented to study inclusion. All participants completed the necessary stations without significant time delays. Eighteen staff members were required to conduct interviews, simulation, debriefing, and personality testing. Participants rated the simulation station to be acceptable, fair, and relevant and as providing an opportunity to demonstrate abilities. Personality testing was rated less fair, less relevant, and less acceptable, and as giving less opportunity to demonstrate abilities. Participants reported that simulation was equally as stressful as the interview, whereas personality testing was rated less stressful. Assessors rated both personality testing and simulation as acceptable and able to provide additional information about candidates. The Ottawa GRS showed moderate interrater concordance. There was moderate concordance between rankings based on traditional selection methods and Ottawa GRS rankings (ρ = 0.52; 95% confidence interval, -0.02 to 0.82; P = 0.06). A multistation selection process involving interviews, simulation, and personality testing is feasible and has face validity. A potential barrier to adoption is the high number of faculty required to conduct the process.

Estimation of distributional parameters for censored trace level water quality data: 1. Estimation techniques

USGS Publications Warehouse

Gilliom, Robert J.; Helsel, Dennis R.

1986-01-01

A recurring difficulty encountered in investigations of many metals and organic contaminants in ambient waters is that a substantial portion of water sample concentrations are below limits of detection established by analytical laboratories. Several methods were evaluated for estimating distributional parameters for such censored data sets using only uncensored observations. Their reliabilities were evaluated by a Monte Carlo experiment in which small samples were generated from a wide range of parent distributions and censored at varying levels. Eight methods were used to estimate the mean, standard deviation, median, and interquartile range. Criteria were developed, based on the distribution of uncensored observations, for determining the best performing parameter estimation method for any particular data set. The most robust method for minimizing error in censored-sample estimates of the four distributional parameters over all simulation conditions was the log-probability regression method. With this method, censored observations are assumed to follow the zero-to-censoring level portion of a lognormal distribution obtained by a least squares regression between logarithms of uncensored concentration observations and their z scores. When method performance was separately evaluated for each distributional parameter over all simulation conditions, the log-probability regression method still had the smallest errors for the mean and standard deviation, but the lognormal maximum likelihood method had the smallest errors for the median and interquartile range. When data sets were classified prior to parameter estimation into groups reflecting their probable parent distributions, the ranking of estimation methods was similar, but the accuracy of error estimates was markedly improved over those without classification.

Estimation of distributional parameters for censored trace level water quality data. 1. Estimation Techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilliom, R.J.; Helsel, D.R.

1986-02-01

A recurring difficulty encountered in investigations of many metals and organic contaminants in ambient waters is that a substantial portion of water sample concentrations are below limits of detection established by analytical laboratories. Several methods were evaluated for estimating distributional parameters for such censored data sets using only uncensored observations. Their reliabilities were evaluated by a Monte Carlo experiment in which small samples were generated from a wide range of parent distributions and censored at varying levels. Eight methods were used to estimate the mean, standard deviation, median, and interquartile range. Criteria were developed, based on the distribution of uncensoredmore » observations, for determining the best performing parameter estimation method for any particular data det. The most robust method for minimizing error in censored-sample estimates of the four distributional parameters over all simulation conditions was the log-probability regression method. With this method, censored observations are assumed to follow the zero-to-censoring level portion of a lognormal distribution obtained by a least squares regression between logarithms of uncensored concentration observations and their z scores. When method performance was separately evaluated for each distributional parameter over all simulation conditions, the log-probability regression method still had the smallest errors for the mean and standard deviation, but the lognormal maximum likelihood method had the smallest errors for the median and interquartile range. When data sets were classified prior to parameter estimation into groups reflecting their probable parent distributions, the ranking of estimation methods was similar, but the accuracy of error estimates was markedly improved over those without classification.« less

Estimation of distributional parameters for censored trace-level water-quality data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilliom, R.J.; Helsel, D.R.

1984-01-01

A recurring difficulty encountered in investigations of many metals and organic contaminants in ambient waters is that a substantial portion of water-sample concentrations are below limits of detection established by analytical laboratories. Several methods were evaluated for estimating distributional parameters for such censored data sets using only uncensored observations. Their reliabilities were evaluated by a Monte Carlo experiment in which small samples were generated from a wide range of parent distributions and censored at varying levels. Eight methods were used to estimate the mean, standard deviation, median, and interquartile range. Criteria were developed, based on the distribution of uncensored observations,more » for determining the best-performing parameter estimation method for any particular data set. The most robust method for minimizing error in censored-sample estimates of the four distributional parameters over all simulation conditions was the log-probability regression method. With this method, censored observations are assumed to follow the zero-to-censoring level portion of a lognormal distribution obtained by a least-squares regression between logarithms of uncensored concentration observations and their z scores. When method performance was separately evaluated for each distributional parameter over all simulation conditions, the log-probability regression method still had the smallest errors for the mean and standard deviation, but the lognormal maximum likelihood method had the smallest errors for the median and interquartile range. When data sets were classified prior to parameter estimation into groups reflecting their probable parent distributions, the ranking of estimation methods was similar, but the accuracy of error estimates was markedly improved over those without classification. 6 figs., 6 tabs.« less

The application of PGNAA borehole logging for copper grade estimation at Chuquicamata mine.

PubMed

Charbucinski, J; Duran, O; Freraut, R; Heresi, N; Pineyro, I

2004-05-01

The field trials of a prompt gamma neutron activation (PGNAA) spectrometric logging method and instrumentation (SIROLOG) for copper grade estimation in production holes of a porphyry type copper ore mine, Chuquicamata in Chile, are described. Examples of data analysis, calibration procedures and copper grade profiles are provided. The field tests have proved the suitability of the PGNAA logging system for in situ quality control of copper ore.

Comparison of 3 in vivo methods for assessment of alcohol-based hand rubs.

PubMed

Edmonds-Wilson, Sarah; Campbell, Esther; Fox, Kyle; Macinga, David

2015-05-01

Alcohol-based hand rubs (ABHRs) are the primary method of hand hygiene in health-care settings. ICPs increasingly are assessing ABHR product efficacy data as improved products and test methods are developed. As a result, ICPs need better tools and recommendations for how to assess and compare ABHRs. Two ABHRs (70% ethanol) were tested according to 3 in vivo methods approved by ASTM International: E1174, E2755, and E2784. Log10 reductions were measured after a single test product use and after 10 consecutive uses at an application volume of 2 mL. The test method used had a significant influence on ABHR efficacy; however, in this study the test product (gel or foam) did not significantly influence efficacy. In addition, for all test methods, log10 reductions obtained after a single application were not predictive of results after 10 applications. Choice of test method can significantly influence efficacy results. Therefore, when assessing antimicrobial efficacy data of hand hygiene products, ICPs should pay close attention to the test method used, and ensure that product comparisons are made head to head in the same study using the same test methodology. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Accounting for Uncertainty in Decision Analytic Models Using Rank Preserving Structural Failure Time Modeling: Application to Parametric Survival Models.

PubMed

Bennett, Iain; Paracha, Noman; Abrams, Keith; Ray, Joshua

2018-01-01

Rank Preserving Structural Failure Time models are one of the most commonly used statistical methods to adjust for treatment switching in oncology clinical trials. The method is often applied in a decision analytic model without appropriately accounting for additional uncertainty when determining the allocation of health care resources. The aim of the study is to describe novel approaches to adequately account for uncertainty when using a Rank Preserving Structural Failure Time model in a decision analytic model. Using two examples, we tested and compared the performance of the novel Test-based method with the resampling bootstrap method and with the conventional approach of no adjustment. In the first example, we simulated life expectancy using a simple decision analytic model based on a hypothetical oncology trial with treatment switching. In the second example, we applied the adjustment method on published data when no individual patient data were available. Mean estimates of overall and incremental life expectancy were similar across methods. However, the bootstrapped and test-based estimates consistently produced greater estimates of uncertainty compared with the estimate without any adjustment applied. Similar results were observed when using the test based approach on a published data showing that failing to adjust for uncertainty led to smaller confidence intervals. Both the bootstrapping and test-based approaches provide a solution to appropriately incorporate uncertainty, with the benefit that the latter can implemented by researchers in the absence of individual patient data. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Cost-effectiveness of quantitative hepatitis B virus surface antigen testing in pregnancy in predicting vertical transmission risk.

PubMed

Samadi Kochaksaraei, Golasa; Congly, Stephen E; Matwiy, Trudy; Castillo, Eliana; Martin, Steven R; Charlton, Carmen L; Coffin, Carla S

2016-11-01

Vertical transmission of hepatitis B virus (HBV) can occur despite immunoprophylaxis in mothers with high HBV DNA levels (>5-7 log 10 IU/ml). Quantitative hepatitis B surface antigen (qHBsAg) testing could be used as a surrogate marker to identify high viral load carriers, but there is limited data in pregnancy. We conducted a prospective observational study to determine the cost-effectiveness and utility of qHBsAg as a valid surrogate marker of HBV DNA. Pregnant patients with chronic hepatitis B were recruited from a tertiary referral centre. HBV DNA levels and qHBsAg were assessed in the second to third trimester. Statistical analysis was performed by Spearman's rank correlation and student's t-test. The cost-effectiveness of qHBsAg as compared to HBV DNA testing was calculated. Ninety nine women with 103 pregnancies, median age 32 years, 65% Asian, 23% African and 12% other [Hispanic, Caucasian] were enrolled. Overall, 23% (23/99) were HBV e Ag (HBeAg)-positive. A significant correlation between qHBsAg and HBV DNA levels was noted in HBeAg-positive patients (r = 0.79, P < 0.05) but not in HBeAg-negative patients (r = 0.17, P = 0.06). In receiver operating characteristic analysis, the optimal qHBsAg cut-off values for predicting maternal viraemia associated with immunoprophylaxis failure (i.e., HBV DNA ≥7 log 10 IU/ml) was 4.3 log 10 IU/ml (accuracy 98.7%, sensitivity 94.7%, specificity 94.4%) (95% CI, 97-100%, P < 0.05). Use of HBV DNA as compared to qHBsAg costs approximately $20 000 more per infection prevented. In resource poor regions, qHBsAg could be used as a more cost-effective marker for high maternal viraemia, and indicate when anti-HBV nucleos/tide analogue therapy should be used to prevent HBV immunoprophylaxis failure. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Efficacy of Pimobendan in the Prevention of Congestive Heart Failure or Sudden Death in Doberman Pinschers with Preclinical Dilated Cardiomyopathy (The PROTECT Study)

PubMed Central

Summerfield, NJ; Boswood, A; O'Grady, MR; Gordon, SG; Dukes-McEwan, J; Oyama, MA; Smith, S; Patteson, M; French, AT; Culshaw, GJ; Braz-Ruivo, L; Estrada, A; O'Sullivan, ML; Loureiro, J; Willis, R; Watson, P

2012-01-01

Background The benefit of pimobendan in delaying the progression of preclinical dilated cardiomyopathy (DCM) in Dobermans is not reported. Hypothesis That chronic oral administration of pimobendan to Dobermans with preclinical DCM will delay the onset of CHF or sudden death and improve survival. Animals Seventy-six client-owned Dobermans recruited at 10 centers in the UK and North America. Methods The trial was a randomized, blinded, placebo-controlled, parallel group multicenter study. Dogs were allocated in a 1:1 ratio to receive pimobendan (Vetmedin capsules) or visually identical placebo. The composite primary endpoint was prospectively defined as either onset of CHF or sudden death. Time to death from all causes was a secondary endpoint. Results The proportion of dogs reaching the primary endpoint was not significantly different between groups (P = .1). The median time to the primary endpoint (onset of CHF or sudden death) was significantly longer in the pimobendan (718 days, IQR 441–1152 days) versus the placebo group (441 days, IQR 151–641 days) (log-rank P = 0.0088). The median survival time was significantly longer in the pimobendan (623 days, IQR 491–1531 days) versus the placebo group (466 days, IQR 236–710 days) (log-rank P = .034). Conclusion and Clinical Importance The administration of pimobendan to Dobermans with preclinical DCM prolongs the time to the onset of clinical signs and extends survival. Treatment of dogs in the preclinical phase of this common cardiovascular disorder with pimobendan can lead to improved outcome. PMID:23078651

Rank-based testing of equal survivorship based on cross-sectional survival data with or without prospective follow-up.

PubMed

Chan, Kwun Chuen Gary; Qin, Jing

2015-10-01

Existing linear rank statistics cannot be applied to cross-sectional survival data without follow-up since all subjects are essentially censored. However, partial survival information are available from backward recurrence times and are frequently collected from health surveys without prospective follow-up. Under length-biased sampling, a class of linear rank statistics is proposed based only on backward recurrence times without any prospective follow-up. When follow-up data are available, the proposed rank statistic and a conventional rank statistic that utilizes follow-up information from the same sample are shown to be asymptotically independent. We discuss four ways to combine these two statistics when follow-up is present. Simulations show that all combined statistics have substantially improved power compared with conventional rank statistics, and a Mantel-Haenszel test performed the best among the proposal statistics. The method is applied to a cross-sectional health survey without follow-up and a study of Alzheimer's disease with prospective follow-up. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Quality Australian Journals in the Humanities and Social Sciences

ERIC Educational Resources Information Center

Haddow, Gaby

2008-01-01

A pilot study was undertaken to test the journal diffusion factor (JDF) as an alternative to journal impact factors (JIFs) for ranking journals. Bibliometric research methods were applied to rank Australian architecture, communications and education journals by the JDF; this was with the total number of citations they attract in ISI indexed…

A Comparison of Didactic and Inquiry Teaching Methods in a Rural Community College Earth Science Course

NASA Astrophysics Data System (ADS)

Beam, Margery Elizabeth

The combination of increasing enrollment and the importance of providing transfer students a solid foundation in science calls for science faculty to evaluate teaching methods in rural community colleges. The purpose of this study was to examine and compare the effectiveness of two teaching methods, inquiry teaching methods and didactic teaching methods, applied in a rural community college earth science course. Two groups of students were taught the same content via inquiry and didactic teaching methods. Analysis of quantitative data included a non-parametric ranking statistical testing method in which the difference between the rankings and the median of the post-test scores was analyzed for significance. Results indicated there was not a significant statistical difference between the teaching methods for the group of students participating in the research. The practical and educational significance of this study provides valuable perspectives on teaching methods and student learning styles in rural community colleges.

Intrusion detection using rough set classification.

PubMed

Zhang, Lian-hua; Zhang, Guan-hua; Zhang, Jie; Bai, Ying-cai

2004-09-01

Recently machine learning-based intrusion detection approaches have been subjected to extensive researches because they can detect both misuse and anomaly. In this paper, rough set classification (RSC), a modern learning algorithm, is used to rank the features extracted for detecting intrusions and generate intrusion detection models. Feature ranking is a very critical step when building the model. RSC performs feature ranking before generating rules, and converts the feature ranking to minimal hitting set problem addressed by using genetic algorithm (GA). This is done in classical approaches using Support Vector Machine (SVM) by executing many iterations, each of which removes one useless feature. Compared with those methods, our method can avoid many iterations. In addition, a hybrid genetic algorithm is proposed to increase the convergence speed and decrease the training time of RSC. The models generated by RSC take the form of "IF-THEN" rules, which have the advantage of explication. Tests and comparison of RSC with SVM on DARPA benchmark data showed that for Probe and DoS attacks both RSC and SVM yielded highly accurate results (greater than 99% accuracy on testing set).

Comparisons of two methods of harvesting biomass for energy

Treesearch

W.F. Watson; B.J. Stokes; I.W. Savelle

1986-01-01

Two harvesting methods for utilization of understory biomass were tested against a conventional harvesting method to determine relative costs. The conventional harvesting method tested removed all pine 6 inches diameter at breast height (DBH) and larger and hardwood sawlogs as tree length logs. The two intensive harvesting methods were a one-pass and a two-pass method...

Outcome for Patients with Triple-Negative Breast Cancer Is Not Dependent on Race/Ethnicity

PubMed Central

Chu, Quyen D.; Henderson, Amanda E.; Ampil, Fred; Li, Benjamin D. L.

2012-01-01

Introduction. Triple negative breast cancer (TNBC) is biologically aggressive and is associated with a worse prognosis. To understand the impact of race/ethnicity on outcome for patients with TNBC, confounding factors such as socioeconomic status (SES) need to be controlled. We examined the impact of race/ethnicity on a cohort of patients of low SES who have TNBC. Methods. 786 patients with Stage 0–III breast cancer were evaluated. Of these, 202 patients had TNBC (26%). Primary endpoints were cancer recurrence and death. ZIP code-based income tract and institutional financial data were used to assess SES. Data were analyzed using Kaplan-Meier survival analysis, log-rank tests, Cox Proportional hazard regression, chi square test, and t-tests. A P value ≤0.05 was considered statistically significant. Results. Of the 468 African-Americans (60%) in the database, 138 had TNBC; 64 of 318 Caucasians had TNBC. 80% of patients had an annual income of ≤$20,000. The 5-year overall survival was 77% for African-American women versus 72% for Caucasian women (P = 0.95). On multivariate analysis, race/ethnicity had an impact on disease-free survival (P = 0.027) but not on overall survival (P = 0.98). Conclusion. In a predominantly indigent population, race/ethnicity had no impact on overall survival for patients with triple negative breast cancer. PMID:22645687

Application of the BAR score as a predictor of short- and long-term survival in liver transplantation patients.

PubMed

de Campos Junior, Ivan Dias; Stucchi, Raquel Silveira Bello; Udo, Elisabete Yoko; Boin, Ilka de Fátima Santana Ferreira

2015-01-01

The balance of risk (BAR) is a prediction system after liver transplantation. To assess the BAR system, a retrospective observational study was performed in 402 patients who had transplant surgery between 1997 and 2012. The BAR score was computed for each patient. Receiver operating characteristic curve analysis with the Hosmer-Lemeshow test was used to calculate sensitivity, specificity, and model calibration. The cutoff value with the best Youden index was selected. Statistical analysis employed the Kaplan-Meier method (log-rank test) for survival, the Mann-Whitney test for group comparison, and multiple logistic regression analysis. 3-month survival was 46% for BAR ≥ 11 and 77% for BAR <11 (p = 0.001); 12-month survival was 44% for BAR ≥ 11 and 69% for BAR <11 (p = 0.001). Factors of survival <3 months were BAR ≥ 11 [odds ratio (OR) 3.08; 95% confidence interval (CI) 1.75-5.42; p = 0.001] and intrasurgical use of packed red blood cells (RBC) above 6 units (OR 4.49; 95% CI 2.73-7.39; p = 0.001). For survival <12 months, factors were BAR ≥ 11 (OR 2.94; 95% CI 1.67-5.16; p = 0.001) and RBC >6 units (OR 2.99; 95% CI 1.92-4.64; p = 0.001). Our study contributes to the incorporation of the BAR system into Brazilian transplantation centers.

Multicenter Comparison of the Etest and EUCAST Methods for Antifungal Susceptibility Testing of Candida Isolates to Micafungin

PubMed Central

Bougnoux, M.-E.; Accoceberry, I.; Angoulvant, A.; Bailly, E.; Botterel, F.; Chevrier, S.; Chouaki, T.; Dalle, F.; Datry, A.; Dupuis, A.; Fekkar, A.; Gangneux, J. P.; Guitard, J.; Hennequin, C.; Le Govic, Y.; Le Pape, P.; Maubon, D.; Sautour, M.; Sendid, B.; Chandenier, J.

2016-01-01

In vitro susceptibility of 933 Candida isolates, from 16 French hospitals, to micafungin was determined using the Etest in each center. All isolates were then sent to a single center for determination of MICs by the EUCAST reference method. Overall essential agreement between the two tests was 98.5% at ±2 log2 dilutions and 90.2% at ±1 log2 dilutions. Categorical agreement was 98.2%. The Etest is a valuable alternative to EUCAST for the routine determination of micafungin MICs in medical mycology laboratories. PMID:27297480

Hydrogeologic data from test drilling near Verna, Florida, 1978

USGS Publications Warehouse

Barker, Michael; Bowman, Geronia; Sutcliffe, Horace

1981-01-01

Four test wells were drilled in the vicinity of the city of Sarasota well field near Verna, Fla., to provide hydrologic and geologic information. An expedient and economical method of air lifting water samples from isolated water-producing zones while drilling was utilized. Lithologic logs of drill cuttings and geophysical logs, including point resistance and spontaneous potential electric logs, gamma-ray logs, and caliper logs, were made. Chemical quality of water was determined for principal producing zones at each well. Dissolved solids from composite water samples ranged from 313 milligrams per liter in test well 0-1 north of the well field to 728 milligrams per liter in test well 0-3 within the well field. Each test well was pumped to determine maximum discharge, water-level drawdown, and recovery time. A leaking pump column on test well 0-1 prevented accurate measurement of drawdown on the well. Test well 0-2, located east of the well field, had a pumping rate of 376 gallons per minute and 13.11 feet of drawdown after 3 hours and 50 minutes; test well 0-3 had a maximum yield of 320 gallons per minute, a drawdown of 31.91 feet after 2 hours and 35 minutes of pumping, had a recovery time of 20 minutes; and test well 0-4, south of the well field, had a pumping rate of 200 gallons per minute with 63.34 feet of drawdown after 2 hours and 35 minutes. (USGS)

Pearson's chi-square test and rank correlation inferences for clustered data.

PubMed

Shih, Joanna H; Fay, Michael P

2017-09-01

Pearson's chi-square test has been widely used in testing for association between two categorical responses. Spearman rank correlation and Kendall's tau are often used for measuring and testing association between two continuous or ordered categorical responses. However, the established statistical properties of these tests are only valid when each pair of responses are independent, where each sampling unit has only one pair of responses. When each sampling unit consists of a cluster of paired responses, the assumption of independent pairs is violated. In this article, we apply the within-cluster resampling technique to U-statistics to form new tests and rank-based correlation estimators for possibly tied clustered data. We develop large sample properties of the new proposed tests and estimators and evaluate their performance by simulations. The proposed methods are applied to a data set collected from a PET/CT imaging study for illustration. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Gamma Knife radiosurgery for intracranial hemangioblastoma.

PubMed

Silva, Danilo; Grabowski, Mathew M; Juthani, Rupa; Sharma, Mayur; Angelov, Lilyana; Vogelbaum, Michael A; Chao, Samuel; Suh, John; Mohammadi, Alireza; Barnett, Gene H

2016-09-01

Gamma knife radiosurgery (GKRS) has become a treatment option for intracranial hemangioblastomas, especially in patients with poor clinical status and also high-risk surgical candidates. The objective of this study was to analyze clinical outcome and tumor control rates. Retrospective chart review revealed 12 patients with a total of 20 intracranial hemangioblastomas treated with GKRS from May 1998 until December 2014. Kaplan-Meier plots were used to calculate the actuarial local tumor control rates and rate of recurrence following GKRS. Univariate analysis, including log rank test and Wilcoxon test were used on the Kaplan-Meier plots to evaluate the predictors of tumor progression. Two-tailed p value of <0.05 was considered as significant. Median follow-up was 64months (2-184). Median tumor volume pre-GKRS was 946mm(3) (79-15970), while median tumor volume post-GKRS was 356mm(3) (30-5404). Complications were seen in two patients. Tumor control rates were 100% at 1year, 90% at 3years, and 85% at 5years, using the Kaplan-Meier method. There were no statistically significant univariate predictors of progression identified, although there was a trend towards successful tumor control in solid tumors (p=0.07). GKRS is an effective and safe option for treating intracranial hemangioblastoma with favorable tumor control rates. Copyright © 2016 Elsevier Ltd. All rights reserved.

Big genomics and clinical data analytics strategies for precision cancer prognosis.

PubMed

Ow, Ghim Siong; Kuznetsov, Vladimir A

2016-11-07

The field of personalized and precise medicine in the era of big data analytics is growing rapidly. Previously, we proposed our model of patient classification termed Prognostic Signature Vector Matching (PSVM) and identified a 37 variable signature comprising 36 let-7b associated prognostic significant mRNAs and the age risk factor that stratified large high-grade serous ovarian cancer patient cohorts into three survival-significant risk groups. Here, we investigated the predictive performance of PSVM via optimization of the prognostic variable weights, which represent the relative importance of one prognostic variable over the others. In addition, we compared several multivariate prognostic models based on PSVM with classical machine learning techniques such as K-nearest-neighbor, support vector machine, random forest, neural networks and logistic regression. Our results revealed that negative log-rank p-values provides more robust weight values as opposed to the use of other quantities such as hazard ratios, fold change, or a combination of those factors. PSVM, together with the classical machine learning classifiers were combined in an ensemble (multi-test) voting system, which collectively provides a more precise and reproducible patient stratification. The use of the multi-test system approach, rather than the search for the ideal classification/prediction method, might help to address limitations of the individual classification algorithm in specific situation.

Effect of Bromocriptine-QR (a Quick-Release Formulation of Bromocriptine Mesylate) on Major Adverse Cardiovascular Events in Type 2 Diabetes Subjects

PubMed Central

Gaziano, J. Michael; Cincotta, Anthony H.; Vinik, Aaron; Blonde, Lawrence; Bohannon, Nancy; Scranton, Richard

2012-01-01

Background Bromocriptine-QR (a quick-release formulation of bromocriptine mesylate), a dopamine D2 receptor agonist, is a US Food and Drug Administrration–approved treatment for type 2 diabetes mellitus (T2DM). A 3070-subject randomized trial demonstrated a significant, 40% reduction in relative risk among bromocriptine-QR-treated subjects in a prespecified composite cardiovascular (CV) end point that included ischemic-related (myocardial infarction and stroke) and nonischemic-related (hospitalization for unstable angina, congestive heart failure [CHF], or revascularization surgery) end points, but did not include cardiovascular death as a component of this composite. The present investigation was undertaken to more critically evaluate the impact of bromocriptine-QR on cardiovascular outcomes in this study subject population by (1) including CV death in the above-described original composite analysis and then stratifying this new analysis on the basis of multiple demographic subgroups and (2) analyzing the influence of this intervention on only the “hard” CV end points of myocardial infarction, stroke, and CV death (major adverse cardiovascular events [MACEs]). Methods and Results Three thousand seventy T2DM subjects on stable doses of ≤2 antidiabetes medications (including insulin) with HbA1c ≤10.0 (average baseline HbA1c=7.0) were randomized 2:1 to bromocriptine-QR (1.6 to 4.8 mg/day) or placebo for a 52-week treatment period. Subjects with heart failure (New York Heart Classes I and II) and precedent myocardial infarction or revascularization surgery were allowed to participate in the trial. Study outcomes included time to first event for each of the 2 CV composite end points described above. The relative risk comparing bromocriptine-QR with the control for the cardiovascular outcomes was estimated as a hazard ratio with 95% confidence interval on the basis of Cox proportional hazards regression. The statistical significance of any between-group difference in the cumulative percentage of CV events over time (derived from a Kaplan–Meier curve) was determined by a log-rank test on the intention-to-treat population. Study subjects were in reasonable metabolic control, with an average baseline HbA1c of 7.0±1.1, blood pressure of 128/76±14/9, and total and LDL cholesterol of 179±42 and 98±32, respectively, with 88%, 77%, and 69% of subjects being treated with antidiabetic, antihypertensive, and antihyperlipidemic agents, respectively. Ninety-one percent of the expected person-year outcome ascertainment was obtained in this study. Respecting the CV-inclusive composite cardiovascular end point, there were 39 events (1.9%) among 2054 bromocriptine-QR-treated subjects versus 33 events (3.2%) among 1016 placebo subjects, yielding a significant, 39% reduction in relative risk in this end point with bromocriptine-QR exposure (P=0.0346; log-rank test) that was not influenced by age, sex, race, body mass index, duration of diabetes, or preexisting cardiovascular disease. In addition, regarding the MACE end point, there were 14 events (0.7%) among 2054 bromocriptine-QR-treated subjects and 15 events (1.5%) among 1016 placebo-treated subjects, yielding a significant, 52% reduction in relative risk in this end point with bromocriptine-QR exposure (P<0.05; log-rank test). Conclusions These findings reaffirm and extend the original observation of relative risk reduction in cardiovascular adverse events among type 2 diabetes subjects treated with bromocriptine-QR and suggest that further investigation into this impact of bromocriptine-QR is warranted. Clinical Trial Registration URL: http://clinicaltrials.gov. Unique Identifier: NCT00377676 PMID:23316290

Kriging for Simulation Metamodeling: Experimental Design, Reduced Rank Kriging, and Omni-Rank Kriging

NASA Astrophysics Data System (ADS)

Hosking, Michael Robert

This dissertation improves an analyst's use of simulation by offering improvements in the utilization of kriging metamodels. There are three main contributions. First an analysis is performed of what comprises good experimental designs for practical (non-toy) problems when using a kriging metamodel. Second is an explanation and demonstration of how reduced rank decompositions can improve the performance of kriging, now referred to as reduced rank kriging. Third is the development of an extension of reduced rank kriging which solves an open question regarding the usage of reduced rank kriging in practice. This extension is called omni-rank kriging. Finally these results are demonstrated on two case studies. The first contribution focuses on experimental design. Sequential designs are generally known to be more efficient than "one shot" designs. However, sequential designs require some sort of pilot design from which the sequential stage can be based. We seek to find good initial designs for these pilot studies, as well as designs which will be effective if there is no following sequential stage. We test a wide variety of designs over a small set of test-bed problems. Our findings indicate that analysts should take advantage of any prior information they have about their problem's shape and/or their goals in metamodeling. In the event of a total lack of information we find that Latin hypercube designs are robust default choices. Our work is most distinguished by its attention to the higher levels of dimensionality. The second contribution introduces and explains an alternative method for kriging when there is noise in the data, which we call reduced rank kriging. Reduced rank kriging is based on using a reduced rank decomposition which artificially smoothes the kriging weights similar to a nugget effect. Our primary focus will be showing how the reduced rank decomposition propagates through kriging empirically. In addition, we show further evidence for our explanation through tests of reduced rank kriging's performance over different situations. In total, reduced rank kriging is a useful tool for simulation metamodeling. For the third contribution we will answer the question of how to find the best rank for reduced rank kriging. We do this by creating an alternative method which does not need to search for a particular rank. Instead it uses all potential ranks; we call this approach omnirank kriging. This modification realizes the potential gains from reduced rank kriging and provides a workable methodology for simulation metamodeling. Finally, we will demonstrate the use and value of these developments on two case studies, a clinic operation problem and a location problem. These cases will validate the value of this research. Simulation metamodeling always attempts to extract maximum information from limited data. Each one of these contributions will allow analysts to make better use of their constrained computational budgets.

Estimation of the chemical rank for the three-way data: a principal norm vector orthogonal projection approach.

PubMed

Hong-Ping, Xie; Jian-Hui, Jiang; Guo-Li, Shen; Ru-Qin, Yu

2002-01-01

A new approach for estimating the chemical rank of the three-way array called the principal norm vector orthogonal projection method has been proposed. The method is based on the fact that the chemical rank of the three-way data array is equal to one of the column space of the unfolded matrix along the spectral or chromatographic mode. A vector with maximum Frobenius norm is selected among all the column vectors of the unfolded matrix as the principal norm vector (PNV). A transformation is conducted for the column vectors with an orthogonal projection matrix formulated by PNV. The mathematical rank of the column space of the residual matrix thus obtained should decrease by one. Such orthogonal projection is carried out repeatedly till the contribution of chemical species to the signal data is all deleted. At this time the decrease of the mathematical rank would equal that of the chemical rank, and the remaining residual subspace would entirely be due to the noise contribution. The chemical rank can be estimated easily by using an F-test. The method has been used successfully to the simulated HPLC-DAD type three-way data array and two real excitation-emission fluorescence data sets of amino acid mixtures and dye mixtures. The simulation with added relatively high level noise shows that the method is robust in resisting the heteroscedastic noise. The proposed algorithm is simple and easy to program with quite light computational burden.

Gamma-index method sensitivity for gauging plan delivery accuracy of volumetric modulated arc therapy.

PubMed

Park, Jong In; Park, Jong Min; Kim, Jung-In; Park, So-Yeon; Ye, Sung-Joon

2015-12-01

The aim of this study was to investigate the sensitivity of the gamma-index method according to various gamma criteria for volumetric modulated arc therapy (VMAT). Twenty head and neck (HN) and twenty prostate VMAT plans were retrospectively selected for this study. Both global and local 2D gamma evaluations were performed with criteria of 3%/3 mm, 2%/2 mm, 1%/2 mm and 2%/1 mm. In this study, the global and local gamma-index calculated the differences in doses relative to the maximum dose and the dose at the current measurement point, respectively. Using log files acquired during delivery, the differences in parameters at every control point between the VMAT plans and the log files were acquired. The differences in dose-volumetric parameters between reconstructed VMAT plans using the log files and the original VMAT plans were calculated. The Spearman's rank correlation coefficients (rs) were calculated between the passing rates and those differences. Considerable correlations with statistical significances were observed between global 1%/2 mm, local 1%/2 mm and local 2%/1 mm and the MLC position differences (rs = -0.712, -0.628 and -0.581). The numbers of rs values with statistical significance between the passing rates and the changes in dose-volumetric parameters were largest in global 2%/2 mm (n = 16), global 2%/1 mm (n = 15) and local 2%/1 mm (n = 13) criteria. Local gamma-index method with 2%/1 mm generally showed higher sensitivity to detect deviations between a VMAT plan and the delivery of the VMAT plan. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Quantification of heterogeneity observed in medical images.

PubMed

Brooks, Frank J; Grigsby, Perry W

2013-03-02

There has been much recent interest in the quantification of visually evident heterogeneity within functional grayscale medical images, such as those obtained via magnetic resonance or positron emission tomography. In the case of images of cancerous tumors, variations in grayscale intensity imply variations in crucial tumor biology. Despite these considerable clinical implications, there is as yet no standardized method for measuring the heterogeneity observed via these imaging modalities. In this work, we motivate and derive a statistical measure of image heterogeneity. This statistic measures the distance-dependent average deviation from the smoothest intensity gradation feasible. We show how this statistic may be used to automatically rank images of in vivo human tumors in order of increasing heterogeneity. We test this method against the current practice of ranking images via expert visual inspection. We find that this statistic provides a means of heterogeneity quantification beyond that given by other statistics traditionally used for the same purpose. We demonstrate the effect of tumor shape upon our ranking method and find the method applicable to a wide variety of clinically relevant tumor images. We find that the automated heterogeneity rankings agree very closely with those performed visually by experts. These results indicate that our automated method may be used reliably to rank, in order of increasing heterogeneity, tumor images whether or not object shape is considered to contribute to that heterogeneity. Automated heterogeneity ranking yields objective results which are more consistent than visual rankings. Reducing variability in image interpretation will enable more researchers to better study potential clinical implications of observed tumor heterogeneity.

[Establishment of simultaneous measurement method of 8 salivary components using urinary test paper and clinical evaluation of oral environment].

PubMed

Yuuki, Kenji; Tsukasaki, Hiroaki; Kawawa, Tadaharu; Shiba, Akihiko; Shiba, Kiyoko

2008-07-01

Clinical findings were compared with glucose, protein, albumin, bilirubin, creatinine, pH, occult blood, ketone body, nitrite, and white blood cells contained in whole saliva to investigate the components that most markedly reflect the periodontal condition. The subjects were staff of the Prosthodontics Department, Showa University, and patients who visited for dental treatments (57 subjects in total). At the first time, saliva samples were gargled with 1.5 ml of distilled water for 15 seconds and collected by spitting out into a paper cup. At the second time, saliva samples were collected by the same method. At the third time, saliva samples after chewing paraffin gum for 60 seconds were collected by spitting out into a paper cup. Thus whole saliva collecting that was divided on three times. After sampling, 8 mul of the saliva sample was dripped in reagent sticks for the 10 items of urinary test paper and the reflectance was measured using a specific reflectometer. In the periodontal tissue evaluation, the degree of alveolar bone resorption, probing value, and tooth mobility and the presence or absence of lesions in the root furcation were examined and classified into 4 ranks. The mean values in each periodontal disease rank and correlation between the periodontal disease ranks and the components were statistically analyzed. Bilirubin and ketone body were not measurable. The components density of the 8 items was increased as the periodontal disease rank increased. Regarding the correlation between the periodontal disease ranks and the components, high correlations were noted for protein, albumin, creatinine, pH, and white blood cells. The simultaneous measurement method of 8 salivary components using test paper may be very useful for the diagnosis of periodontal disease of abutment teeth.

Improvement of human cell line activation test (h-CLAT) using short-time exposure methods for prevention of false-negative results.

PubMed

Narita, Kazuto; Ishii, Yuuki; Vo, Phuc Thi Hong; Nakagawa, Fumiko; Ogata, Shinichi; Yamashita, Kunihiko; Kojima, Hajime; Itagaki, Hiroshi

2018-01-01

Recently, animal testing has been affected by increasing ethical, social, and political concerns regarding animal welfare. Several in vitro safety tests for evaluating skin sensitization, such as the human cell line activation test (h-CLAT), have been proposed. However, similar to other tests, the h-CLAT has produced false-negative results, including in tests for acid anhydride and water-insoluble chemicals. In a previous study, we demonstrated that the cause of false-negative results from phthalic anhydride was hydrolysis by an aqueous vehicle, with IL-8 release from THP-1 cells, and that short-time exposure to liquid paraffin (LP) dispersion medium could reduce false-negative results from acid anhydrides. In the present study, we modified the h-CLAT by applying this exposure method. We found that the modified h-CLAT is a promising method for reducing false-negative results obtained from acid anhydrides and chemicals with octanol-water partition coefficients (LogK ow ) greater than 3.5. Based on the outcomes from the present study, a combination of the original and the modified h-CLAT is suggested for reducing false-negative results. Notably, the combination method provided a sensitivity of 95% (overall chemicals) or 93% (chemicals with LogK ow > 2.0), and an accuracy of 88% (overall chemicals) or 81% (chemicals with LogK ow > 2.0). We found that the combined method is a promising evaluation scheme for reducing false-negative results seen in existing in vitro skin-sensitization tests. In the future, we expect a combination of original and modified h-CLAT to be applied in a newly developed in vitro test for evaluating skin sensitization.

Coagulation, flocculation, dissolved air flotation and filtration in the removal of Giardia spp. and Cryptosporidium spp. from water supply.

PubMed

Andreoli, Fernando César; Sabogal-Paz, Lyda Patricia

2017-11-15

Removing protozoa from a water supply using coagulation, flocculation, dissolved air flotation (DAF) and filtration on a bench scale was evaluated. Calcium carbonate flocculation with and without immunomagnetic separation (IMS) was chosen to detect Giardia spp. cysts and Cryptosporidium spp. oocysts in the studied samples. The results indicated that DAF removed between 1.31 log and 1.79 log of cysts and between 1.08 log and 1.42 log of oocysts. The performance was lower in filtration, with the removal of 1.07 log-1.44 log for cysts and 0.82 log-0.98 log for oocysts. The coagulation, flocculation, DAF and filtration steps removed more than 2.2 log of cysts and oocysts from the water studied. However, protozoa were detected in the filtered water, even with turbidity values of 0.2 NTU. The recovery of the detection method met the international criteria and was higher when there was no IMS. Including the third acid dissociation in the IMS was critical to improve the performance of the protocol tested. However, there was an increase in the technical and analytical complexity and costs. It was also observed that the efficiency of the treatment was linked to the performance of the selected method of detecting protozoa.

A generic standard additions based method to determine endogenous analyte concentrations by immunoassays to overcome complex biological matrix interference.

PubMed

Pang, Susan; Cowen, Simon

2017-12-13

We describe a novel generic method to derive the unknown endogenous concentrations of analyte within complex biological matrices (e.g. serum or plasma) based upon the relationship between the immunoassay signal response of a biological test sample spiked with known analyte concentrations and the log transformed estimated total concentration. If the estimated total analyte concentration is correct, a portion of the sigmoid on a log-log plot is very close to linear, allowing the unknown endogenous concentration to be estimated using a numerical method. This approach obviates conventional relative quantification using an internal standard curve and need for calibrant diluent, and takes into account the individual matrix interference on the immunoassay by spiking the test sample itself. This technique is based on standard additions for chemical analytes. Unknown endogenous analyte concentrations within even 2-fold diluted human plasma may be determined reliably using as few as four reaction wells.

A new formulation of Gamma Delta Tocotrienol has superior bioavailability compared to existing Tocotrienol-Rich Fraction in healthy human subjects

PubMed Central

Meganathan, Puvaneswari; Jabir, Rafid Salim; Fuang, Ho Gwo; Bhoo-Pathy, Nirmala; Choudhury, Roma Basu; Taib, Nur Aishah; Nesaretnam, Kalanithi; Chik, Zamri

2015-01-01

Gamma and delta tocotrienols are isomers of Vitamin E with established potency in pre-clinical anti-cancer research. This single-dose, randomized, crossover study aimed to compare the safety and bioavailability of a new formulation of Gamma Delta Tocotrienol (GDT) in comparison with the existing Tocotrienol-rich Fraction (TRF) in terms of gamma and delta isomers in healthy volunteers. Subjects were given either two 300 mg GDT (450 mg γ-T3 and 150 mg δ-T3) capsules or four 200 mg TRF (451.2 mg γ-T3 & 102.72 mg δ-T3) capsules and blood samples were taken at several time points over 24 hours. Plasma tocotrienol concentrations were determined using HPLC method. The 90% CI for gamma and delta tocotrienols for the ratio of log-transformation of GDT/TRF for Cmax and AUC0–∞ (values were anti-logged and expressed as a percentage) were beyond the bioequivalence limits (106.21–195.46, 154.11–195.93 and 52.35–99.66, 74.82–89.44 respectively). The Wilcoxon Signed Rank Test for Tmax did not show any significant difference between GDT and TRF for both isomers (p > 0.05). No adverse events were reported during the entire period of study. GDT was found not bioequivalent to TRF, in terms of AUC and Cmax. Gamma tocotrienol in GDT showed superior bioavailability whilst delta tocotrienol showed less bioavailability compared to TRF. PMID:26323969

A new physical method to assess handle properties of fabrics made from wood-based fibers

NASA Astrophysics Data System (ADS)

Abu-Rous, M.; Liftinger, E.; Innerlohinger, J.; Malengier, B.; Vasile, S.

2017-10-01

In this work, the handfeel of fabrics made of wood-based fibers such as viscose, modal and Lyocell was investigated in relation to cotton fabrics applying the Tissue Softness Analyzer (TSA) method in comparison to other classical methods. Two different construction groups of textile were investigated. The validity of TSA in assessing textile softness of these constructions was tested. TSA results were compared to human hand evaluation as well as to classical physical measurements like drape coefficient, ring pull-through and Handle-o-meter, as well as a newer device, the Fabric Touch Tester (FTT). Physical methods as well as human hand assessments mostly agreed on the softest and smoothest range, but showed different rankings in the harder/rougher side fabrics. TSA ranking of softness and smoothness corresponded to the rankings by other physical methods as well as with human hand feel for the basic textile constructions.

Identifying and classifying hyperostosis frontalis interna via computerized tomography.

PubMed

May, Hila; Peled, Nathan; Dar, Gali; Hay, Ori; Abbas, Janan; Masharawi, Youssef; Hershkovitz, Israel

2010-12-01

The aim of this study was to recognize the radiological characteristics of hyperostosis frontalis interna (HFI) and to establish a valid and reliable method for its identification and classification. A reliability test was carried out on 27 individuals who had undergone a head computerized tomography (CT) scan. Intra-observer reliability was obtained by examining the images three times, by the same researcher, with a 2-week interval between each sample ranking. The inter-observer test was performed by three independent researchers. A validity test was carried out using two methods for identifying and classifying HFI: 46 cadaver skullcaps were ranked twice via computerized tomography scans and then by direct observation. Reliability and validity were calculated using Kappa test (SPSS 15.0). Reliability tests of ranking HFI via CT scans demonstrated good results (K > 0.7). As for validity, a very good consensus was obtained between the CT and direct observation, when moderate and advanced types of HFI were present (K = 0.82). The suggested classification method for HFI, using CT, demonstrated a sensitivity of 84%, specificity of 90.5%, and positive predictive value of 91.3%. In conclusion, volume rendering is a reliable and valid tool for identifying HFI. The suggested three-scale classification is most suitable for radiological diagnosis of the phenomena. Considering the increasing awareness of HFI as an early indicator of a developing malady, this study may assist radiologists in identifying and classifying the phenomena.

Information needs for increasing log transport efficiency

Treesearch

Timothy P. McDonald; Steven E. Taylor; Robert B. Rummer; Jorge Valenzuela

2001-01-01

Three methods of dispatching trucks to loggers were tested using a log transport simulation model: random allocation, fixed assignment of trucks to loggers, and dispatch based on knowledge of the current status of trucks and loggers within the system. This 'informed' dispatch algorithm attempted to minimize the difference in time between when a logger would...

Chromosomal Aberrations and Survival after Unrelated Donor Hematopoietic Stem Cell Transplant in Patients with Fanconi Anemia.

PubMed

Wang, Youjin; Zhou, Weiyin; Alter, Blanche P; Wang, Tao; Spellman, Stephen R; Haagenson, Michael; Yeager, Meredith; Lee, Stephanie J; Chanock, Stephen J; Savage, Sharon A; Gadalla, Shahinaz M

2018-06-04

Studies of chromosomal aberrations in blood or bone marrow of patients with Fanconi anemia (FA) have focused on their associations with leukemic transformation. The role of such abnormalities on outcomes after hematopoietic cell transplantation (HCT) is unclear. We used genome-wide single nucleotide polymorphism arrays to identify chromosomal aberrations in pre-HCT blood samples from 73 patients with FA who received unrelated donor HCT for severe aplastic anemia between 1991 and 2007. Outcome data and blood samples were available through the Center for International Blood and Marrow Transplant Research. For survival analyses, we used the Kaplan-Meier estimator to calculate the survival probabilities and the exact log-rank test to compare the survival differences across groups. Chromosomal aberrations were detected in 16 (22%) patients; most frequent were clonal copy loss in chromosome 7 (9.6%), clonal copy gains in the long arm (q) of chromosome 1 (chr1q + ) (8.2%), and clonal or complete copy gains in the q arm of chromosome 3 (chr3q + ) (8.2%). Seven (9.6%) patients had alterations in 3 or more chromosomes. Poor post-HCT overall survival (OS) was noted in patients with chr3q +  (P = .04), or those with abnormalities in ≥3 chromosomes (P = .03). The 1-year OS was 0% versus 45% in patients with either alteration versus its absence. No statistically significant differences in 1-year OS were noted in patients carrying deletions in chr7 (29% versus 42%; log-rank P = .74). The study is limited by the small sample size. A larger, prospective study is warranted to validate our findings in light of recent improvement in transplant modalities and outcomes. Copyright © 2018. Published by Elsevier Inc.

Adverse pathology and undetectable ultrasensitive prostate-specific antigen after radical prostatectomy: is adjuvant radiation warranted?

PubMed

Simon, Ross M; Howard, Lauren E; Freedland, Stephen J; Aronson, William J; Terris, Martha K; Kane, Christopher J; Amling, Christopher L; Cooperberg, Matthew R; Vidal, Adriana C

2016-06-01

To determine if men with adverse pathology but undetectable ultrasensitive (<0.01 ng/mL) PSA are at high-risk for biochemical recurrence (BCR), or if there is a subset of patients at low-risk for whom the benefit of adjuvant radiation therapy might be limited. We evaluated 411 patients treated with RP from 2001 to 2013 without adjuvant radiation who had an undetectable (<0.01 ng/mL) PSA level after RP but with adverse pathology [positive surgical margins (PSMs), extraprostatic extension (EPE), and/or seminal vesicle invasion (SVI)]. Multivariable Cox regression analyses tested the relationship between pathological characteristics and BCR to identify groups of men at highest risk of early BCR. On multivariable analysis, only pathological Gleason 7 (4 + 3), Gleason ≥8, and SVI independently predicted BCR (P = 0.019, P < 0.001, and P = 0.001, respectively), although on two-way analysis men with Gleason 7 (4 + 3) did not have significantly higher rates of BCR compared with patients with Gleason ≤6 (log-rank, P = 0.074). Men with either Gleason ≥8 (with PSMs or EPE) or SVI (15% of the cohort) defined a high-risk group vs men without these characteristics (3-year BCR risk of 50.4% vs 11.9%, log-rank, P < 0.001). Among men with adverse pathology but an undetectable (<0.01 ng/mL) PSA level after RP, the benefits of adjuvant radiation are probably limited except for men with Gleason 8-10 (with PSMs or EPE) or SVI who are at high-risk of early BCR. © 2015 The Authors BJU International © 2015 BJU International Published by John Wiley & Sons Ltd.

Abnormal glucose tolerance post-gestational diabetes mellitus as defined by the International Association of Diabetes and Pregnancy Study Groups criteria.

PubMed

Noctor, Eoin; Crowe, Catherine; Carmody, Louise A; Saunders, Jean A; Kirwan, Breda; O'Dea, Angela; Gillespie, Paddy; Glynn, Liam G; McGuire, Brian E; O'Neill, Ciarán; O'Shea, P M; Dunne, F P

2016-10-01

An increase in gestational diabetes mellitus (GDM) prevalence has been demonstrated across many countries with adoption of the International Association of the Diabetes and Pregnancy Study Groups (IADPSG) diagnostic criteria. Here, we determine the cumulative incidence of abnormal glucose tolerance among women with previous GDM, and identify clinical risk factors predicting this. Two hundred and seventy women with previous IADPSG-defined GDM were prospectively followed up for 5years (mean 2.6) post-index pregnancy, and compared with 388 women with normal glucose tolerance (NGT) in pregnancy. Cumulative incidence of abnormal glucose tolerance (using American Diabetes Association criteria for impaired fasting glucose, impaired glucose tolerance and diabetes) was determined using the Kaplan-Meier method of survival analysis. Cox regression models were constructed to test for factors predicting abnormal glucose tolerance. Twenty-six percent of women with previous GDM had abnormal glucose tolerance vs 4% with NGT, with the log-rank test demonstrating significantly different survival curves (P<0.001). Women meeting IADPSG, but not the World Health Organization (WHO) 1999 criteria, had a lower cumulative incidence than women meeting both sets of criteria, both in the early post-partum period (4.2% vs 21.7%, P<0.001) and at longer-term follow-up (13.7% vs 32.6%, P<0.001). Predictive factors were glucose levels on the pregnancy oral glucose tolerance test, family history of diabetes, gestational week at testing, and BMI at follow-up. The proportion of women developing abnormal glucose tolerance remains high among those with IADPSG-defined GDM. This demonstrates the need for continued close follow-up, although the optimal frequency and method needs further study. © 2016 European Society of Endocrinology.

Crush testing, characterizing, and modeling the crashworthiness of composite laminates

NASA Astrophysics Data System (ADS)

Garner, David Michael, Jr.

Research in the field of crashworthiness of composite materials is presented. A new crush test method was produced to characterize the crush behavior of composite laminates. In addition, a model of the crush behavior and a method for rank ordering the energy absorption capability of various laminates were developed. The new crush test method was used for evaluating the crush behavior of flat carbon/epoxy composite specimens at quasi-static and dynamic rates. The University of Utah crush test fixture was designed to support the flat specimen against catastrophic buckling. A gap, where the specimen is unsupported, allowed unhindered crushing of the specimen. In addition, the specimen's failure modes could be clearly observed during crush testing. Extensive crush testing was conducted wherein the crush force and displacement data were collected to calculate the energy absorption, and high speed video was captured during dynamic testing. Crush tests were also performed over a range of fixture gap heights. The basic failure modes were buckling, crack growth, and fracture. Gap height variations resulted in poorly, properly, and overly constrained specimens. In addition, guidelines for designing a composite laminate for crashworthiness were developed. Modeling of the crush behavior consisted of the delamination and fracture of a single ply or group of like plies during crushing. Delamination crack extension was modeled using the mode I energy release rate, G lc, where an elastica approach was used to obtain the strain energy. Variations in Glc were briefly explored with double cantilever beam tests wherein crack extension occurred along a multidirectional ply interface. The model correctly predicted the failure modes for most of the test cases, and offered insight into how the input parameters affect the model. The ranking method related coefficients of the laminate and sublaminate stiffness matrices, the ply locations within the laminate, and the laminate thickness. The ranking method correctly ordered the laminates tested in this study with respect to their energy absorption.

Linking multimetric and multivariate approaches to assess the ecological condition of streams.

PubMed

Collier, Kevin J

2009-10-01

Few attempts have been made to combine multimetric and multivariate analyses for bioassessment despite recognition that an integrated method could yield powerful tools for bioassessment. An approach is described that integrates eight macroinvertebrate community metrics into a Principal Components Analysis to develop a Multivariate Condition Score (MCS) from a calibration dataset of 511 samples. The MCS is compared to an Index of Biotic Integrity (IBI) derived using the same metrics based on the ratio to the reference site mean. Both approaches were highly correlated although the MCS appeared to offer greater potential for discriminating a wider range of impaired conditions. Both the MCS and IBI displayed low temporal variability within reference sites, and were able to distinguish between reference conditions and low levels of catchment modification and local habitat degradation, although neither discriminated among three levels of low impact. Pseudosamples developed to test the response of the metric aggregation approaches to organic enrichment, urban, mining, pastoral and logging stressor scenarios ranked pressures in the same order, but the MCS provided a lower score for the urban scenario and a higher score for the pastoral scenario. The MCS was calculated for an independent test dataset of urban and reference sites, and yielded similar results to the IBI. Although both methods performed comparably, the MCS approach may have some advantages because it removes the subjectivity of assigning thresholds for scoring biological condition, and it appears to discriminate a wider range of degraded conditions.

“URM Candidates Are Encouraged to Apply”: A National Study to Identify Effective Strategies to Enhance Racial and Ethnic Faculty Diversity in Academic Departments of Medicine

PubMed Central

Peek, Monica E.; Kim, Karen E.; Johnson, Julie K.; Vela, Monica B.

2016-01-01

Purpose There is little evidence regarding which factors and strategies are associated with high proportions of underrepresented minority (URM) faculty in academic medicine. The authors conducted a national study of U.S. academic medicine departments to better understand the challenges, successful strategies, and predictive factors for enhancing racial and ethnic diversity among faculty (i.e., physicians with an academic position or rank). Method This was a mixed-methods study using quantitative and qualitative methods. The authors conducted a cross-sectional study of eligible departments of medicine in 125 accredited U.S. medical schools, dichotomized into low-URM (bottom 50%) versus high-URM rank (top 50%). They used t tests and chi-squared tests to compare departments by geographic region, academic school rank, city type, and composite measures of “diversity best practices.” The authors also conducted semistructured in-depth interviews with a subsample from the highest-and lowest-quartile medical schools in terms of URM rank. Results Eighty-two medical schools responded (66%). Geographic region and academic rank were statistically associated with URM rank, but not city type or composite measures of diversity best practices. Key themes emerged from interviews regarding successful strategies for URM faculty recruitment and retention including institutional leadership, the use of human capital and social relationships and strategic deployment of institutional resources. Conclusions Departments of medicine with high proportions of URM faculty employ a number of successful strategies and programs for recruitment and retention. More research is warranted to identify new successful strategies and to determine the impact of specific strategies on establishing and maintaining workforce diversity. PMID:23348090

Consistency of QSAR models: Correct split of training and test sets, ranking of models and performance parameters.

PubMed

Rácz, A; Bajusz, D; Héberger, K

2015-01-01

Recent implementations of QSAR modelling software provide the user with numerous models and a wealth of information. In this work, we provide some guidance on how one should interpret the results of QSAR modelling, compare and assess the resulting models, and select the best and most consistent ones. Two QSAR datasets are applied as case studies for the comparison of model performance parameters and model selection methods. We demonstrate the capabilities of sum of ranking differences (SRD) in model selection and ranking, and identify the best performance indicators and models. While the exchange of the original training and (external) test sets does not affect the ranking of performance parameters, it provides improved models in certain cases (despite the lower number of molecules in the training set). Performance parameters for external validation are substantially separated from the other merits in SRD analyses, highlighting their value in data fusion.

Compressed sparse tensor based quadrature for vibrational quantum mechanics integrals

DOE PAGES

Rai, Prashant; Sargsyan, Khachik; Najm, Habib N.

2018-03-20

A new method for fast evaluation of high dimensional integrals arising in quantum mechanics is proposed. Here, the method is based on sparse approximation of a high dimensional function followed by a low-rank compression. In the first step, we interpret the high dimensional integrand as a tensor in a suitable tensor product space and determine its entries by a compressed sensing based algorithm using only a few function evaluations. Secondly, we implement a rank reduction strategy to compress this tensor in a suitable low-rank tensor format using standard tensor compression tools. This allows representing a high dimensional integrand function asmore » a small sum of products of low dimensional functions. Finally, a low dimensional Gauss–Hermite quadrature rule is used to integrate this low-rank representation, thus alleviating the curse of dimensionality. Finally, numerical tests on synthetic functions, as well as on energy correction integrals for water and formaldehyde molecules demonstrate the efficiency of this method using very few function evaluations as compared to other integration strategies.« less

Compressed sparse tensor based quadrature for vibrational quantum mechanics integrals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rai, Prashant; Sargsyan, Khachik; Najm, Habib N.

A new method for fast evaluation of high dimensional integrals arising in quantum mechanics is proposed. Here, the method is based on sparse approximation of a high dimensional function followed by a low-rank compression. In the first step, we interpret the high dimensional integrand as a tensor in a suitable tensor product space and determine its entries by a compressed sensing based algorithm using only a few function evaluations. Secondly, we implement a rank reduction strategy to compress this tensor in a suitable low-rank tensor format using standard tensor compression tools. This allows representing a high dimensional integrand function asmore » a small sum of products of low dimensional functions. Finally, a low dimensional Gauss–Hermite quadrature rule is used to integrate this low-rank representation, thus alleviating the curse of dimensionality. Finally, numerical tests on synthetic functions, as well as on energy correction integrals for water and formaldehyde molecules demonstrate the efficiency of this method using very few function evaluations as compared to other integration strategies.« less

Learning to Rank the Severity of Unrepaired Cleft Lip Nasal Deformity on 3D Mesh Data.

PubMed

Wu, Jia; Tse, Raymond; Shapiro, Linda G

2014-08-01

Cleft lip is a birth defect that results in deformity of the upper lip and nose. Its severity is widely variable and the results of treatment are influenced by the initial deformity. Objective assessment of severity would help to guide prognosis and treatment. However, most assessments are subjective. The purpose of this study is to develop and test quantitative computer-based methods of measuring cleft lip severity. In this paper, a grid-patch based measurement of symmetry is introduced, with which a computer program learns to rank the severity of cleft lip on 3D meshes of human infant faces. Three computer-based methods to define the midfacial reference plane were compared to two manual methods. Four different symmetry features were calculated based upon these reference planes, and evaluated. The result shows that the rankings predicted by the proposed features were highly correlated with the ranking orders provided by experts that were used as the ground truth.

Ranking nano-enabled hybrid media for simultaneous removal of contaminants with different chemistries: Pseudo-equilibrium sorption tests versus column tests.

PubMed

Custodio, Tomas; Garcia, Jose; Markovski, Jasmina; McKay Gifford, James; Hristovski, Kiril D; Olson, Larry W

2017-12-15

The underlying hypothesis of this study was that pseudo-equilibrium and column testing conditions would provide the same sorbent ranking trends although the values of sorbents' performance descriptors (e.g. sorption capacity) may vary because of different kinetics and competition effects induced by the two testing approaches. To address this hypothesis, nano-enabled hybrid media were fabricated and its removal performances were assessed for two model contaminants under multi-point batch pseudo-equilibrium and continuous-flow conditions. Calculation of simultaneous removal capacity indices (SRC) demonstrated that the more resource demanding continuous-flow tests are able to generate the same performance rankings as the ones obtained by conducing the simpler pseudo-equilibrium tests. Furthermore, continuous overlap between the 98% confidence boundaries for each SRC index trend, not only validated the hypothesis that both testing conditions provide the same ranking trends, but also pointed that SRC indices are statistically the same for each media, regardless of employed method. In scenarios where rapid screening of new media is required to obtain the best performing synthesis formulation, use of pseudo-equilibrium tests proved to be reliable. Considering that kinetics induced effects on sorption capacity must not be neglected, more resource demanding column test could be conducted only with the top performing media that exhibit the highest sorption capacity. Copyright © 2017 Elsevier B.V. All rights reserved.

Nucleated red blood cells as predictors of mortality in patients with acute respiratory distress syndrome (ARDS): an observational study.

PubMed

Menk, Mario; Giebelhäuser, Lena; Vorderwülbecke, Gerald; Gassner, Martina; Graw, Jan A; Weiss, Björn; Zimmermann, Mathias; Wernecke, Klaus-D; Weber-Carstens, Steffen

2018-03-27

Nucleated red blood cells (NRBCs) in critically ill patients are associated with increased mortality and poor outcome. The aim of the present study was to evaluate the predictive value of NRBCs in patients with acute respiratory distress syndrome (ARDS). This observational study was conducted at an ARDS referral center and included patients from 2007 to 2014. Daily NRBC counts were assessed and the predictive validity of NRBCs on mortality was statistically evaluated. A cutoff for prediction of mortality based on NRBCs was evaluated using ROC analysis and specified according to Youden's method. Multivariate nonparametric analysis for longitudinal data was applied to prove for differences between groups over the whole time course. Independent predictors of mortality were identified with multiple logistic and Cox' regression analyses. Kaplan-Meier estimations visualized the survival; the corresponding curves were tested for differences with the log-rank test. A total of 404 critically ill ARDS patients were analyzed. NRBCs were found in 75.5% of the patients, which was associated with longer length of ICU stay [22 (11; 39) vs. 14 (7; 26) days; p < 0.05] and higher mortality rates (50.8 vs. 27.3%; p < 0.001). Logistic regression analysis with mortality as response showed NRBC positivity per se to be an independent risk factor for mortality in ARDS with a doubled risk for ICU death (OR 2.03; 95% CI 1.16-3.55; p < 0.05). Also, NRBC value at ICU admission was found to be an independent risk factor for mortality (OR 3.25; 95% CI 1.09-9.73, p = 0.035). A cutoff level of 220 NRBC/µl was associated with a more than tripled risk of ICU death (OR 3.2; 95% CI 1.93-5.35; p < 0.0001). ARDS patients below this threshold level had a significant survival advantage (median survival 85 days vs. 29 days; log rank p < 0.001). Presence of a severe ARDS was identified as independent risk factor for the occurrence of NRBCs > 220/µl (OR 1.81; 95% CI 1.1-2.97; p < 0.05). NRBCs may predict mortality in ARDS with high prognostic power. The presence of NRBCs in the blood might be regarded as a marker of disease severity indicating a higher risk of ICU death.

Iterative deblending of simultaneous-source data using a coherency-pass shaping operator

NASA Astrophysics Data System (ADS)

Zu, Shaohuan; Zhou, Hui; Mao, Weijian; Zhang, Dong; Li, Chao; Pan, Xiao; Chen, Yangkang

2017-10-01

Simultaneous-source acquisition helps greatly boost an economic saving, while it brings an unprecedented challenge of removing the crosstalk interference in the recorded seismic data. In this paper, we propose a novel iterative method to separate the simultaneous source data based on a coherency-pass shaping operator. The coherency-pass filter is used to constrain the model, that is, the unblended data to be estimated, in the shaping regularization framework. In the simultaneous source survey, the incoherent interference from adjacent shots greatly increases the rank of the frequency domain Hankel matrix that is formed from the blended record. Thus, the method based on rank reduction is capable of separating the blended record to some extent. However, the shortcoming is that it may cause residual noise when there is strong blending interference. We propose to cascade the rank reduction and thresholding operators to deal with this issue. In the initial iterations, we adopt a small rank to severely separate the blended interference and a large thresholding value as strong constraints to remove the residual noise in the time domain. In the later iterations, since more and more events have been recovered, we weaken the constraint by increasing the rank and shrinking the threshold to recover weak events and to guarantee the convergence. In this way, the combined rank reduction and thresholding strategy acts as a coherency-pass filter, which only passes the coherent high-amplitude component after rank reduction instead of passing both signal and noise in traditional rank reduction based approaches. Two synthetic examples are tested to demonstrate the performance of the proposed method. In addition, the application on two field data sets (common receiver gathers and stacked profiles) further validate the effectiveness of the proposed method.

Some design issues of strata-matched non-randomized studies with survival outcomes.

PubMed

Mazumdar, Madhu; Tu, Donsheng; Zhou, Xi Kathy

2006-12-15

Non-randomized studies for the evaluation of a medical intervention are useful for quantitative hypothesis generation before the initiation of a randomized trial and also when randomized clinical trials are difficult to conduct. A strata-matched non-randomized design is often utilized where subjects treated by a test intervention are matched to a fixed number of subjects treated by a standard intervention within covariate based strata. In this paper, we consider the issue of sample size calculation for this design. Based on the asymptotic formula for the power of a stratified log-rank test, we derive a formula to calculate the minimum number of subjects in the test intervention group that is required to detect a given relative risk between the test and standard interventions. When this minimum number of subjects in the test intervention group is available, an equation is also derived to find the multiple that determines the number of subjects in the standard intervention group within each stratum. The methodology developed is applied to two illustrative examples in gastric cancer and sarcoma.

A coalition partnership of vision health through a health-promoting school program for primary school students in Taiwan.

PubMed

Chang, Li-Chun; Guo, Jong-Long; Liao, Li-Ling; Peng, Hsiu-Ying; Hsieh, Pei-Lin

2017-09-01

Myopia, the most common refractive error, is the most common cause of avoidable visual impairment among children and has reached epidemic proportions among children and young adults in urban areas of East and Southeast Asia that contain populations of Chinese ancestry. Moreover, vision health is an important theme of the health-promoting school program issued by the Ministry of Education in Taiwan. The aim of this study is to assess the impact of pre- and post-intervention proposed by the health-promoting school (HPS) model. The objectives are to understand whether the HPS model influenced the vision screening results and the attitude, knowledge level, and vision care behavior of the students involved. A prospective cohort study design was used to evaluate a vision health program. Four elementary schools, local education authorities, and one university in northern Taiwan established a coalition partnership to design a six-month program to combat myopia among students. The target population was 6668 school children from local elementary schools. For the purpose of this study, the outcome of visual acuity testing (in logMAR) was analyzed with a sampling of 373 school children (aged 11-12 years old) who were chosen from high prevalence of poor vision classes. After the HPS program, the attitudes, behaviors, and knowledge levels of the school children regarding vision health were significantly improved. The pre-intervention mean logMAR of all participating students ( N = 373) was -.10, which increased to -.19 after the intervention. Analysis using the Wilcoxon signed-rank test showed that the logMAR value was significantly improved after the intervention ( t = 2.13, p < 0.05). Our findings highlight the relevance and effectiveness of the coalition's efforts, which reinforces the usefulness of co-operatively implementing the HPS program.

p63 and Ki-67 immunostainings in laryngeal squamous cell carcinoma are related to survival.

PubMed

Re, M; Zizzi, A; Ferrante, L; Stramazzotti, D; Goteri, G; Gioacchini, F M; Olivieri, F; Magliulo, G; Rubini, C

2014-06-01

To examine the prognostic significance of the immunohistochemical expression of p63 and Ki-67 oncoproteins in patients with laryngeal squamous cell carcinoma, a retrospective evaluation was carried out on a cohort of 108 patients with primary laryngeal squamous cell carcinoma (LSCC) treated by primary surgery. For the immunohistochemical evaluation, tissue section obtained by formalin-fixed and paraffin-embedded tissue blocks from resection of each patient was used. Clinicopathologic data were associated with the immunostaining results. The association among the considered variables was assessed by Fisher's exact test, Mann-Whitney test, non-parametric χ(2) test, and Spearman's rho rank test was used to assess the relations among them. Differences in p63 and Ki-67 immunoreactivity among the different groups were compared via Kruskal-Wallis test and post hoc tests were performed using Mann-Whitney test with Bonferroni correction. The overall survival rate was estimated via Kaplan-Meier method, and the cumulative incidence functions for different groups were compared using log-rank statistics. Cox proportional hazard model was employed in a multivariate analysis to assess the effect of prognostic factors in the overall survival rate. Furthermore, taking into account death due to other causes, we estimated LSCC-related survival and disease-free survival rates using competing risk analysis. The results of immunohistochemical examination showed a statistically significant relationship between the up-regulation of P63 and Ki-67, an increase in histological grading, and primary tumours associated with lymph node metastases. p63 and Ki-67 up-regulation was related to a shorter disease-free survival and a significant association was found between p63 and Ki-67 percentage of positive cells and patient survival. Finally, we noticed a significant relation between p63 and Ki-67 (ρ = 0.87). On the other hand, no statistically significant associations were found between p63 and Ki-67 down-regulation and clinicopathologic data. Our findings suggest that abnormal p63 and Ki-67 immunoreactivity may be involved in the early phases of laryngeal tumorigenesis and may become a significant prognostic predictor for both overall and disease-free survivals. These biomarkers could thus help in the selection of high-risk patients with LSCC who may benefit from more aggressive therapy or chemoprevention.

MDM2 promoter polymorphism and p53 codon 72 polymorphism in chronic myeloid leukemia: the association between MDM2 promoter genotype and disease susceptibility, age of onset, and blast-free survival in chronic phase patients receiving imatinib.

PubMed

Liu, Yi-Chang; Hsiao, Hui-Hua; Yang, Wen-Chi; Liu, Ta-Chih; Chang, Chao-Sung; Yang, Ming-Yu; Lin, Pai-Mei; Hsu, Jui-Feng; Lee, Ching-Ping; Lin, Sheng-Fung

2014-12-01

The genetic or functional inactivation of the p53 pathway plays an important role with regards to disease progression from the chronic phase (CP) to blast phase (BP) and imatinib treatment response in chronic myeloid leukemia (CML). Two functional single nucleotide polymorphisms (SNPs), p53 R72P and MDM2 SNP309, are associated with alternation of p53 activity, however the association regarding CML susceptibility and BP transformation under imatinib treatment is unclear. The MDM2 SNP309 genotype was determined by polymerase chain reaction-restriction fragment length polymorphism and confirmed by direct sequencing from 116 CML patients, including 104 in the CP at diagnosis, and 162 healthy Taiwanese controls. The p53 R72P polymorphism was examined in all CML patients. The SNP309 G/G genotype was associated with an increased risk of CML susceptibility (OR: 1.82, 95% CI: 1.03-3.22, P = 0.037), and an earlier age of disease onset (log-rank P = 0.005) compared with the T/T + T/G genotypes. Higher MDM2 mRNA expression was found in G/G genotype compared with T/T (P = 0.034) and T/T + T/G (P = 0.056) genotypes. No associations were found between the p53 R72P genotypes and clinical parameters and survival outcomes. Among 62 CP patients receiving imatinib as first-line therapy, the G/G genotype was associated with a shorter blast-free survival (log-rank P = 0.048) and more clonal evolution compared with the T/T + T/G genotypes. In patients with advanced diseases at diagnosis, the G/G genotype was associated with a poor overall survival (log-rank P = 0.006). Closely monitoring CML patients harboring the G/G genotype and further large-scale studies are warranted. © 2013 Wiley Periodicals, Inc.

Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera.

PubMed

De Marchi, Tommaso; Kuhn, Erik; Dekker, Lennard J; Stingl, Christoph; Braakman, Rene B H; Opdam, Mark; Linn, Sabine C; Sweep, Fred C G J; Span, Paul N; Luider, Theo M; Foekens, John A; Martens, John W M; Carr, Steven A; Umar, Arzu

2016-04-01

We recently reported on the development of a 4-protein-based classifier (PDCD4, CGN, G3BP2, and OCIAD1) capable of predicting outcome to tamoxifen treatment in recurrent, estrogen-receptor-positive breast cancer based on high-resolution MS data. A precise and high-throughput assay to measure these proteins in a multiplexed, targeted fashion would be favorable to measure large numbers of patient samples to move these findings toward a clinical setting. By coupling immunoprecipitation to multiple reaction monitoring (MRM) MS and stable isotope dilution, we developed a high-precision assay to measure the 4-protein signature in 38 primary breast cancer whole tissue lysates (WTLs). Furthermore, we evaluated the presence and patient stratification capabilities of our signature in an independent set of 24 matched (pre- and post-therapy) sera. We compared the performance of immuno-MRM (iMRM) with direct MRM in the absence of fractionation and shotgun proteomics in combination with label-free quantification (LFQ) on both WTL and laser capture microdissected (LCM) tissues. Measurement of the 4-proteins by iMRM showed not only higher accuracy in measuring proteotypic peptides (Spearman r: 0.74 to 0.93) when compared with MRM (Spearman r: 0.0 to 0.76) but also significantly discriminated patient groups based on treatment outcome (hazard ratio [HR]: 10.96; 95% confidence interval [CI]: 4.33 to 27.76; Log-rank P < 0.001) when compared with LCM (HR: 2.85; 95% CI: 1.24 to 6.54; Log-rank P = 0.013) and WTL (HR: 1.16; 95% CI: 0.57 to 2.33; Log-rank P = 0.680) LFQ-based predictors. Serum sample analysis by iMRM confirmed the detection of the four proteins in these samples. We hereby report that iMRM outperformed regular MRM, confirmed our previous high-resolution MS results in tumor tissues, and has shown that the 4-protein signature is measurable in serum samples.

Comparison of long-term results between laparoscopy-assisted gastrectomy and open gastrectomy with D2 lymph node dissection for advanced gastric cancer.

PubMed

Hamabe, Atsushi; Omori, Takeshi; Tanaka, Koji; Nishida, Toshirou

2012-06-01

Laparoscopy-assisted gastrectomy (LAG) has been established as a low-invasive surgery for early gastric cancer. However, it remains unknown whether it is applicable also for advanced gastric cancer, mainly because the long-term results of LAG with D2 lymph node dissection for advanced gastric cancer have not been well validated compared with open gastrectomy (OG). A retrospective cohort study was performed to compare LAG and OG with D2 lymph node dissection. For this study, 167 patients (66 LAG and 101 OG patients) who underwent gastrectomy with D2 lymph node dissection for advanced gastric cancer were reviewed. Recurrence-free survival and overall survival time were estimated using Kaplan-Meier curves. Stratified log-rank statistical evaluation was used to compare the difference between the LAG and OG groups stratified by histologic type, pathologic T status, N status, and postoperative adjuvant chemotherapy. The adjusted Cox proportional hazards regression models were used to calculate the hazard ratios (HRs) of LAG. The 5-year recurrence-free survival rate was 89.6% in the LAG group and 75.8% in the OG group (nonsignificant difference; stratified log-rank statistic, 3.11; P = 0.0777). The adjusted HR of recurrence for LAG compared with OG was 0.389 [95% confidence interval (CI) 0.131-1.151]. The 5-year overall survival rate was 94.4% in the LAG group and 78.5% in the OG group (nonsignificant difference; stratified log-rank statistic, 0.4817; P = 0.4877). The adjusted HR of death for LAG compared with OG was 0.633 (95% CI 0.172-2.325). The findings show that LAG with D2 lymph node dissection is acceptable in terms of long-term results for advanced gastric cancer cases and may be applicable for advanced gastric cancer treatment.

Outcomes after radical prostatectomy for patients with clinical stages T1-T2 prostate cancer with pathologically positive lymph nodes in the prostate-specific antigen era.

PubMed

Dorin, Ryan P; Lieskovsky, Gary; Fairey, Adrian S; Cai, Jie; Daneshmand, Siamak

2013-11-01

To evaluate the outcomes of radical prostatectomy (RP) and pelvic lymph node dissection (PLND) for clinically organ confined prostate cancer (CaP) with regional lymph node metastases (pN1) treated in the era of prostate-specific antigen (PSA) screening. A single institution cohort of 2,487 men with cT1-T2 CaP treated with open radical prostatectomy and pelvic lymph node dissection between 1988 and 2008 were analyzed. Kaplan-Meier and Cox proportional regression models were used to analyze overall survival (OS), clinical recurrence-free survival (cRFS), and biochemical recurrence-free survival (bRFS). Overall, 150 out of 2,487 patients (6%) had pN1 disease, with a median follow-up of 10.4 years. The predicted 10-year OS, cRFS, and bRFS rates for patients with pN0 and pN1 were 86% and 74% (Log rank P < 0.001), 97% and 84% (Log rank P < 0.001), and 88% and 57% (Log rank P < 0.001), respectively. In the subset of pN1 patients treated with surgery only (n = 49), the predicted 10-year OS, cRFS, and bRFS rates were 81%, 80%, and 59%, respectively. Exploratory univariate regression analysis showed that age (P = 0.003), total number of lymph nodes identified (P = 0.040), and total number of positive lymph nodes identified (P = 0.004) were associated with OS. Total number of positive lymph nodes (LNs) identified was also significantly associated with cRFS (P = 0.05). The incidence of pN1 in patients with cT1-T2 CaP treated with surgery in the era of PSA screening was low. RP and PLND demonstrated therapeutic efficacy in a subset of pN1 patients treated with surgery alone. Copyright © 2013 Elsevier Inc. All rights reserved.

Development of Castration Resistant Prostate Cancer can be Predicted by a DNA Hypermethylation Profile.

PubMed

Angulo, Javier C; Andrés, Guillermo; Ashour, Nadia; Sánchez-Chapado, Manuel; López, Jose I; Ropero, Santiago

2016-03-01

Detection of DNA hypermethylation has emerged as a novel molecular biomarker for prostate cancer diagnosis and evaluation of prognosis. We sought to define whether a hypermethylation profile of patients with prostate cancer on androgen deprivation would predict castrate resistant prostate cancer. Genome-wide methylation analysis was performed using a methylation cancer panel in 10 normal prostates and 45 tumor samples from patients placed on androgen deprivation who were followed until castrate resistant disease developed. Castrate resistant disease was defined according to EAU (European Association of Urology) guideline criteria. Two pathologists reviewed the Gleason score, Ki-67 index and neuroendocrine differentiation. Hierarchical clustering analysis was performed and relationships with outcome were investigated by Cox regression and log rank analysis. We found 61 genes that were significantly hypermethylated in greater than 20% of tumors analyzed. Three clusters of patients were characterized by a DNA methylation profile, including 1 at risk for earlier castrate resistant disease (log rank p = 0.019) and specific mortality (log rank p = 0.002). Hypermethylation of ETV1 (HR 3.75) and ZNF215 (HR 2.89) predicted disease progression despite androgen deprivation. Hypermethylation of IRAK3 (HR 13.72), ZNF215 (HR 4.81) and SEPT9 (HR 7.64) were independent markers of prognosis. Prostate specific antigen greater than 25 ng/ml, Gleason pattern 5, Ki-67 index greater than 12% and metastasis at diagnosis also predicted a negative response to androgen deprivation. Study limitations included the retrospective design and limited number of cases. Epigenetic silencing of the mentioned genes could be novel molecular markers for the prognosis of advanced prostate cancer. It might predict castrate resistance during hormone deprivation and, thus, disease specific mortality. Gene hypermethylation is associated with disease progression in patients who receive hormone therapy. It could serve as a marker of the treatment response. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Statistical grand rounds: a review of analysis and sample size calculation considerations for Wilcoxon tests.

PubMed

Divine, George; Norton, H James; Hunt, Ronald; Dienemann, Jacqueline

2013-09-01

When a study uses an ordinal outcome measure with unknown differences in the anchors and a small range such as 4 or 7, use of the Wilcoxon rank sum test or the Wilcoxon signed rank test may be most appropriate. However, because nonparametric methods are at best indirect functions of standard measures of location such as means or medians, the choice of the most appropriate summary measure can be difficult. The issues underlying use of these tests are discussed. The Wilcoxon-Mann-Whitney odds directly reflects the quantity that the rank sum procedure actually tests, and thus it can be a superior summary measure. Unlike the means and medians, its value will have a one-to-one correspondence with the Wilcoxon rank sum test result. The companion article appearing in this issue of Anesthesia & Analgesia ("Aromatherapy as Treatment for Postoperative Nausea: A Randomized Trial") illustrates these issues and provides an example of a situation for which the medians imply no difference between 2 groups, even though the groups are, in fact, quite different. The trial cited also provides an example of a single sample that has a median of zero, yet there is a substantial shift for much of the nonzero data, and the Wilcoxon signed rank test is quite significant. These examples highlight the potential discordance between medians and Wilcoxon test results. Along with the issues surrounding the choice of a summary measure, there are considerations for the computation of sample size and power, confidence intervals, and multiple comparison adjustment. In addition, despite the increased robustness of the Wilcoxon procedures relative to parametric tests, some circumstances in which the Wilcoxon tests may perform poorly are noted, along with alternative versions of the procedures that correct for such limitations. 

The Continuized Log-Linear Method: An Alternative to the Kernel Method of Continuization in Test Equating

ERIC Educational Resources Information Center

Wang, Tianyou

2008-01-01

Von Davier, Holland, and Thayer (2004) laid out a five-step framework of test equating that can be applied to various data collection designs and equating methods. In the continuization step, they presented an adjusted Gaussian kernel method that preserves the first two moments. This article proposes an alternative continuization method that…

Comparison of liquid chemical sterilization with peracetic acid and ethylene oxide sterilization for long narrow lumens.

PubMed

Alfa, M J; DeGagne, P; Olson, N; Hizon, R

1998-10-01

The aim of this study was to determine how well peracetic acid liquid chemical sterilization (LCPAS) killed test organisms in the presence of 10% fetal bovine serum and 0.65% salt challenge (RPMI-S) compared with a 100% ethylene oxide (ETO) sterilizer and an ETO hydrochlorofluorocarbon (ETO-HCFC) sterilization method with long (125 cm), narrow (3-mm internal diameter) flexible lumens as the test carrier. The inoculated lumens were dried overnight before processing. The test organisms included Mycobacterium chelonei, Enterococcus faecalis, and Bacillus subtilis. For all 3 organisms tested, the LCPAS process resulted in a 6 log10 reduction in bacterial load compared with a 2.5 log10 to 6 log10 reduction for the 100% ETO and ETO-HCFC sterilizers. Sterilization was achieved for 100%, 61%, and 67% of the lumen test carriers for the LCPAS, 100% ETO, and ETO-HCFC sterilizers, respectively. The data indicate that of the sterilization methods evaluated, LCPAS was the most effective for sterilizing narrow flexible lumens in the presence of residual inorganic and organic soil. This effectiveness was achieved through a combination of organism wash-off and peracetic acid sterilant killing of organisms. Salt was the major compounding factor for effective ETO gas sterilization, because carriers inoculated with organisms in 10% fetal bovine serum alone all were sterilized by both 100% ETO and ETO-HCFC sterilization methods. Our data support the critical need to ensure adequate precleaning of narrow flexible lumen endoscopes before any sterilization method.

Multicenter Comparison of the Etest and EUCAST Methods for Antifungal Susceptibility Testing of Candida Isolates to Micafungin.

PubMed

Bougnoux, M-E; Dannaoui, E; Accoceberry, I; Angoulvant, A; Bailly, E; Botterel, F; Chevrier, S; Chouaki, T; Cornet, M; Dalle, F; Datry, A; Dupuis, A; Fekkar, A; Gangneux, J P; Guitard, J; Hennequin, C; Le Govic, Y; Le Pape, P; Maubon, D; Ranque, S; Sautour, M; Sendid, B; Chandenier, J

2016-08-01

In vitro susceptibility of 933 Candida isolates, from 16 French hospitals, to micafungin was determined using the Etest in each center. All isolates were then sent to a single center for determination of MICs by the EUCAST reference method. Overall essential agreement between the two tests was 98.5% at ±2 log2 dilutions and 90.2% at ±1 log2 dilutions. Categorical agreement was 98.2%. The Etest is a valuable alternative to EUCAST for the routine determination of micafungin MICs in medical mycology laboratories. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Long-term prognosis in patients continuing taking antithrombotics after peptic ulcer bleeding.

PubMed

Wang, Xi-Xu; Dong, Bo; Hong, Biao; Gong, Yi-Qun; Wang, Wei; Wang, Jue; Zhou, Zhen-Yu; Jiang, Wei-Jun

2017-01-28

To investigate the long-term prognosis in peptic ulcer patients continuing taking antithrombotics after ulcer bleeding, and to determine the risk factors that influence the prognosis. All clinical data of peptic ulcer patients treated from January 1, 2009 to January 1, 2014 were retrospectively collected and analyzed. Patients were divided into either a continuing group to continue taking antithrombotic drugs after ulcer bleeding or a discontinuing group to discontinue antithrombotic drugs. The primary outcome of follow-up in peptic ulcer bleeding patients was recurrent bleeding, and secondary outcome was death or acute cardiovascular disease occurrence. The final date of follow-up was December 31, 2014. Basic demographic data, complications, and disease classifications were analyzed and compared by t - or χ 2 -test. The number of patients that achieved various outcomes was counted and analyzed statistically. A survival curve was drawn using the Kaplan-Meier method, and the difference was compared using the log-rank test. COX regression multivariate analysis was applied to analyze risk factors for the prognosis of peptic ulcer patients. A total of 167 patients were enrolled into this study. As for the baseline information, differences in age, smoking, alcohol abuse, and acute cardiovascular diseases were statistically significant between the continuing and discontinuing groups (70.8 ± 11.4 vs 62.4 ± 12.0, P < 0.001; 8 (8.2%) vs 15 (21.7%), P < 0.05; 65 (66.3%) vs 13 (18.8%), P < 0.001). At the end of the study, 18 patients had recurrent bleeding and three patients died or had acute cardiovascular disease in the continuing group, while four patients had recurrent bleeding and 15 patients died or had acute cardiovascular disease in the discontinuing group. The differences in these results were statistically significant ( P = 0.022, P = 0.000). The Kaplan-Meier survival curve indicated that the incidence of recurrent bleeding was higher in patients in the continuing group, and the risk of death and developing acute cardiovascular disease was higher in patients in the discontinuing group (log-rank test, P = 0.000 for both). Furthermore, COX regression multivariate analysis revealed that the hazard ratio (HR) for recurrent bleeding was 2.986 (95%CI: 067-8.356, P = 0.015) in the continuing group, while HR for death or acute cardiovascular disease was 5.216 (95%CI: 1.035-26.278, P = 0.028). After the occurrence of peptic ulcer bleeding, continuing antithrombotics increases the risk of recurrent bleeding events, while discontinuing antithrombotics would increase the risk of death and developing cardiovascular disease. This suggests that clinicians should comprehensively consider the use of antithrombotics after peptic ulcer bleeding.

The Role of 3T Magnetic Resonance Imaging for Targeting the Human Subthalamic Nucleus in Deep Brain Stimulation for Parkinson Disease.

PubMed

Longhi, Michele; Ricciardi, Giuseppe; Tommasi, Giorgio; Nicolato, Antonio; Foroni, Roberto; Bertolasi, Laura; Beltramello, Alberto; Moretto, Giuseppe; Tinazzi, Michele; Gerosa, Massimo

2015-05-01

Chronic stimulation of the human subthalamic nucleus (STN) is gradually becoming accepted as a long-term therapeutic option for patients with advanced Parkinson disease (PD). 3Tesla (T) magnetic resonance imaging (MRI) improves contrast resolution in basal ganglia nuclei containing high levels of iron, because of magnetic susceptibility effects that increase significantly as the magnetic field gets higher. This phenomenon can be used for better visualization of the STN and may reduce the time necessary for detailed microrecording (MER) mapping, increasing surgery efficacy and lowering morbidity. The objective of this retrospective study is to analyze a population of 20 deep brain stimulation (DBS) electrode implanted patients with PD divided into two groups in which different targeting methods were used. Mean age was 56 years (range 37 to 69 years). Mean disease duration was 11.6 years. Mean follow-up was 12 months (range 6 to 36 months). Patients were divided into two groups: Group A contained 6 patients who underwent STN targeting using 1T stereotactic (T1w + T2w) MRI plus STN indirect atlas derived targeting. Group B consisted of 14 patients who underwent STN targeting using 3T nonstereotactic (T2w) MRI fused with 1T T1w stereotactic MRI and STN direct targeting. For statistical analysis, we compared (five different parameters in both (matched) groups: Unified Parkinson's disease rating scale (UPDRS) score reduction (medication off before surgery against stimulation on/medication off after surgery), postoperative drug reduction, duration of surgery, the "central preoperative track" chosen as final implantation track during surgery, and correspondence between the targeted STN and the intraoperative neurophysiologic data. Mean UPDRS III score reduction (medication off/stimulation on versus preoperative medication off) was 69% in Group A and 74% in Group B (p = 0.015, log-rank test) respectively. Postoperatively, antiparkinsonian treatment was reduced by 66% in Group A and 75% in Group B (p = 0.006, log-rank test). The preoperative "central" track (which corresponds to ideal STN targeting) proved to be the most clinically effective in 2/12 leads for Group A versus 21/28 for Group B (p < 0.001).Neurophysiologic data confirmed these results; the hypothetical target was confirmed by MER data in 76% of tracks in Group A, and in 75% of tracks in Group B (p < 0.001, univariate and multivariate analysis). 3T MRI appears to be a useful tool in STN-DBS preoperative targeting. Neurophysiologic testing remains fundamental to determine lead deepness (and prevent clinical side effects. Georg Thieme Verlag KG Stuttgart · New York.

Socially transmitted diffusion of a novel behaviour from subordinate chimpanzees

PubMed Central

Watson, Stuart K; Reamer, Lisa A; Mareno, Mary Catherine; Vale, Gillian; Harrison, Rachel A; Lambeth, Susan P; Schapiro, Steven J; Whiten, Andrew

2017-01-01

Chimpanzees (Pan troglodytes) demonstrate much cultural diversity in the wild, yet a majority of novel behaviours do not become group-wide traditions. Since many such novel behaviours are introduced by low-ranking individuals, a bias toward copying dominant individuals (‘rank-bias’) has been proposed as an explanation for their limited diffusion. Previous experimental work showed that chimpanzees (Pan troglodytes) preferentially copy dominant over low-rank models. We investigated whether low ranking individuals may nevertheless successfully seed a beneficial behaviour as a tradition if there are no ‘competing’ models. In each of four captive groups, either a single high-rank (HR, n=2) or a low-rank (LR, n=2) chimpanzee model was trained on one method of opening a two-action puzzle-box, before demonstrating the trained method in a group context. This was followed by eight hours of group-wide, open-access to the puzzle-box. Successful manipulations and observers of each manipulation were recorded. Barnard’s exact tests showed that individuals in the LR groups used the seeded method as their first-choice option at significantly above chance levels, whereas those in the HR groups did not. Furthermore, individuals in the LR condition used the seeded method on their first attempt significantly more often than those in the HR condition. A network-based diffusion analysis revealed that the best supported statistical models were those in which social transmission occurred only in groups with subordinate models. Finally, we report an innovation by a subordinate individual that built cumulatively on existing methods of opening the puzzle-box and was subsequently copied by a dominant observer. These findings illustrate that chimpanzees are motivated to copy rewarding novel behaviours that are demonstrated by subordinate individuals and that, in some cases, social transmission may be constrained by high-rank demonstrators. PMID:28171684

Handwashing and Ebola virus disease outbreaks: A randomized comparison of soap, hand sanitizer, and 0.05% chlorine solutions on the inactivation and removal of model organisms Phi6 and E. coli from hands and persistence in rinse water

PubMed Central

Gallandat, Karin; Daniels, Kyle; Desmarais, Anne Marie; Scheinman, Pamela; Lantagne, Daniele

2017-01-01

To prevent Ebola transmission, frequent handwashing is recommended in Ebola Treatment Units and communities. However, little is known about which handwashing protocol is most efficacious. We evaluated six handwashing protocols (soap and water, alcohol-based hand sanitizer (ABHS), and 0.05% sodium dichloroisocyanurate, high-test hypochlorite, and stabilized and non-stabilized sodium hypochlorite solutions) for 1) efficacy of handwashing on the removal and inactivation of non-pathogenic model organisms and, 2) persistence of organisms in rinse water. Model organisms E. coli and bacteriophage Phi6 were used to evaluate handwashing with and without organic load added to simulate bodily fluids. Hands were inoculated with test organisms, washed, and rinsed using a glove juice method to retrieve remaining organisms. Impact was estimated by comparing the log reduction in organisms after handwashing to the log reduction without handwashing. Rinse water was collected to test for persistence of organisms. Handwashing resulted in a 1.94–3.01 log reduction in E. coli concentration without, and 2.18–3.34 with, soil load; and a 2.44–3.06 log reduction in Phi6 without, and 2.71–3.69 with, soil load. HTH performed most consistently well, with significantly greater log reductions than other handwashing protocols in three models. However, the magnitude of handwashing efficacy differences was small, suggesting protocols are similarly efficacious. Rinse water demonstrated a 0.28–4.77 log reduction in remaining E. coli without, and 0.21–4.49 with, soil load and a 1.26–2.02 log reduction in Phi6 without, and 1.30–2.20 with, soil load. Chlorine resulted in significantly less persistence of E. coli in both conditions and Phi6 without soil load in rinse water (p<0.001). Thus, chlorine-based methods may offer a benefit of reducing persistence in rinse water. We recommend responders use the most practical handwashing method to ensure hand hygiene in Ebola contexts, considering the potential benefit of chlorine-based methods in rinse water persistence. PMID:28231311

The combined use of heat-pulse flowmeter logging and packer testing for transmissive fracture recognition

NASA Astrophysics Data System (ADS)

Lo, Hung-Chieh; Chen, Po-Jui; Chou, Po-Yi; Hsu, Shih-Meng

2014-06-01

This paper presents an improved borehole prospecting methodology based on a combination of techniques in the hydrogeological characterization of fractured rock aquifers. The approach is demonstrated by on-site tests carried out in the Hoshe Experimental Forest site and the Tailuge National Park, Taiwan. Borehole televiewer logs are used to obtain fracture location and distribution along boreholes. The heat-pulse flow meter log is used to measure vertical velocity flow profiles which can be analyzed to estimate fracture transmissivity and to indicate hydraulic connectivity between fractures. Double-packer hydraulic tests are performed to determine the rock mass transmissivity. The computer program FLASH is used to analyze the data from the flowmeter logs. The FLASH program is confirmed as a useful tool which quantitatively predicts the fracture transmissivity in comparison to the hydraulic properties obtained from packer tests. The location of conductive fractures and their transmissivity is identified, after which the preferential flow paths through the fracture network are precisely delineated from a cross-borehole test. The results provide robust confirmation of the use of combined flowmeter and packer methods in the characterization of fractured-rock aquifers, particularly in reference to the investigation of groundwater resource and contaminant transport dynamics.

The Activity of Antimicrobial Surfaces Varies by Testing Protocol Utilized

PubMed Central

Campos, Matias D.; Zucchi, Paola C.; Phung, Ann; Leonard, Steven N.; Hirsch, Elizabeth B.

2016-01-01

Background Contaminated hospital surfaces are an important source of nosocomial infections. A major obstacle in marketing antimicrobial surfaces is a lack of efficacy data based on standardized testing protocols. Aim We compared the efficacy of multiple testing protocols against several “antimicrobial” film surfaces. Methods Four clinical isolates were used: one Escherichia coli, one Klebsiella pneumoniae, and two Staphylococcus aureus strains. Two industry methods (modified ISO 22196 and ASTM E2149), a “dried droplet”, and a “transfer” method were tested against two commercially available antimicrobial films, one film in development, an untreated control, and a positive (silver) control film. At 2 (only ISO) and 24 hours following inoculation, bacteria were collected from film surfaces and enumerated. Results Compared to untreated films in all protocols, there were no significant differences in recovery on either commercial brand at 2 or 24 hours after inoculation. The silver surface demonstrated significant microbicidal activity (mean loss 4.9 Log10 CFU/ml) in all methods and time points with the exception of 2 hours in the ISO protocol and the transfer method. Using our novel droplet method, no differences between placebo and active surfaces were detected. The surface in development demonstrated variable activity depending on method, organism, and time point. The ISO demonstrated minimal activity at 2 hours but significant activity at 24 hours (mean 4.5 Log10 CFU/ml difference versus placebo). The ASTEM protocol exhibited significant differences in recovery of staphylococci (mean 5 Log10 CFU/ml) but not Gram-negative isolates (10 fold decrease). Minimal activity was observed with this film in the transfer method. Conclusions Varying results between protocols suggested that efficacy of antimicrobial surfaces cannot be easily and reproducibly compared. Clinical use should be considered and further development of representative methods is needed. PMID:27494336

Effectiveness of combined macular buckle under direct vision and vitrectomy with ILM peeling in refractory macular hole retinal detachment with extreme high axial myopia: a 24-month comparative study.

PubMed

Ma, Jin; Li, Honghui; Ding, Xiaohu; Tanumiharjo, Silvia; Lu, Lin

2017-10-01

To evaluate the efficacy of a combined macular buckle under direct vision and 23-gauge pars plana vitrectomy (PPV) with internal limiting membrane (ILM) peeling in refractory macular hole retinal detachment (MHRD) with extreme high axial myopia. Prospective, randomised controlled study. The study included 98 eyes of 98 patients of MHRD with extreme high axial (>30 mm) myopia. Patients were randomly assigned to undergo PPV with ILM peeling (group 1, n=52) or PPV with ILM peeling combined with macular buckle under direct vision (group 2, n=46). Complete ocular examination included best-corrected visual acuity (BCVA) (LogMAR), applanation tonometry, optical biometry, slit-lamp biomicroscopy, colour fundus photography, ultrasound examination and optical coherence tomography at baseline and every follow-up visit. Initial retinal reattachment rate was significantly higher in group 2 than in group 1 at 12-month postoperatively (χ 2 test, p=0.020). Macular hole closure rate in group 2 was significantly higher than that in group 1 at 3, 12, 18 and 24 months postoperatively (Fisher's exact test, p<0.05). In initial retinal reattachment cases, the mean BCVA decreased significantly in group 2 than in group 1 at 3 months postoperatively (Wilcoxon matched pairs signed rank test, p=0.036), and had increased significantly in group 2 than in group 1 since 6 months postoperatively (Wilcoxon matched pairs signed rank test, p<0.05). Mean axial lengths in group 2 were significantly shorter than that of group 1 at each follow-up time point (Wilcoxon matched pairs signed rank test, p<0.05). Combined macular buckle under direct vision and PPV with ILM peeling is more effective in treatment of MHRD with extreme high axial (>30 mm) myopia. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Comparison of Superelasticity of Nickel Titanium Orthodontic Arch wires using Mechanical Tensile Testing and Correlating with Electrical Resistivity

PubMed Central

Sivaraj, Aravind

2013-01-01

Background: Application of light and continuous forces for optimum physiological response and least damage to the tooth supporting structures should be the primary aim of the orthodontist. Nickel titanium alloys with the properties of excellent spring back, super elasticity and wide range of action is one of the natural choices for the clinicians to achieve this goal. In recent periods, various wire manufacturers have come with a variety of wires exhibiting different properties. It is the duty of the clinician to select appropriate wires during various stages of treatment for excellent results. For achieving this evaluation of the properties of these wires is essential. Materials & Methods: This study is focussed on evaluating the super elastic property of eight groups of austenite active nickel titanium wires. Eight groups of archwires bought from eight different manufacturers were studied. These wires were tested through mechanical tensile testing and electrical resistivity methods. Results: Unloading curves were carefully assessed for superelastic behaviour on deactivation. Rankings of the wires tested were based primarily upon the unloading curve’s slope Conclusion: Ortho organisers wires ranked first and superior, followed by American Orthodontics and Ormco A wires. Morelli and GAClowland NiTi wires were ranked last. It can be concluded that the performance of these wires based on rankings should be further evaluated by clinical studies. How to cite this article: Sivaraj A. Comparison of Superelasticity of Nickel Titanium Orthodontic Arch wires using Mechanical Tensile Testing and Correlating with Electrical Resistivity. J Int Oral Health 2013; 5(3):1-12. PMID:24155596

Body size and hosts of Triatoma infestans populations affect the size of bloodmeal contents and female fecundity in rural northwestern Argentina

PubMed Central

Fernández, María del Pilar; Cecere, María Carla; Cohen, Joel E.

2017-01-01

Human sleeping quarters (domiciles) and chicken coops are key source habitats of Triatoma infestans—the principal vector of the infection that causes Chagas disease—in rural communities in northern Argentina. Here we investigated the links among individual bug bloodmeal contents (BMC, mg), female fecundity, body length (L, mm), host blood sources and habitats. We tested whether L, habitat and host blood conferred relative fitness advantages using generalized linear mixed-effects models and a multimodel inference approach with model averaging. The data analyzed include 769 late-stage triatomines collected in 120 sites from six habitats in 87 houses in Figueroa, Santiago del Estero, during austral spring. L correlated positively with other body-size surrogates and was modified by habitat type, bug stage and recent feeding. Bugs from chicken coops were significantly larger than pig-corral and kitchen bugs. The best-fitting model of log BMC included habitat, a recent feeding, bug stage, log Lc (mean-centered log L) and all two-way interactions including log Lc. Human- and chicken-fed bugs had significantly larger BMC than bugs fed on other hosts whereas goat-fed bugs ranked last, in consistency with average blood-feeding rates. Fecundity was maximal in chicken-fed bugs from chicken coops, submaximal in human- and pig-fed bugs, and minimal in goat-fed bugs. This study is the first to reveal the allometric effects of body-size surrogates on BMC and female fecundity in a large set of triatomine populations occupying multiple habitats, and discloses the links between body size, microsite temperatures and various fitness components that affect the risks of transmission of Trypanosoma cruzi. PMID:29211791

Body size and hosts of Triatoma infestans populations affect the size of bloodmeal contents and female fecundity in rural northwestern Argentina.

PubMed

Gürtler, Ricardo E; Fernández, María Del Pilar; Cecere, María Carla; Cohen, Joel E

2017-12-01

Human sleeping quarters (domiciles) and chicken coops are key source habitats of Triatoma infestans-the principal vector of the infection that causes Chagas disease-in rural communities in northern Argentina. Here we investigated the links among individual bug bloodmeal contents (BMC, mg), female fecundity, body length (L, mm), host blood sources and habitats. We tested whether L, habitat and host blood conferred relative fitness advantages using generalized linear mixed-effects models and a multimodel inference approach with model averaging. The data analyzed include 769 late-stage triatomines collected in 120 sites from six habitats in 87 houses in Figueroa, Santiago del Estero, during austral spring. L correlated positively with other body-size surrogates and was modified by habitat type, bug stage and recent feeding. Bugs from chicken coops were significantly larger than pig-corral and kitchen bugs. The best-fitting model of log BMC included habitat, a recent feeding, bug stage, log Lc (mean-centered log L) and all two-way interactions including log Lc. Human- and chicken-fed bugs had significantly larger BMC than bugs fed on other hosts whereas goat-fed bugs ranked last, in consistency with average blood-feeding rates. Fecundity was maximal in chicken-fed bugs from chicken coops, submaximal in human- and pig-fed bugs, and minimal in goat-fed bugs. This study is the first to reveal the allometric effects of body-size surrogates on BMC and female fecundity in a large set of triatomine populations occupying multiple habitats, and discloses the links between body size, microsite temperatures and various fitness components that affect the risks of transmission of Trypanosoma cruzi.

Fat Composition Changes in Bone Marrow During Chemotherapy and Radiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carmona, Ruben; Pritz, Jakub; Bydder, Mark

Purpose: To quantify changes in bone marrow fat fraction and determine associations with peripheral blood cell counts. Methods and Materials: In this prospective study, 19 patients received either highly myelotoxic treatment (radiation therapy plus cisplatin, 5-fluorouracil mitomycin C [FU/MMC], or cisplatin/5-FU/cetuximab) or less myelotoxic treatment (capecitabine-radiation therapy or no concurrent chemotherapy). Patients underwent MR imaging and venipuncture at baseline, midtreatment, and posttreatment visits. We performed mixed effects modeling of the mean proton density fat fraction (PDFF[%]) by linear time, treatment, and vertebral column region (lumbar [L]4-sacral [S]2 vs thoracic [T]10-L3 vs cervical[C]3-T9), while controlling for cumulative mean dose and other confounders. Spearmanmore » rank correlations were performed by white blood cell (WBC) counts versus the differences in PDFF(%) before and after treatment. Results: Cumulative mean dose was associated with a 0.43% per Gy (P=.004) increase in PDFF(%). In the highly myelotoxic group, we observed significant changes in PDFF(%) per visit within L4-S2 (10.1%, P<.001) and within T10-L3 (3.93%, P=.01), relative to the reference C3-T9. In the less myelotoxic group, we did not observe significant changes in PDFF(%) per visit according to region. Within L4-S2, we observed a significant difference between treatment groups in the change in PDFF(%) per visit (5.36%, P=.04). Rank correlations of the inverse log differences in WBC versus the differences in PDFF(%) overall and within T10-S2 ranged from 0.69 to 0.78 (P<.05). Rank correlations of the inverse log differences in absolute neutrophil counts versus the differences in PDFF(%) overall and within L4-S2 ranged from 0.79 to 0.81 (P<.05). Conclusions: Magnetic resonance imaging fat quantification is sensitive to marrow composition changes that result from chemoradiation therapy. These changes are associated with peripheral blood cell counts. This study supports a rationale for bone marrow-sparing treatment planning to reduce the risk of hematologic toxicity.« less

A European multicientre study on the comparison of HBV viral loads between VERIS HBV assay and Roche COBAS® TAQMAN® HBV test, Abbott RealTime HBV assay, Siemens VERSANT HBV assay, and Qiagen artus HBV RG kit.

PubMed

Braun, Patrick; Delgado, Rafael; Drago, Monica; Fanti, Diana; Fleury, Hervé; Izopet, Jacques; Lombardi, Alessandra; Marcos, MaAngeles; Sauné, Karine; O'Shea, Siobhan; Pérez-Rivilla, Alfredo; Ramble, John; Trimoulet, Pascale; Vila, Jordi; Whittaker, Duncan; Artus, Alain; Rhodes, Daniel

2017-10-01

Hepatitis B viral load testing is essential to treatment and monitoring decisions in patients with chronic Hepatitis B. Beckman Coulter has developed the VERIS HBV Assay (Veris) for use on the fully automated DxN VERIS Molecular Diagnostics System. 1 OBJECTIVES: To evaluate the clinical performance of the Veris HBV Assay at multiple EU laboratories STUDY DESIGN: Method comparison was performed with a total of 344 plasma specimens from HBV infected patients tested with Veris and COBAS ® TaqMan ® HBV Test (Cobas), 207 specimens tested with Veris and RealTime HBV Assay (RealTime), 86 specimens tested with Veris and VERSANT ® HBV Assay (Versant), and 74 specimens tested with Veris and artus ® HBV RG PCR kit (artus). Bland-Altman analysis showed average bias of -0.46 log 10 IU/mL between Veris and Cobas, -0.46 log 10 IU/mL between Veris and RealTime, -0.36 log 10 IU/mL between Veris and Versant, and -0.12 log 10 IU/mL between Veris and artus. Bias was consistent across the assay range. Patient monitoring results using Veris demonstrated similar viral load trends over time to Cobas, RealTime, and artus. The VERIS HBV Assay demonstrated comparable clinical performance, with varying degrees of negative bias, compared to other currently marketed assays for HBV DNA monitoring. This negative bias should be taken into consideration if switching monitoring methods to Veris. Copyright © 2017 Elsevier B.V. All rights reserved.

Metabolic acidosis status and mortality in patients on the end stage of renal disease.

PubMed

Raikou, Vaia D

2016-12-01

Uncorrected metabolic acidosis leads to higher death risk in dialysis patients. We observed the relationship between metabolic acidosis status and mortality rate in patients on renal replacement therapy during a median follow up time of 60 months. We studied 76 patients on an on-line hemodiafiltration. The dialysis adequacy was defined by Kt/V for urea. The Framingham risk score (FRS) points were used to determine the 10-year risk for coronary heart disease. We examined the impact of high or low serum bicarbonate concentrations on mortality rate and on 10-year risk for coronary heart disease via the Kaplan-Meier method. Cox's model was used to evaluate a combination of prognostic variables, such as dialysis adequacy defined by Kt/V for urea, age and serum bicarbonate concentrations. We divided the enrolled patients in three groups according to serum bicarbonate concentrations (< 20 mmol/L, 20-22 mmol/L and > 22 mmol/L). Kaplan-Meier survival curve for the impact of serum bicarbonate concentrations on overall mortality was found significant (log-rank = 7.8, P = 0.02). The prevalence of serum bicarbonate less or more than 20 mmol/L on high FRS (> 20%) by Kaplan-Meier curve was also found significant (log-rank = 4.9, P = 0.02). Cox's model revealed the significant predictive effect of serum bicarbonate on overall mortality ( P = 0.006, OR = 1.5, 95% CI = 1.12-1.98) in combination to Kt/V for urea and age. Uncorrected severe metabolic acidosis, defined by serum bicarbonate concentrations less than 20 mmol/L, is associated with a 10-year risk for coronary heart disease more than 20% and high overall mortality in patients on renal replacement therapy.

SU-F-R-24: Identifying Prognostic Imaging Biomarkers in Early Stage Lung Cancer Using Radiomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeng, X; Wu, J; Cui, Y

2016-06-15

Purpose: Patients diagnosed with early stage lung cancer have favorable outcomes when treated with surgery or stereotactic radiotherapy. However, a significant proportion (∼20%) of patients will develop metastatic disease and eventually die of the disease. The purpose of this work is to identify quantitative imaging biomarkers from CT for predicting overall survival in early stage lung cancer. Methods: In this institutional review board-approved HIPPA-compliant retrospective study, we retrospectively analyzed the diagnostic CT scans of 110 patients with early stage lung cancer. Data from 70 patients were used for training/discovery purposes, while those of remaining 40 patients were used for independentmore » validation. We extracted 191 radiomic features, including statistical, histogram, morphological, and texture features. Cox proportional hazard regression model, coupled with the least absolute shrinkage and selection operator (LASSO), was used to predict overall survival based on the radiomic features. Results: The optimal prognostic model included three image features from the Law’s feature and wavelet texture. In the discovery cohort, this model achieved a concordance index or CI=0.67, and it separated the low-risk from high-risk groups in predicting overall survival (hazard ratio=2.72, log-rank p=0.007). In the independent validation cohort, this radiomic signature achieved a CI=0.62, and significantly stratified the low-risk and high-risk groups in terms of overall survival (hazard ratio=2.20, log-rank p=0.042). Conclusion: We identified CT imaging characteristics associated with overall survival in early stage lung cancer. If prospectively validated, this could potentially help identify high-risk patients who might benefit from adjuvant systemic therapy.« less

Co-morbid pain and opioid addiction: Long term effect of opioid maintenance on acute pain

PubMed Central

Wachholtz, Amy; Gonzalez, Gerardo

2014-01-01

Introduction Medication assisted treatment for opioid dependence alters the pain experience. This study will evaluate changes pain sensitivity and tolerance with opioid treatments; and duration of this effect after treatment cessation. Method 120 individuals with chronic pain were recruited in 4 groups (n=30): 1-methadone for opioid addiction; 2-buprenorphine for opioid addiction; 3-history of opioid maintenance treatment for opioid addiction but with prolonged abstinence (M=121 weeks; SD=23.3); and 4-opioid naïve controls. Participants completed a psychological assessment and a cold water task including, time to first pain (sensitivity) and time to stopping the pain task (tolerance). Data analysis used survival analyses. Results A Kaplan-Meier-Cox survival analysis showed group differences for both pain sensitivity (Log rank=15.50; p<.001) and tolerance (Log rank=20.11; p<.001). Current or historical use of opioid maintenance resulted in differing pain sensitivity compared to opioid naïve (p’s<.01). However, tolerance to pain was better among those with a history of opioid maintenance compared to active methadone patients (p<.05), with the highest tolerance found among opioid naïve control group participants (p’s<.001). Correlations within the prolonged abstinent group indicated pain tolerance was significantly improved as length of opioid abstinence increased (R=.37; p<.05); but duration of abstinence did not alter sensitivity (ns). Conclusion Among individuals with a history of prolonged opioid maintenance, there appears to be long-term differences in pain sensitivity that do not resolve with discontinuation of opioid maintenance. Although pain sensitivity does not change, pain tolerance does improve after opioid maintenance cessation. Implications for treating co-morbid opioid addiction and pain (acute and chronic) are discussed. PMID:25456326

Early Probiotic Supplementation for Eczema and Asthma Prevention: A Randomized Controlled Trial.

PubMed

Cabana, Michael D; McKean, Michelle; Caughey, Aaron B; Fong, Lawrence; Lynch, Susan; Wong, Angela; Leong, Russell; Boushey, Homer A; Hilton, Joan F

2017-09-01

To determine if probiotic administration during the first 6 months of life decreases childhood asthma and eczema. We conducted a randomized, double-blind controlled trial of Lactobacillus rhamnosus GG (LGG) supplementation on the cumulative incidence of eczema (primary end point) and asthma and rhinitis (secondary end points) in high-risk infants. For the first 6 months of life, intervention infants ( n = 92) received a daily dose of 10 billion colony-forming units of LGG and 225 mg of inulin (Amerifit Brands, Cromwell, CT), and control infants ( n = 92) received 325 mg of inulin alone. We used survival analysis methods to estimate disease incidences in the presence or absence of LGG and to estimate the efficacy of LGG in delaying or preventing these diseases. Infants were accrued over a 6-year period (median follow-up: 4.6 years; 95% retention rate at 2 years). At 2 years of age, the estimated cumulative incidence of eczema was 30.9% (95% confidence interval [CI], 21.4%-40.4%) in the control arm and 28.7% (95% CI, 19.4%-38.0%) in the LGG arm, for a hazard ratio of 0.95 (95% CI, 0.59-1.53) (log-rank P = .83). At 5 years of age, the cumulative incidence of asthma was 17.4% (95% CI, 7.6%-27.1%) in the control arm and 9.7% (95% CI, 2.7%-16.6%) in the LGG arm, for a hazard ratio of 0.88 (95% CI, 0.41-1.87) (log-rank P = .25). For high-risk infants, early LGG supplementation for the first 6 months of life does not appear to prevent the development of eczema or asthma at 2 years of age. Copyright © 2017 by the American Academy of Pediatrics.

Impact of Paclitaxel-Eluting Balloons Compared to Second-Generation Drug-Eluting Stents for of In-Stent Restenosis in a Primarily Acute Coronary Syndrome Population

PubMed Central

Marquis-Gravel, Guillaume; Matteau, Alexis; Potter, Brian J; Gobeil, François; Noiseux, Nicolas; Stevens, Louis-Mathieu; Mansour, Samer

2017-01-01

Background The place of drug-eluting balloons (DEB) in the treatment of in-stent restenosis (ISR) is not well-defined, particularly in a population of all-comers with acute coronary syndromes (ACS). Objective Compare the clinical outcomes of DEB with second-generation drug-eluting stents (DES) for the treatment of ISR in a real-world population with a high proportion of ACS. Methods A retrospective analysis of consecutive patients with ISR treated with a DEB compared to patients treated with a second-generation DES was performed. The primary endpoint was a composite of major adverse cardiovascular events (MACE: all-cause death, non-fatal myocardial infarction, and target lesion revascularization). Comparisons were performed using Cox proportional hazards multivariate adjustment and Kaplan-Meier analysis with log-rank. Results The cohort included 91 patients treated with a DEB and 89 patients treated with a DES (74% ACS). Median follow-up was 26 months. MACE occurred in 33 patients (36%) in the DEB group, compared to 17 patients (19%) in the DES group (p log-rank = 0.02). After multivariate adjustment, there was no significant difference between the groups (HR for DEB = 1.45 [95%CI: 0.75-2.83]; p = 0.27). Mortality rates at 1 year were 11% with DEB, and 3% with DES (p = 0.04; adjusted HR = 2.85 [95%CI: 0.98-8.32]; p = 0.06). Conclusion In a population with a high proportion of ACS, a non-significant numerical signal towards increased rates of MACE with DEB compared to second-generation DES for the treatment of ISR was observed, mainly driven by a higher mortality rate. An adequately-powered randomized controlled trial is necessary to confirm these findings. PMID:28977052