A Re-Analysis of the Collaborative Knowledge Transcripts from a Noncombatant Evacuation Operation Scenario: The Next Phase in the Evolution of a Team Collaboration Model

DTIC Science & Technology

2008-04-15

65 E. Scoring Matrix for the NEO Scenario ............................................................................ 69 F. Experimenter...the unclassified scenario. Warner, Wroblewski, and Shuck (2004) also developed a scoring matrix for the final NEO plan (see appendix E). They did...this with input from military operational personnel who had experience in actual NEO scenarios. The researchers created the matrix so that they

Decision to abort after a prenatal diagnosis of sex chromosome abnormality: a systematic review of the literature.

PubMed

Jeon, Kwon Chan; Chen, Lei-Shih; Goodson, Patricia

2012-01-01

We performed a systematic review of factors affecting parental decisions to continue or terminate a pregnancy after prenatal diagnosis of a sex chromosome abnormality, as reported in published studies from 1987 to May 2011. Based on the Matrix Method for systematic reviews, 19 studies were found in five electronic databases, meeting specific inclusion/exclusion criteria. Abstracted data were organized in a matrix. Alongside the search for factors influencing parental decisions, each study was judged on its methodological quality and assigned a methodological quality score. Decisions either to terminate or to continue a sex chromosome abnormality-affected pregnancy shared five similar factors: specific type of sex chromosome abnormality, gestational week at diagnosis, parents' age, providers' genetic expertise, and number of children/desire for (more) children. Factors unique to termination decisions included parents' fear/anxiety and directive counseling. Factors uniquely associated with continuation decisions were parents' socioeconomic status and ethnicity. The studies' average methodological quality score was 10.6 (SD = 1.67; range, 8-14). Findings from this review can be useful in adapting and modifying guidelines for genetic counseling after prenatal diagnosis of a sex chromosome abnormality. Moreover, improving the quality of future studies on this topic may allow clearer understanding of the most influential factors affecting parental decisions.

Epithelial expression of extracellular matrix metalloproteinase inducer/CD147 and matrix metalloproteinase-2 in neoplasms and precursor lesions derived from cutaneous squamous cells: An immunohistochemical study.

PubMed

Ayva, Sebnem Kupana; Karabulut, Ayse Anil; Akatli, Ayşe Nur; Atasoy, Pinar; Bozdogan, Onder

2013-10-01

Extracellular matrix metalloproteinase inducer (CD147) is a transmembrane glycoprotein involved in the regulation of matrix metalloproteinases (MMPs). The study investigated CD147 and MMP-2 expression in epidermis of cutaneous squamous lesions. CD147 and MMP-2 expressions were evaluated immunohistochemically in 44 specimens: 18 actinic keratoses (AK), 6 squamous cell carcinomas in situ (SCCIS), 13 squamous cell carcinomas (SCC; peritumoral and invasive portions assessed), and 7 normal skins. Patterns of expression were assessed, with MMP-2 in nuclei (MMP-2n) and cytoplasm (MMP-2c) evaluated separately. The expression of each marker was quantified using a calculated immunohistochemical/histologic score (H-score). Correlations were analyzed for the marker H-scores in each study group. Associations between H-scores and histopathologic parameters were also evaluated. CD147 H-score was the highest in SCC (invasive islands), followed by AK, SCCIS, and control specimens, respectively. MMP-2n and MMP-2c H-scores were the highest in AK, followed by SCCIS, SCC, and control specimens, respectively. MMP-2c and MMP-2n H-scores were significantly higher in peritumoral epidermis than in invasive islands of SCC. MMP-2c and CD147 H-scores were positively correlated in the peritumoral SCCs. CD147 H-score was positively correlated with tumor differentiation in SCC. The findings suggest that overexpression of CD147 plays a role in the development of SCC. Copyright © 2013 Elsevier GmbH. All rights reserved.

Optimization and critical evaluation of decellularization strategies to develop renal extracellular matrix scaffolds as biological templates for organ engineering and transplantation.

PubMed

Caralt, M; Uzarski, J S; Iacob, S; Obergfell, K P; Berg, N; Bijonowski, B M; Kiefer, K M; Ward, H H; Wandinger-Ness, A; Miller, W M; Zhang, Z J; Abecassis, M M; Wertheim, J A

2015-01-01

The ability to generate patient-specific cells through induced pluripotent stem cell (iPSC) technology has encouraged development of three-dimensional extracellular matrix (ECM) scaffolds as bioactive substrates for cell differentiation with the long-range goal of bioengineering organs for transplantation. Perfusion decellularization uses the vasculature to remove resident cells, leaving an intact ECM template wherein new cells grow; however, a rigorous evaluative framework assessing ECM structural and biochemical quality is lacking. To address this, we developed histologic scoring systems to quantify fundamental characteristics of decellularized rodent kidneys: ECM structure (tubules, vessels, glomeruli) and cell removal. We also assessed growth factor retention--indicating matrix biofunctionality. These scoring systems evaluated three strategies developed to decellularize kidneys (1% Triton X-100, 1% Triton X-100/0.1% sodium dodecyl sulfate (SDS) and 0.02% Trypsin-0.05% EGTA/1% Triton X-100). Triton and Triton/SDS preserved renal microarchitecture and retained matrix-bound basic fibroblast growth factor and vascular endothelial growth factor. Trypsin caused structural deterioration and growth factor loss. Triton/SDS-decellularized scaffolds maintained 3 h of leak-free blood flow in a rodent transplantation model and supported repopulation with human iPSC-derived endothelial cells and tubular epithelial cells ex vivo. Taken together, we identify an optimal Triton/SDS-based decellularization strategy that produces a biomatrix that may ultimately serve as a rodent model for kidney bioengineering. © Copyright 2014 The American Society of Transplantation and the American Society of Transplant Surgeons.

Kernel analysis of partial least squares (PLS) regression models.

PubMed

Shinzawa, Hideyuki; Ritthiruangdej, Pitiporn; Ozaki, Yukihiro

2011-05-01

An analytical technique based on kernel matrix representation is demonstrated to provide further chemically meaningful insight into partial least squares (PLS) regression models. The kernel matrix condenses essential information about scores derived from PLS or principal component analysis (PCA). Thus, it becomes possible to establish the proper interpretation of the scores. A PLS model for the total nitrogen (TN) content in multiple Thai fish sauces is built with a set of near-infrared (NIR) transmittance spectra of the fish sauce samples. The kernel analysis of the scores effectively reveals that the variation of the spectral feature induced by the change in protein content is substantially associated with the total water content and the protein hydration. Kernel analysis is also carried out on a set of time-dependent infrared (IR) spectra representing transient evaporation of ethanol from a binary mixture solution of ethanol and oleic acid. A PLS model to predict the elapsed time is built with the IR spectra and the kernel matrix is derived from the scores. The detailed analysis of the kernel matrix provides penetrating insight into the interaction between the ethanol and the oleic acid.

In Spite of Indeterminacy Many Common Factor Score Estimates Yield an Identical Reproduced Covariance Matrix

ERIC Educational Resources Information Center

Beauducel, Andre

2007-01-01

It was investigated whether commonly used factor score estimates lead to the same reproduced covariance matrix of observed variables. This was achieved by means of Schonemann and Steiger's (1976) regression component analysis, since it is possible to compute the reproduced covariance matrices of the regression components corresponding to different…

MRL and SuperFine+MRL: new supertree methods

PubMed Central

2012-01-01

Background Supertree methods combine trees on subsets of the full taxon set together to produce a tree on the entire set of taxa. Of the many supertree methods, the most popular is MRP (Matrix Representation with Parsimony), a method that operates by first encoding the input set of source trees by a large matrix (the "MRP matrix") over {0,1, ?}, and then running maximum parsimony heuristics on the MRP matrix. Experimental studies evaluating MRP in comparison to other supertree methods have established that for large datasets, MRP generally produces trees of equal or greater accuracy than other methods, and can run on larger datasets. A recent development in supertree methods is SuperFine+MRP, a method that combines MRP with a divide-and-conquer approach, and produces more accurate trees in less time than MRP. In this paper we consider a new approach for supertree estimation, called MRL (Matrix Representation with Likelihood). MRL begins with the same MRP matrix, but then analyzes the MRP matrix using heuristics (such as RAxML) for 2-state Maximum Likelihood. Results We compared MRP and SuperFine+MRP with MRL and SuperFine+MRL on simulated and biological datasets. We examined the MRP and MRL scores of each method on a wide range of datasets, as well as the resulting topological accuracy of the trees. Our experimental results show that MRL, coupled with a very good ML heuristic such as RAxML, produced more accurate trees than MRP, and MRL scores were more strongly correlated with topological accuracy than MRP scores. Conclusions SuperFine+MRP, when based upon a good MP heuristic, such as TNT, produces among the best scores for both MRP and MRL, and is generally faster and more topologically accurate than other supertree methods we tested. PMID:22280525

Prospective randomized comparison of scar appearances between cograft of acellular dermal matrix with autologous split-thickness skin and autologous split-thickness skin graft alone for full-thickness skin defects of the extremities.

PubMed

Yi, Ju Won; Kim, Jae Kwang

2015-03-01

The purpose of this study was to evaluate the clinical outcomes of cografting of acellular dermal matrix with autologous split-thickness skin and autologous split-thickness skin graft alone for full-thickness skin defects on the extremities. In this prospective randomized study, 19 consecutive patients with full-thickness skin defects on the extremities following trauma underwent grafting using either cograft of acellular dermal matrix with autologous split-thickness skin graft (nine patients, group A) or autologous split-thickness skin graft alone (10 patients, group B) from June of 2011 to December of 2012. The postoperative evaluations included observation of complications (including graft necrosis, graft detachment, or seroma formation) and Vancouver Scar Scale score. No statistically significant difference was found regarding complications, including graft necrosis, graft detachment, or seroma formation. At week 8, significantly lower Vancouver Scar Scale scores for vascularity, pliability, height, and total score were found in group A compared with group B. At week 12, lower scores for pliability and height and total scores were identified in group A compared with group B. For cases with traumatic full-thickness skin defects on the extremities, a statistically significant better result was achieved with cograft of acellular dermal matrix with autologous split-thickness skin graft than with autologous split-thickness skin graft alone in terms of Vancouver Scar Scale score. Therapeutic, II.

Stage scoring of liver fibrosis using Mueller matrix microscope

NASA Astrophysics Data System (ADS)

Zhou, Jialing; He, Honghui; Wang, Ye; Ma, Hui

2016-10-01

Liver fibrosis is a common pathological process of varied chronic liver diseases including alcoholic hepatitis, virus hepatitis, and so on. Accurate evaluation of liver fibrosis is necessary for effective therapy and a five-stage grading system was developed. Currently, experienced pathologists use stained liver biopsies to assess the degree of liver fibrosis. But it is difficult to obtain highly reproducible results because of huge discrepancy among different observers. Polarization imaging technique has the potential of scoring liver fibrosis since it is capable of probing the structural and optical properties of samples. Considering that the Mueller matrix measurement can provide comprehensive microstructural information of the tissues, in this paper, we apply the Mueller matrix microscope to human liver fibrosis slices in different fibrosis stages. We extract the valid regions and adopt the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters for quantitative analysis. We also use the Monte Carlo simulation to analyze the relationship between the microscopic Mueller matrix parameters and the characteristic structural changes during the fibrosis process. The experimental and Monte Carlo simulated results show good consistency. We get a positive correlation between the parameters and the stage of liver fibrosis. The results presented in this paper indicate that the Mueller matrix microscope can provide additional information for the detections and fibrosis scorings of liver tissues and has great potential in liver fibrosis diagnosis.

Genetic parameter estimates for carcass traits and visual scores including or not genomic information.

PubMed

Gordo, D G M; Espigolan, R; Tonussi, R L; Júnior, G A F; Bresolin, T; Magalhães, A F Braga; Feitosa, F L; Baldi, F; Carvalheiro, R; Tonhati, H; de Oliveira, H N; Chardulo, L A L; de Albuquerque, L G

2016-05-01

The objective of this study was to determine whether visual scores used as selection criteria in Nellore breeding programs are effective indicators of carcass traits measured after slaughter. Additionally, this study evaluated the effect of different structures of the relationship matrix ( and ) on the estimation of genetic parameters and on the prediction accuracy of breeding values. There were 13,524 animals for visual scores of conformation (CS), finishing precocity (FP), and muscling (MS) and 1,753, 1,747, and 1,564 for LM area (LMA), backfat thickness (BF), and HCW, respectively. Of these, 1,566 animals were genotyped using a high-density panel containing 777,962 SNP. Six analyses were performed using multitrait animal models, each including the 3 visual scores and 1 carcass trait. For the visual scores, the model included direct additive genetic and residual random effects and the fixed effects of contemporary group (defined by year of birth, management group at yearling, and farm) and the linear effect of age of animal at yearling. The same model was used for the carcass traits, replacing the effect of age of animal at yearling with the linear effect of age of animal at slaughter. The variance and covariance components were estimated by the REML method in analyses using the numerator relationship matrix () or combining the genomic and the numerator relationship matrices (). The heritability estimates for the visual scores obtained with the 2 methods were similar and of moderate magnitude (0.23-0.34), indicating that these traits should response to direct selection. The heritabilities for LMA, BF, and HCW were 0.13, 0.07, and 0.17, respectively, using matrix and 0.29, 0.16, and 0.23, respectively, using matrix . The genetic correlations between the visual scores and carcass traits were positive, and higher correlations were generally obtained when matrix was used. Considering the difficulties and cost of measuring carcass traits postmortem, visual scores of CS, FP, and MS could be used as selection criteria to improve HCW, BF, and LMA. The use of genomic information permitted the detection of greater additive genetic variability for LMA and BF. For HCW, the high magnitude of the genetic correlations with visual scores was probably sufficient to recover genetic variability. The methods provided similar breeding value accuracies, especially for the visual scores.

Aortic Wall Extracellular Matrix Proteins Correlate with Syntax Score in Patients Undergoing Coronary Artery Bypass Surgery

PubMed Central

Chiong, Terri; Cheow, Esther S. H.; Woo, Chin C.; Lin, Xiao Y.; Khin, Lay W.; Lee, Chuen N.; Hartman, Mikael; Sze, Siu K.; Sorokin, Vitaly A.

2016-01-01

Aims: The SYNTAX score correlate with major cardiovascular events post-revascularization, although the histopathological basis is unclear. We aim to evaluate the association between syntax score and extracellular matrix histological characteristics of aortic punch tissue obtained during coronary artery bypass surgery (CABG). This analysis compares coronary artery bypass surgery patients with High and Low syntax score which were followed up for one year period. Methods and Results: Patients with High (score ≥ 33, (n=77)) and Low Syntax Scores (score ≤ 22, (n=71)) undergoing elective CABG were recruited prospectively. Baseline clinical characteristics and surgical risks were well matched. At 1 year, EMACCE (Sum of cardiovascular death, stroke, congestive cardiac failure, and limb, gut and myocardial ischemia) was significantly elevated in the High syntax group (P=0.022). Mass spectrometry (MS)-based quantitative iTRAQ proteomic results validated on independent cohort by immunohistochemistry (IHC) revealed that the High syntax group had significantly upraised Collagen I (P<0.0001) and Elastin (P<0.0001) content in ascending aortic wall. Conclusion: This study shows that aortic extracellular matrix (ECM) differ between High and Low syntax groups with up-regulation of Collagen I and Elastin level in High Syntax Score group. This identifies aortic punches collected during CABG as another biomarker source related with atherosclerosis severity and possible clinical outcome. PMID:27347220

Environmental impact assessment of Gonabad municipal waste landfill site using Leopold Matrix

PubMed Central

Sajjadi, Seyed Ali; Aliakbari, Zohreh; Matlabi, Mohammad; Biglari, Hamed; Rasouli, Seyedeh Samira

2017-01-01

Introduction An environmental impact assessment (EIA) before embarking on any project is a useful tool to reduce the potential effects of each project, including landfill, if possible. The main objective of this study was to assess the environmental impact of the current municipal solid waste disposal site of Gonabad by using the Iranian Leopold matrix method. Methods This cross-sectional study was conducted to assess the environmental impacts of a landfill site in Gonabad in 2015 by an Iranian matrix (modified Leopold matrix). This study was conducted based on field visits of the landfill, and collected information from various sources and analyzing and comparing between five available options, including the continuation of the current disposal practices, construction of new sanitary landfills, recycling plans, composting, and incineration plants was examined. The best option was proposed to replace the existing landfill. Results The current approach has a score of 2.35, the construction of new sanitary landfill has a score of 1.59, a score of 1.57 for the compost plant, and recycling and incineration plant, respectively, have scores of 1.68 and 2.3. Conclusion Results showed that continuation of the current method of disposal, due to severe environmental damage and health problems, is rejected. A compost plant with the lowest negative score is the best option for the waste disposal site of Gonabad City and has priority over the other four options. PMID:28465797

Environmental impact assessment of Gonabad municipal waste landfill site using Leopold Matrix.

PubMed

Sajjadi, Seyed Ali; Aliakbari, Zohreh; Matlabi, Mohammad; Biglari, Hamed; Rasouli, Seyedeh Samira

2017-02-01

An environmental impact assessment (EIA) before embarking on any project is a useful tool to reduce the potential effects of each project, including landfill, if possible. The main objective of this study was to assess the environmental impact of the current municipal solid waste disposal site of Gonabad by using the Iranian Leopold matrix method. This cross-sectional study was conducted to assess the environmental impacts of a landfill site in Gonabad in 2015 by an Iranian matrix (modified Leopold matrix). This study was conducted based on field visits of the landfill, and collected information from various sources and analyzing and comparing between five available options, including the continuation of the current disposal practices, construction of new sanitary landfills, recycling plans, composting, and incineration plants was examined. The best option was proposed to replace the existing landfill. The current approach has a score of 2.35, the construction of new sanitary landfill has a score of 1.59, a score of 1.57 for the compost plant, and recycling and incineration plant, respectively, have scores of 1.68 and 2.3. Results showed that continuation of the current method of disposal, due to severe environmental damage and health problems, is rejected. A compost plant with the lowest negative score is the best option for the waste disposal site of Gonabad City and has priority over the other four options.

Assessing Fit of Item Response Models Using the Information Matrix Test

ERIC Educational Resources Information Center

Ranger, Jochen; Kuhn, Jorg-Tobias

2012-01-01

The information matrix can equivalently be determined via the expectation of the Hessian matrix or the expectation of the outer product of the score vector. The identity of these two matrices, however, is only valid in case of a correctly specified model. Therefore, differences between the two versions of the observed information matrix indicate…

Controlled ecological evaluation of an implemented exercise training programme to prevent lower limb injuries in sport: differences in implementation activity.

PubMed

Donaldson, Alex; Gabbe, Belinda J; Lloyd, David G; Cook, Jill; Finch, Caroline F

2018-04-24

The public health benefits of injury prevention programmes are maximised when programmes are widely adopted and adhered to. Therefore, these programmes require appropriate implementation support. This study evaluated implementation activity outcomes associated with the implementation of FootyFirst, an exercise training injury prevention programme for community Australian football, both with (FootyFirst+S) and without (FootyFirst+NS) implementation support. An evaluation plan based on the Reach Effectiveness Adoption Implementation Maintenance (RE-AIM) Sports Setting Matrix was applied in a controlled ecological evaluation of the implementation of FootyFirst. RE-AIM dimension-specific (range: 0-2) and total RE-AIM scores (range: 0-10) were derived by triangulating data from a number of sources (including surveys, interviews, direct observations and notes) describing FootyFirst implementation activities. The mean dimension-specific and total scores were compared for clubs in regions receiving FootyFirst+S and FootyFirst+NS, through analysis of variance. The mean total RE-AIM score forclubs in the FootyFirst+S regions was 2.4 times higher than for clubs in the FootyFirst+NS region (4.73 vs 1.94; 95% CI for the difference: 1.64 to 3.74). Similarly, all dimension-specific scores were significantly higher for clubs in the FootyFirst+S regions compared with clubs in the FootyFirst+NS region. In all regions, the dimension-specific scores were highest for reach and adoption, and lowest for implementation. Implementing exercise training injury prevention programmes in community sport is challenging. Delivering programme content supported by a context-specific and evidence-informed implementation plan leads to greater implementation activity, which is an important precursor to injury reductions. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

All-Arthroscopic Autologous Matrix-Induced Chondrogenesis-Aided Repair of a Patellar Cartilage Defect Using Dry Arthroscopy and a Retraction System.

PubMed

Sadlik, Boguslaw; Puszkarz, Mariusz; Kosmalska, Lidia; Wiewiorski, Martin

2017-11-01

The technique of all-arthroscopic autologous matrix-induced chondrogenesis (AMIC)-aided repair of patellar cartilage lesions using a retraction system and dry arthroscopy has been recently described. We report the first clinical and radiological data at a short-term follow-up. Twelve patients underwent AMIC-aided cartilage repair for a patellar lesion. All steps of the procedure were performed arthroscopically, which include the use of an intra-articularly placed retraction plate for distraction of the patellofemoral joint and evacuation of saline solution for collagen matrix insertion and fixation. Clinical assessment performed before surgery and at a mean follow-up time of 38 months (range: 24-70) included the following scores: Knee Injury and Osteoarthritis Outcome Score (KOOS), International Knee Documentation Committee (IKDC), and visual analog scale (VAS). Magnetic resonance imaging was performed at the follow-up examination, including the magnetic resonance observation of cartilage repair tissue (MOCART) score. The mean KOOS and IKDC scores increased significantly ( p  < 0.01) from 50.3 and 37.4 points preoperatively to 90.1 and 79.4 postoperatively. The VAS score decreased from 7.8 to 2.3 points. Mean MOCART score at follow-up was 58.3 points. Cartilage repair of patellar lesions aided by a retraction system in a dry arthroscopy setup is a promising approach. Further studies are needed to evaluate this procedure and compare it to existing matrix implantation techniques. The level of evidence for the study is 4 (case series). Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues.

PubMed

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health.Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper,we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameter scan provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues

NASA Astrophysics Data System (ADS)

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health. Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper, we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameters can provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

Exploring syndrome differentiation using non-negative matrix factorization and cluster analysis in patients with atopic dermatitis.

PubMed

Yun, Younghee; Jung, Wonmo; Kim, Hyunho; Jang, Bo-Hyoung; Kim, Min-Hee; Noh, Jiseong; Ko, Seong-Gyu; Choi, Inhwa

2017-08-01

Syndrome differentiation (SD) results in a diagnostic conclusion based on a cluster of concurrent symptoms and signs, including pulse form and tongue color. In Korea, there is a strong interest in the standardization of Traditional Medicine (TM). In order to standardize TM treatment, standardization of SD should be given priority. The aim of this study was to explore the SD, or symptom clusters, of patients with atopic dermatitis (AD) using non-negative factorization methods and k-means clustering analysis. We screened 80 patients and enrolled 73 eligible patients. One TM dermatologist evaluated the symptoms/signs using an existing clinical dataset from patients with AD. This dataset was designed to collect 15 dermatologic and 18 systemic symptoms/signs associated with AD. Non-negative matrix factorization was used to decompose the original data into a matrix with three features and a weight matrix. The point of intersection of the three coordinates from each patient was placed in three-dimensional space. With five clusters, the silhouette score reached 0.484, and this was the best silhouette score obtained from two to nine clusters. Patients were clustered according to the varying severity of concurrent symptoms/signs. Through the distribution of the null hypothesis generated by 10,000 permutation tests, we found significant cluster-specific symptoms/signs from the confidence intervals in the upper and lower 2.5% of the distribution. Patients in each cluster showed differences in symptoms/signs and severity. In a clinical situation, SD and treatment are based on the practitioners' observations and clinical experience. SD, identified through informatics, can contribute to development of standardized, objective, and consistent SD for each disease. Copyright © 2017. Published by Elsevier Ltd.

Mining for class-specific motifs in protein sequence classification

PubMed Central

2013-01-01

Background In protein sequence classification, identification of the sequence motifs or n-grams that can precisely discriminate between classes is a more interesting scientific question than the classification itself. A number of classification methods aim at accurate classification but fail to explain which sequence features indeed contribute to the accuracy. We hypothesize that sequences in lower denominations (n-grams) can be used to explore the sequence landscape and to identify class-specific motifs that discriminate between classes during classification. Discriminative n-grams are short peptide sequences that are highly frequent in one class but are either minimally present or absent in other classes. In this study, we present a new substitution-based scoring function for identifying discriminative n-grams that are highly specific to a class. Results We present a scoring function based on discriminative n-grams that can effectively discriminate between classes. The scoring function, initially, harvests the entire set of 4- to 8-grams from the protein sequences of different classes in the dataset. Similar n-grams of the same size are combined to form new n-grams, where the similarity is defined by positive amino acid substitution scores in the BLOSUM62 matrix. Substitution has resulted in a large increase in the number of discriminatory n-grams harvested. Due to the unbalanced nature of the dataset, the frequencies of the n-grams are normalized using a dampening factor, which gives more weightage to the n-grams that appear in fewer classes and vice-versa. After the n-grams are normalized, the scoring function identifies discriminative 4- to 8-grams for each class that are frequent enough to be above a selection threshold. By mapping these discriminative n-grams back to the protein sequences, we obtained contiguous n-grams that represent short class-specific motifs in protein sequences. Our method fared well compared to an existing motif finding method known as Wordspy. We have validated our enriched set of class-specific motifs against the functionally important motifs obtained from the NLSdb, Prosite and ELM databases. We demonstrate that this method is very generic; thus can be widely applied to detect class-specific motifs in many protein sequence classification tasks. Conclusion The proposed scoring function and methodology is able to identify class-specific motifs using discriminative n-grams derived from the protein sequences. The implementation of amino acid substitution scores for similarity detection, and the dampening factor to normalize the unbalanced datasets have significant effect on the performance of the scoring function. Our multipronged validation tests demonstrate that this method can detect class-specific motifs from a wide variety of protein sequence classes with a potential application to detecting proteome-specific motifs of different organisms. PMID:23496846

A DEIM Induced CUR Factorization

DTIC Science & Technology

2015-09-18

CUR approximate matrix factorization based on the Discrete Empirical Interpolation Method (DEIM). For a given matrix A, such a factorization provides a...CUR approximations based on leverage scores. 1 Introduction This work presents a new CUR matrix factorization based upon the Discrete Empirical...SUPPLEMENTARY NOTES 14. ABSTRACT We derive a CUR approximate matrix factorization based on the Discrete Empirical Interpolation Method (DEIM). For a given

Estimating Total-Test Scores from Partial Scores in a Matrix Sampling Design.

ERIC Educational Resources Information Center

Sachar, Jane; Suppes, Patrick

1980-01-01

The present study compared six methods, two of which utilize the content structure of items, to estimate total-test scores using 450 students and 60 items of the 110-item Stanford Mental Arithmetic Test. Three methods yielded fairly good estimates of the total-test score. (Author/RL)

Improved detection of DNA-binding proteins via compression technology on PSSM information.

PubMed

Wang, Yubo; Ding, Yijie; Guo, Fei; Wei, Leyi; Tang, Jijun

2017-01-01

Since the importance of DNA-binding proteins in multiple biomolecular functions has been recognized, an increasing number of researchers are attempting to identify DNA-binding proteins. In recent years, the machine learning methods have become more and more compelling in the case of protein sequence data soaring, because of their favorable speed and accuracy. In this paper, we extract three features from the protein sequence, namely NMBAC (Normalized Moreau-Broto Autocorrelation), PSSM-DWT (Position-specific scoring matrix-Discrete Wavelet Transform), and PSSM-DCT (Position-specific scoring matrix-Discrete Cosine Transform). We also employ feature selection algorithm on these feature vectors. Then, these features are fed into the training SVM (support vector machine) model as classifier to predict DNA-binding proteins. Our method applys three datasets, namely PDB1075, PDB594 and PDB186, to evaluate the performance of our approach. The PDB1075 and PDB594 datasets are employed for Jackknife test and the PDB186 dataset is used for the independent test. Our method achieves the best accuracy in the Jacknife test, from 79.20% to 86.23% and 80.5% to 86.20% on PDB1075 and PDB594 datasets, respectively. In the independent test, the accuracy of our method comes to 76.3%. The performance of independent test also shows that our method has a certain ability to be effectively used for DNA-binding protein prediction. The data and source code are at https://doi.org/10.6084/m9.figshare.5104084.

PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants.

PubMed

Krystkowiak, Izabella; Manguy, Jean; Davey, Norman E

2018-06-05

There is a pressing need for in silico tools that can aid in the identification of the complete repertoire of protein binding (SLiMs, MoRFs, miniMotifs) and modification (moiety attachment/removal, isomerization, cleavage) motifs. We have created PSSMSearch, an interactive web-based tool for rapid statistical modeling, visualization, discovery and annotation of protein motif specificity determinants to discover novel motifs in a proteome-wide manner. PSSMSearch analyses proteomes for regions with significant similarity to a motif specificity determinant model built from a set of aligned motif-containing peptides. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the motif specificity determinant model. This model can then be modified by a user to add prior knowledge of specificity determinants through an interactive PSSM heatmap. PSSMSearch includes a statistical framework to calculate the significance of specificity determinant model matches against a proteome of interest. PSSMSearch also includes the SLiMSearch framework's annotation, motif functional analysis and filtering tools to highlight relevant discriminatory information. Additional tools to annotate statistically significant shared keywords and GO terms, or experimental evidence of interaction with a motif-recognizing protein have been added. Finally, PSSM-based conservation metrics have been created for taxonomic range analyses. The PSSMSearch web server is available at http://slim.ucd.ie/pssmsearch/.

Rapid motif compliance scoring with match weight sets.

PubMed

Venezia, D; O'Hara, P J

1993-02-01

Most current implementations of motif matching in biological sequences have sacrificed the generality of weight matrix scoring for shorter runtimes. The program MOTIF incorporates a weight matrix and a rapid, backtracking tree-search algorithm to score motif compliance with greatly enhanced performance while placing no constraints on the motif. In addition, any positions within a motif can be marked as 'inviolate', thereby requiring an exact match. MOTIF allows a choice of regular expression formats and can use both motif and sequence libraries as either targets or queries. Nucleic acid sequences can optionally be translated by MOTIF in any frame(s) and used against peptide motifs.

Possible pathways used to predict different stages of lung adenocarcinoma.

PubMed

Chen, Xiaodong; Duan, Qiongyu; Xuan, Ying; Sun, Yunan; Wu, Rong

2017-04-01

We aimed to find some specific pathways that can be used to predict the stage of lung adenocarcinoma.RNA-Seq expression profile data and clinical data of lung adenocarcinoma (stage I [37], stage II 161], stage III [75], and stage IV [45]) were obtained from the TCGA dataset. The differentially expressed genes were merged, correlation coefficient matrix between genes was constructed with correlation analysis, and unsupervised clustering was carried out with hierarchical clustering method. The specific coexpression network in every stage was constructed with cytoscape software. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed with KOBAS database and Fisher exact test. Euclidean distance algorithm was used to calculate total deviation score. The diagnostic model was constructed with SVM algorithm.Eighteen specific genes were obtained by getting intersection of 4 group differentially expressed genes. Ten significantly enriched pathways were obtained. In the distribution map of 10 pathways score in different groups, degrees that sample groups deviated from the normal level were as follows: stage I < stage II < stage III < stage IV. The pathway score of 4 stages exhibited linear change in some pathways, and the score of 1 or 2 stages were significantly different from the rest stages in some pathways. There was significant difference between dead and alive for these pathways except thyroid hormone signaling pathway.Those 10 pathways are associated with the development of lung adenocarcinoma and may be able to predict different stages of it. Furthermore, these pathways except thyroid hormone signaling pathway may be able to predict the prognosis.

Recognition and defect detection of dot-matrix text via variation-model based learning

NASA Astrophysics Data System (ADS)

Ohyama, Wataru; Suzuki, Koushi; Wakabayashi, Tetsushi

2017-03-01

An algorithm for recognition and defect detection of dot-matrix text printed on products is proposed. Extraction and recognition of dot-matrix text contains several difficulties, which are not involved in standard camera-based OCR, that the appearance of dot-matrix characters is corrupted and broken by illumination, complex texture in the background and other standard characters printed on product packages. We propose a dot-matrix text extraction and recognition method which does not require any user interaction. The method employs detected location of corner points and classification score. The result of evaluation experiment using 250 images shows that recall and precision of extraction are 78.60% and 76.03%, respectively. Recognition accuracy of correctly extracted characters is 94.43%. Detecting printing defect of dot-matrix text is also important in the production scene to avoid illegal productions. We also propose a detection method for printing defect of dot-matrix characters. The method constructs a feature vector of which elements are classification scores of each character class and employs support vector machine to classify four types of printing defect. The detection accuracy of the proposed method is 96.68 %.

Development of a clinical diagnostic matrix for characterizing inherited epidermolysis bullosa.

PubMed

Yenamandra, V K; Moss, C; Sreenivas, V; Khan, M; Sivasubbu, S; Sharma, V K; Sethuraman, G

2017-06-01

Accurately diagnosing the subtype of epidermolysis bullosa (EB) is critical for management and genetic counselling. Modern laboratory techniques are largely inaccessible in developing countries, where the diagnosis remains clinical and often inaccurate. To develop a simple clinical diagnostic tool to aid in the diagnosis and subtyping of EB. We developed a matrix indicating presence or absence of a set of distinctive clinical features (as rows) for the nine most prevalent EB subtypes (as columns). To test an individual patient, presence or absence of these features was compared with the findings expected in each of the nine subtypes to see which corresponded best. If two or more diagnoses scored equally, the diagnosis with the greatest number of specific features was selected. The matrix was tested using findings from 74 genetically characterized patients with EB aged > 6 months by an investigator blinded to molecular diagnosis. For concordance, matrix diagnoses were compared with molecular diagnoses. Overall, concordance between the matrix and molecular diagnoses for the four major types of EB was 91·9%, with a kappa coefficient of 0·88 [95% confidence interval (CI) 0·81-0·95; P < 0·001]. The matrix achieved a 75·7% agreement in classifying EB into its nine subtypes, with a kappa coefficient of 0·73 (95% CI 0·69-0·77; P < 0·001). The matrix appears to be simple, valid and useful in predicting the type and subtype of EB. An electronic version will facilitate further testing. © 2016 British Association of Dermatologists.

Aseptic Freeze-Dried versus Sterile Wet-Packaged Human Cadaveric Acellular Dermal Matrix in Immediate Tissue Expander Breast Reconstruction: A Propensity Score Analysis.

PubMed

Hanson, Summer E; Meaike, Jesse D; Selber, Jesse C; Liu, Jun; Li, Liang; Hassid, Victor J; Baumann, Donald P; Butler, Charles E; Garvey, Patrick B

2018-05-01

Although multiple acellular dermal matrix sources exist, it is unclear how its processing impacts complication rates. The authors compared complications between two preparations of human cadaveric acellular dermal matrix (freeze dried and ready-to-use) in immediate tissue expander breast reconstruction to analyze the effect of processing on complications. The authors retrospectively reviewed all alloplastic breast reconstructions with freeze-dried or ready-to-use human acellular dermal matrices between 2006 and 2016. The primary outcome measure was surgical-site occurrence defined as seroma, skin dehiscence, surgical-site infection, or reconstruction failure. The two groups were compared before and after propensity score matching. The authors included 988 reconstructions (freeze-dried, 53.8 percent; ready-to-use, 46.2 percent). Analysis of 384 propensity score-matched pairs demonstrated a slightly higher rate of surgical-site occurrence (21.4 percent versus 16.7 percent; p = 0.10) and surgical-site infection (9.6 percent versus 7.8 percent; p = 0.13) in the freeze-dried group than in the ready-to-use group, but the difference was not significant. However, failure was significantly higher for the freeze-dried versus ready-to-use group (7.8 percent versus 4.4 percent; p = 0.050). This is the largest study comparing the outcomes of alloplastic breast reconstruction using human acellular dermal matrix materials prepared by different methods. The authors demonstrated higher early complications with aseptic, freeze-dried matrix than with sterile ready-to-use matrix; reconstructive failure was the only outcome to achieve statistical significance. The authors conclude that acellular dermal matrix preparation has an independent impact on patient outcomes in their comparison of one company's product. Therapeutic, III.

Estimating injury severity using the Barell matrix

PubMed Central

Clark, D E; Ahmad, S

2006-01-01

Objective To determine whether the Barell matrix (Inj Prev 2002;8:91–6) could effectively categorize injuries by severity. Methods Injury diagnoses of cases in the 2002 US Nationwide Inpatient Sample were classified according to the Barell matrix. For each cell of the matrix, the authors used ICDMAP‐90 to determine the predominant Abbreviated Injury Score (AIS) and body region, and calculated the weighted proportion surviving (bPScell) among patients with any diagnosis in that cell. These findings were used to estimate maximum AIS (bAISmax), ISS (bISS), and the minimum or product of bPScell (bPSmin, bPSprod) for injured patients in the 1996–2000 US National Hospital Discharge Surveys. Case survival was determined for different scores, and outcome models using age, sex, comorbidity, mechanism, and bISS or bPSmin were compared to models using ISS calculated from ICDMAP‐90 (mISS) or using ICISS. Results Case survival decreased with increasing bAISmax or bISS; survival was closely approximated by bPSmin, and also increased monotonically with bPSprod. Outcome models using bISS or bPSmin were similar to those using mISS or ICISS. An Abbreviated Barell Categorization, with only four groups, was also effective. Conclusion Barell matrix categorization of administrative data allows severity scoring similar to that obtainable with ICDMAP‐90 or ICISS. PMID:16595426

Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites.

PubMed

Fang, Chun; Noguchi, Tamotsu; Yamana, Hayato

2014-10-01

Evolutionary conservation information included in position-specific scoring matrix (PSSM) has been widely adopted by sequence-based methods for identifying protein functional sites, because all functional sites, whether in ordered or disordered proteins, are found to be conserved at some extent. However, different functional sites have different conservation patterns, some of them are linear contextual, some of them are mingled with highly variable residues, and some others seem to be conserved independently. Every value in PSSMs is calculated independently of each other, without carrying the contextual information of residues in the sequence. Therefore, adopting the direct output of PSSM for prediction fails to consider the relationship between conservation patterns of residues and the distribution of conservation scores in PSSMs. In order to demonstrate the importance of combining PSSMs with the specific conservation patterns of functional sites for prediction, three different PSSM-based methods for identifying three kinds of functional sites have been analyzed. Results suggest that, different PSSM-based methods differ in their capability to identify different patterns of functional sites, and better combining PSSMs with the specific conservation patterns of residues would largely facilitate the prediction.

General and victim-specific empathy: associations with actuarial risk, treatment outcome, and sexual recidivism.

PubMed

Brown, Sarah; Harkins, Leigh; Beech, Anthony R

2012-10-01

An empathy-related component has been included in most sex offender treatment programs since the 1980s; however, research linking empathy to sexual offending and/or to treatment outcome has produced mixed findings. This study examined the relationship between victim specific empathy, general empathy, and overall treatment change (determined by responses on a battery of psychometric tests) with static risk (Risk Matrix 2000 [RM 2000]) and sexual offense reconviction data in a sample of 105 offenders who completed treatment while in prison or in the community in England and Wales and followed up for an average period of more than 10 years. Victim-specific empathy improved from pretreatment to posttreatment and related to overall treatment change. A small group of offenders, whose victim empathy scores deteriorated from pretreatment to posttreatment, had higher rates of sexual recidivism compared with the rest of the sample. In contrast, neither were any reliable pretreatment to posttreatment changes noted on general empathy scores, except for an indication on the Interpersonal Reactivity Index Personal Distress Scale, nor was any relationship found to sexual recidivism. The implications of these findings are discussed in relation to treatment goals and sexual recidivism.

Formulas for Image Factor Scores

ERIC Educational Resources Information Center

Hakstian, A. Ralph

1973-01-01

Formulas are presented in this paper for computing scores associated with factors of G, the image covariance matrix, under three conditions. The subject of the paper is restricted to "pure" image analysis. (Author/NE)

Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles.

PubMed

Zou, Lingyun; Nan, Chonghan; Hu, Fuquan

2013-12-15

Various human pathogens secret effector proteins into hosts cells via the type IV secretion system (T4SS). These proteins play important roles in the interaction between bacteria and hosts. Computational methods for T4SS effector prediction have been developed for screening experimental targets in several isolated bacterial species; however, widely applicable prediction approaches are still unavailable In this work, four types of distinctive features, namely, amino acid composition, dipeptide composition, .position-specific scoring matrix composition and auto covariance transformation of position-specific scoring matrix, were calculated from primary sequences. A classifier, T4EffPred, was developed using the support vector machine with these features and their different combinations for effector prediction. Various theoretical tests were performed in a newly established dataset, and the results were measured with four indexes. We demonstrated that T4EffPred can discriminate IVA and IVB effectors in benchmark datasets with positive rates of 76.7% and 89.7%, respectively. The overall accuracy of 95.9% shows that the present method is accurate for distinguishing the T4SS effector in unidentified sequences. A classifier ensemble was designed to synthesize all single classifiers. Notable performance improvement was observed using this ensemble system in benchmark tests. To demonstrate the model's application, a genome-scale prediction of effectors was performed in Bartonella henselae, an important zoonotic pathogen. A number of putative candidates were distinguished. A web server implementing the prediction method and the source code are both available at http://bioinfo.tmmu.edu.cn/T4EffPred.

[Correlation between the SF-8 health status questionnaire and JRQLQ in patients with Japanese cedar pollinosis].

PubMed

Fujii, Tsukasa; Ogino, Satoshi; Arimoto, Hiroe; Irifune, Morihiro; Iwata, Nobuko; Ookawachi, Ichiro; Kikumori, Hiroshi; Seo, Ritsu; Takeda, Mariko; Tamaki, Akiko; Baba, Kenji; Nose, Michihiro

2007-02-01

It is reported that the health-related quality of life (HRQL) is an important outcome in the Japanese Cedar Pollinosis (JCP) treatment. In Japan, the disease-specific Japan Rhino-conjunctivitis Quality of Life Questionnaire (JRQLQ) and the generic SF-36 Health Survey (SF-36) has been used. The aim of this study is to investigate more profitable QOL by using both the disease-specific questionnaire and the non-disease-specific questionnaire together. 411 patients with JCP who visited 10 ENT clinics in Osaka from March 14 to March 26 (peak pollen season) in 2005 were questioned, and 240 patients were engaged in this study as subjects. In this study, the QOL scores were evaluated using the JRQLQ and SF-8 Health Survey (Japanese Version), a new, even shorter generic health survey. Using factor analysis and the correlation matrix, we showed that the disease-specific and the general health instrument covered a different half the total measurable HRQL. There was some correlation between the SF-8 items with the JRQLQ domains. There was little correlation between the SF-8 items and symptom scores, while, there was high correlation between the JRQLQ and symptom scores. The "Usual daily activities" domain in the JRQLQ correlated with any rhinoconjunctivitis symptoms. Both JRQLQ and SF-8 can be used to assess the quality of life of patients with JCP. Each instrument measures the aspects of the HRQL that hardly overlaps. For an assessment of the HRQL in JCP that is complete and responsive both instruments should be employed together.

Non-invasive dual fluorescence in vivo imaging for detection of macrophage infiltration and matrix metalloproteinase (MMP) activity in inflammatory arthritic joints

PubMed Central

Cho, Hongsik; Bhatti, Fazal-Ur-Rehman; Yoon, Tae Won; Hasty, Karen A.; Stuart, John M.; Yi, Ae-Kyung

2016-01-01

Detection and intervention at an early stage is a critical factor to impede arthritis progress. Here we present a non-invasive method to detect inflammatory changes in joints of arthritic mice. Inflammation was monitored by dual fluorescence optical imaging for near-infrared fluorescent (750F) matrix-metalloproteinase activatable agent and allophycocyanin-conjugated anti-mouse CD11b. Increased intensity of allophycocyanin (indication of macrophage accumulation) and 750F (indication of matrix-metalloproteinase activity) showed a biological relationship with the arthritis severity score and the histopathology score of arthritic joints. Our results demonstrate that this method can be used to detect early stages of arthritis with minimum intervention in small animal models. PMID:27231625

Evaluating a native collagen matrix dressing in the treatment of chronic wounds of different aetiologies: a case series.

PubMed

Ricci, E; Cutting, K F

2016-11-02

To collate clinical evidence on the use of a native collagen matrix dressing, consisting of a fibrillary collagen network, in patients with a variety of chronic wounds. Patients whose wounds had not improved in the eight weeks before the beginning of the evalutaion were recruited. All participants had their dressings changed twice weekly and received standard adjunctive wound care as part of their treatment. Data, collected over a 4-week period, included: patient demographics, wound surface area measurements, Bates-Jensen score, level of wound pain, wound infection status, wound bed preparation staging score, depth of wound according to tissue type, and photographic imaging of patients' wounds. We recruited 19 patients with 20 wounds and a mean wound duration of 66.6 months (range: 4-480 months). There was a mean decrease in wound surface area of 29% (median reduction: 47%). A reduction in the Bates-Jensen score was demonstrated in 85% of cases. Wound pain reduced by 66.66% and the wound bed preparation score reduced in 16 wounds with four remaining static. No adverse events arose. This case series provides clinical evidence on the use of a native collagen matrix dressing in the management of hard-to-heal wounds that have previously received local standard therapy. The decrease in wound surface area together with other data indicating improved wound status suggests that a native collagen matrix dressing supports healing and improves quality of life through reduction in wound pain.

Subclinical hypothyroidism and cognitive dysfunction in the elderly.

PubMed

Resta, F; Triggiani, V; Barile, G; Benigno, M; Suppressa, P; Giagulli, V A; Guastamacchia, E; Sabbà, C

2012-09-01

While overt hypothyroidism is associated with reversible dementia in the elderly, the relationship of subclinical hypothyroidism with cognition remains a controversial issue. Our aim was to investigate the correlation between subclinical hypothyroidism and cognition in the elderly, with particular reference to long term memory and selective attention. We selected 337 outpatients (177 men and 160 women), mean age 74.3 years, excluding the subjects with thyroid dysfunction and those treated with drugs influencing thyroid function. The score of Mini Mental State Examination (MMSE) was significantly lower in the group of patients with subclinical hypothyroidism than in euthyroid subjects (p<0.03). It was observed that patients with subclinical hypothyroidism had a probability about 2 times greater (RR = 2.028, p<0.05) of developing cognitive impairment. Prose Memory Test (PMT) score resulted significantly lower in subjects with subclinical hypothyroidism (p<0.04). Considering the Matrix Test (MT) score, the performance was slightly reduced in subclinical hypothyroidism (NS). Furthermore, TSH was negatively correlated with MMSE (p<0.04), PMT (p<0.05) and MT score (NS). No correlation was found between FT4 and FT3 and MMSE, PMT and MT score. In the elderly, subclinical hypothyroidism is associated with cognitive impairment, and its impact on specific aspects of cognition (long term memory and selective attention) is less evident.

Use of cell-free collagen type I matrix implants for the treatment of small cartilage defects in the knee: clinical and magnetic resonance imaging evaluation.

PubMed

Schüttler, Karl F; Schenker, Hanno; Theisen, Christina; Schofer, Markus D; Getgood, Alan; Roessler, Philip P; Struewer, Johannes; Rominger, Marga B; Efe, Turgay

2014-06-01

Articular cartilage defects of the knee are a common condition for which several repair techniques have been described. The aim of the present study was to assess medium-term results of a one-step procedure using a cell-free collagen type I matrix. Fifteen patients with articular cartilage defects of the knee were treated with an 11-mm-diameter cell-free collagen type 1 matrix implant. The matrices were implanted in a press-fit manner into the defect after careful debridement down to the subchondral bone but without penetration of this margin. Follow-up examinations were carried out at 6 weeks, 6 months, and at 12, 24, 36, and 48 months after implantation. Clinical assessment included the visual analogue scale (VAS), the Tegner activity scale, and the International Knee Documentation Committee (IKDC) score. Radiological assessment for graft attachment and tissue regeneration was performed using the magnetic observation of cartilage repair tissue (MOCART) score. A total of 15 patients (males: n = 6 and females: n = 9) with a mean age of 26.4 years (range 19-40) were treated. The mean VAS improved significantly when compared to the preoperative values (P < 0.05). Six weeks after implantation, IKDC values were slightly lower than the preoperative values (n.s.), but increased significantly at final follow-up (P < 0.05). At 24 months, there were no significant differences in the median Tegner score between the post-operative values and the preoperative values (n.s.). However, after 36 months, a significant improvement was noted that lasted at least up to 48 months (P < 0.05). The MOCART score improved consistently up to 4 years after implantation, with significant improvements already observed after 12 months (P < 0.05). No correlation between the clinical scores and the MOCART score could be perceived. The present study showed that the use of cell-free collagen type I matrix implants led to a significant and durable improvement in all the clinical and imaging scores investigated 4 years after implantation. IV.

Lung cancer signature biomarkers: tissue specific semantic similarity based clustering of digital differential display (DDD) data.

PubMed

Srivastava, Mousami; Khurana, Pankaj; Sugadev, Ragumani

2012-11-02

The tissue-specific Unigene Sets derived from more than one million expressed sequence tags (ESTs) in the NCBI, GenBank database offers a platform for identifying significantly and differentially expressed tissue-specific genes by in-silico methods. Digital differential display (DDD) rapidly creates transcription profiles based on EST comparisons and numerically calculates, as a fraction of the pool of ESTs, the relative sequence abundance of known and novel genes. However, the process of identifying the most likely tissue for a specific disease in which to search for candidate genes from the pool of differentially expressed genes remains difficult. Therefore, we have used 'Gene Ontology semantic similarity score' to measure the GO similarity between gene products of lung tissue-specific candidate genes from control (normal) and disease (cancer) sets. This semantic similarity score matrix based on hierarchical clustering represents in the form of a dendrogram. The dendrogram cluster stability was assessed by multiple bootstrapping. Multiple bootstrapping also computes a p-value for each cluster and corrects the bias of the bootstrap probability. Subsequent hierarchical clustering by the multiple bootstrapping method (α = 0.95) identified seven clusters. The comparative, as well as subtractive, approach revealed a set of 38 biomarkers comprising four distinct lung cancer signature biomarker clusters (panel 1-4). Further gene enrichment analysis of the four panels revealed that each panel represents a set of lung cancer linked metastasis diagnostic biomarkers (panel 1), chemotherapy/drug resistance biomarkers (panel 2), hypoxia regulated biomarkers (panel 3) and lung extra cellular matrix biomarkers (panel 4). Expression analysis reveals that hypoxia induced lung cancer related biomarkers (panel 3), HIF and its modulating proteins (TGM2, CSNK1A1, CTNNA1, NAMPT/Visfatin, TNFRSF1A, ETS1, SRC-1, FN1, APLP2, DMBT1/SAG, AIB1 and AZIN1) are significantly down regulated. All down regulated genes in this panel were highly up regulated in most other types of cancers. These panels of proteins may represent signature biomarkers for lung cancer and will aid in lung cancer diagnosis and disease monitoring as well as in the prediction of responses to therapeutics.

The effects of occupational class transitions on hypertension: racial disparities among working-age men.

PubMed Central

Waitzman, N J; Smith, K R

1994-01-01

OBJECTIVES. This study was undertaken to examine how the interaction between occupational class transitions and race affects the incidence of hypertension. METHODS. A cohort of 1982 men (183 Black), ages 25 to 55, received a baseline medical exam between 1971 and 1975 and a follow-up between 1982 and 1984. Logistic regressions were estimated for hypertension at follow-up controlling for hypertension at baseline, other risk factors associated with blood pressure, and interaction terms identifying specific occupational class transitions among Blacks and Whites. The occupational class matrix was based largely on scores of US Census Bureau occupations from the Dictionary of Occupational Titles. RESULTS. Relative to Whites who remained in professional and technical jobs between baseline and follow-up, Blacks and Whites who remained in lower occupational classes or made specific transitions--notably into the lowest class--had significantly higher incidence rates of hypertension. These differences were greater among Blacks, who are also more concentrated in and less likely to move upward from the lower end of the occupational class matrix. CONCLUSIONS. Widening racial disparities in high blood pressure over the period of study may be partly attributable to characteristics associated with occupational class position and dynamics. PMID:8203691

The suitability of matrix assisted laser desorption/ionization time of flight mass spectrometry in a laboratory developed test using cystic fibrosis carrier screening as a model.

PubMed

Farkas, Daniel H; Miltgen, Nicholas E; Stoerker, Jay; van den Boom, Dirk; Highsmith, W Edward; Cagasan, Lesley; McCullough, Ron; Mueller, Reinhold; Tang, Lin; Tynan, John; Tate, Courtney; Bombard, Allan

2010-09-01

We designed a laboratory developed test (LDT) by using an open platform for mutation/polymorphism detection. Using a 108-member (mutation plus variant) cystic fibrosis carrier screening panel as a model, we completed the last phase of LDT validation by using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Panel customization was accomplished via specific amplification primer and extension probe design. Amplified genomic DNA was subjected to allele specific, single base extension endpoint analysis by mass spectrometry for inspection of the cystic fibrosis transmembrane regulator gene (NM_000492.3). The panel of mutations and variants was tested against 386 blinded samples supplied by "authority" laboratories highly experienced in cystic fibrosis transmembrane regulator genotyping; >98% concordance was observed. All discrepant and discordant results were resolved satisfactorily. Taken together, these results describe the concluding portion of the LDT validation process and the use of mass spectrometry to detect a large number of complex reactions within a single run as well as its suitability as a platform appropriate for interrogation of scores to hundreds of targets.

Estimating Total-test Scores from Partial Scores in a Matrix Sampling Design.

ERIC Educational Resources Information Center

Sachar, Jane; Suppes, Patrick

It is sometimes desirable to obtain an estimated total-test score for an individual who was administered only a subset of the items in a total test. The present study compared six methods, two of which utilize the content structure of items, to estimate total-test scores using 450 students in grades 3-5 and 60 items of the ll0-item Stanford Mental…

Fisher Scoring Method for Parameter Estimation of Geographically Weighted Ordinal Logistic Regression (GWOLR) Model

NASA Astrophysics Data System (ADS)

Widyaningsih, Purnami; Retno Sari Saputro, Dewi; Nugrahani Putri, Aulia

2017-06-01

GWOLR model combines geographically weighted regression (GWR) and (ordinal logistic reression) OLR models. Its parameter estimation employs maximum likelihood estimation. Such parameter estimation, however, yields difficult-to-solve system of nonlinear equations, and therefore numerical approximation approach is required. The iterative approximation approach, in general, uses Newton-Raphson (NR) method. The NR method has a disadvantage—its Hessian matrix is always the second derivatives of each iteration so it does not always produce converging results. With regard to this matter, NR model is modified by substituting its Hessian matrix into Fisher information matrix, which is termed Fisher scoring (FS). The present research seeks to determine GWOLR model parameter estimation using Fisher scoring method and apply the estimation on data of the level of vulnerability to Dengue Hemorrhagic Fever (DHF) in Semarang. The research concludes that health facilities give the greatest contribution to the probability of the number of DHF sufferers in both villages. Based on the number of the sufferers, IR category of DHF in both villages can be determined.

Quantitative OCT and MRI biomarkers for the differentiation of cartilage degeneration.

PubMed

Nebelung, Sven; Brill, Nicolai; Tingart, Markus; Pufe, Thomas; Kuhl, Christiane; Jahr, Holger; Truhn, Daniel

2016-04-01

To evaluate the usefulness of quantitative parameters obtained by optical coherence tomography (OCT) and magnetic resonance imaging (MRI) in the comprehensive assessment of human articular cartilage degeneration. Human osteochondral samples of variable degeneration (n = 45) were obtained from total knee replacements and assessed by MRI sequences measuring T1, T1ρ, T2 and T2* relaxivity and by OCT-based quantification of irregularity (OII, optical irregularity index), homogeneity (OHI, optical homogeneity index]) and attenuation (OAI, optical attenuation index]). Samples were also assessed macroscopically (Outerbridge classification) and histologically (Mankin classification) as grade-0 (Mankin scores 0-4)/grade-I (scores 5-8)/grade-II (scores 9-10)/grade-III (score 11-14). After data normalisation, differences between Mankin grades and correlations between imaging parameters were assessed using ANOVA and Tukey's post-hoc test and Spearman's correlation coefficients, respectively. Sensitivities and specificities in the detection of Mankin grade-0 were calculated. Significant degeneration-related increases were found for T2 and OII and decreases for OAI, while T1, T1ρ, T2* or OHI did not reveal significant changes in relation to degeneration. A number of significant correlations between imaging parameters and histological (sub)scores were found, in particular for T2 and OII. Sensitivities and specificities in the detection of Mankin grade-0 were highest for OHI/T1 and OII/T1ρ, respectively. Quantitative OCT and MRI techniques seem to complement each other in the comprehensive assessment of cartilage degeneration. Sufficiently large structural and compositional changes in the extracellular matrix may thus be parameterized and quantified, while the detection of early degeneration remains challenging.

A novel anti-EMMPRIN function-blocking antibody reduces T cell proliferation and neurotoxicity: relevance to multiple sclerosis

PubMed Central

2012-01-01

Background Extracellular matrix metalloproteinase inducer (EMMPRIN; CD147, basigin) is an inducer of the expression of several matrix metalloproteinases (MMPs). We reported previously that blocking EMMPRIN activity reduced neuroinflammation and severity of disease in an animal model of multiple sclerosis (MS), experimental autoimmune encephalomyelitis (EAE). Methods To improve upon EMMPRIN blockade, and to help unravel the biological functions of EMMPRIN in inflammatory disorders, we have developed several anti-EMMPRIN monoclonal antibodies. Results Of these monoclonal antibodies, a particular one, clone 10, was efficient in binding mouse and human cells using several methods of detection. The specificity of clone 10 was demonstrated by its lack of staining of EMMPRIN-null embryos compared to heterozygous and wild-type mouse samples. Functionally, human T cells activated with anti-CD3 and anti-CD28 elevated their expression of EMMPRIN and the treatment of these T cells with clone 10 resulted in decreased proliferation and matrix metalloproteinase- 9 (MMP-9) production. Activated human T cells were toxic to human neurons in culture and clone 10 pretreatment reduced T cell cytotoxicity correspondent with decrease of granzyme B levels within T cells. In vivo, EAE mice treated with clone 10 had a markedly reduced disease score compared to mice treated with IgM isotype control. Conclusions We have produced a novel anti-EMMPRIN monoclonal antibody that blocks several aspects of T cell activity, thus highlighting the multiple roles of EMMPRIN in T cell biology. Moreover, clone 10 reduces EAE scores in mice compared to controls, and has activity on human cells, potentially allowing for the testing of anti-EMMPRIN treatment not only in EAE, but conceivably also in MS. PMID:22480370

A novel anti-EMMPRIN function-blocking antibody reduces T cell proliferation and neurotoxicity: relevance to multiple sclerosis.

PubMed

Agrawal, Smriti M; Silva, Claudia; Wang, Janet; Tong, Jade Pui-Wai; Yong, V Wee

2012-04-05

Extracellular matrix metalloproteinase inducer (EMMPRIN; CD147, basigin) is an inducer of the expression of several matrix metalloproteinases (MMPs). We reported previously that blocking EMMPRIN activity reduced neuroinflammation and severity of disease in an animal model of multiple sclerosis (MS), experimental autoimmune encephalomyelitis (EAE). To improve upon EMMPRIN blockade, and to help unravel the biological functions of EMMPRIN in inflammatory disorders, we have developed several anti-EMMPRIN monoclonal antibodies. Of these monoclonal antibodies, a particular one, clone 10, was efficient in binding mouse and human cells using several methods of detection. The specificity of clone 10 was demonstrated by its lack of staining of EMMPRIN-null embryos compared to heterozygous and wild-type mouse samples. Functionally, human T cells activated with anti-CD3 and anti-CD28 elevated their expression of EMMPRIN and the treatment of these T cells with clone 10 resulted in decreased proliferation and matrix metalloproteinase- 9 (MMP-9) production. Activated human T cells were toxic to human neurons in culture and clone 10 pretreatment reduced T cell cytotoxicity correspondent with decrease of granzyme B levels within T cells. In vivo, EAE mice treated with clone 10 had a markedly reduced disease score compared to mice treated with IgM isotype control. We have produced a novel anti-EMMPRIN monoclonal antibody that blocks several aspects of T cell activity, thus highlighting the multiple roles of EMMPRIN in T cell biology. Moreover, clone 10 reduces EAE scores in mice compared to controls, and has activity on human cells, potentially allowing for the testing of anti-EMMPRIN treatment not only in EAE, but conceivably also in MS.

The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Based Typing: Employment of Bioinformatics in a Multicenter Study.

PubMed

Oberle, Michael; Wohlwend, Nadia; Jonas, Daniel; Maurer, Florian P; Jost, Geraldine; Tschudin-Sutter, Sarah; Vranckx, Katleen; Egli, Adrian

2016-01-01

The technical, biological, and inter-center reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) typing data has not yet been explored. The aim of this study is to compare typing data from multiple centers employing bioinformatics using bacterial strains from two past outbreaks and non-related strains. Participants received twelve extended spectrum betalactamase-producing E. coli isolates and followed the same standard operating procedure (SOP) including a full-protein extraction protocol. All laboratories provided visually read spectra via flexAnalysis (Bruker, Germany). Raw data from each laboratory allowed calculating the technical and biological reproducibility between centers using BioNumerics (Applied Maths NV, Belgium). Technical and biological reproducibility ranged between 96.8-99.4% and 47.6-94.4%, respectively. The inter-center reproducibility showed a comparable clustering among identical isolates. Principal component analysis indicated a higher tendency to cluster within the same center. Therefore, we used a discriminant analysis, which completely separated the clusters. Next, we defined a reference center and performed a statistical analysis to identify specific peaks to identify the outbreak clusters. Finally, we used a classifier algorithm and a linear support vector machine on the determined peaks as classifier. A validation showed that within the set of the reference center, the identification of the cluster was 100% correct with a large contrast between the score with the correct cluster and the next best scoring cluster. Based on the sufficient technical and biological reproducibility of MALDI-TOF MS based spectra, detection of specific clusters is possible from spectra obtained from different centers. However, we believe that a shared SOP and a bioinformatics approach are required to make the analysis robust and reliable.

Tissue specificity of the hormonal response in sex accessory tissues is associated with nuclear matrix protein patterns.

PubMed

Getzenberg, R H; Coffey, D S

1990-09-01

The DNA of interphase nuclei have very specific three-dimensional organizations that are different in different cell types, and it is possible that this varying DNA organization is responsible for the tissue specificity of gene expression. The nuclear matrix organizes the three-dimensional structure of the DNA and is believed to be involved in the control of gene expression. This study compares the nuclear structural proteins between two sex accessory tissues in the same animal responding to the same androgen stimulation by the differential expression of major tissue-specific secretory proteins. We demonstrate here that the nuclear matrix is tissue specific in the rat ventral prostate and seminal vesicle, and undergoes characteristic alterations in its protein composition upon androgen withdrawal. Three types of nuclear matrix proteins were observed: 1) nuclear matrix proteins that are different and tissue specific in the rat ventral prostate and seminal vesicle, 2) a set of nuclear matrix proteins that either appear or disappear upon androgen withdrawal, and 3) a set of proteins that are common to both the ventral prostate and seminal vesicle and do not change with the hormonal state of the animal. Since the nuclear matrix is known to bind androgen receptors in a tissue- and steroid-specific manner, we propose that the tissue specificity of the nuclear matrix arranges the DNA in a unique conformation, which may be involved in the specific interaction of transcription factors with DNA sequences, resulting in tissue-specific patterns of secretory protein expression.

Unsupervised Bayesian linear unmixing of gene expression microarrays.

PubMed

Bazot, Cécile; Dobigeon, Nicolas; Tourneret, Jean-Yves; Zaas, Aimee K; Ginsburg, Geoffrey S; Hero, Alfred O

2013-03-19

This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor.

MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs.

PubMed

Kao, Hui-Ju; Weng, Shun-Long; Huang, Kai-Yao; Kaunang, Fergie Joanda; Hsu, Justin Bo-Kai; Huang, Chien-Hsun; Lee, Tzong-Yi

2017-12-21

Carbonylation, which takes place through oxidation of reactive oxygen species (ROS) on specific residues, is an irreversibly oxidative modification of proteins. It has been reported that the carbonylation is related to a number of metabolic or aging diseases including diabetes, chronic lung disease, Parkinson's disease, and Alzheimer's disease. Due to the lack of computational methods dedicated to exploring motif signatures of protein carbonylation sites, we were motivated to exploit an iterative statistical method to characterize and identify carbonylated sites with motif signatures. By manually curating experimental data from research articles, we obtained 332, 144, 135, and 140 verified substrate sites for K (lysine), R (arginine), T (threonine), and P (proline) residues, respectively, from 241 carbonylated proteins. In order to examine the informative attributes for classifying between carbonylated and non-carbonylated sites, multifarious features including composition of twenty amino acids (AAC), composition of amino acid pairs (AAPC), position-specific scoring matrix (PSSM), and positional weighted matrix (PWM) were investigated in this study. Additionally, in an attempt to explore the motif signatures of carbonylation sites, an iterative statistical method was adopted to detect statistically significant dependencies of amino acid compositions between specific positions around substrate sites. Profile hidden Markov model (HMM) was then utilized to train a predictive model from each motif signature. Moreover, based on the method of support vector machine (SVM), we adopted it to construct an integrative model by combining the values of bit scores obtained from profile HMMs. The combinatorial model could provide an enhanced performance with evenly predictive sensitivity and specificity in the evaluation of cross-validation and independent testing. This study provides a new scheme for exploring potential motif signatures at substrate sites of protein carbonylation. The usefulness of the revealed motifs in the identification of carbonylated sites is demonstrated by their effective performance in cross-validation and independent testing. Finally, these substrate motifs were adopted to build an available online resource (MDD-Carb, http://csb.cse.yzu.edu.tw/MDDCarb/ ) and are also anticipated to facilitate the study of large-scale carbonylated proteomes.

Different matrix micro-environments in colon cancer and diverticular disease.

PubMed

Klinge, U; Rosch, R; Junge, K; Krones, C J; Stumpf, M; Lynen-Jansen, P; Mertens, P R; Schumpelick, V

2007-05-01

The extracellular matrix and the interactive signalling between its components are thought to play a pivotal role for tumour development and metastasis formation. An altered matrix composition as potential underlying pathology for the development of colorectal cancer was hypothesized. In a retrospective study of patients with colon cancer, the extracellular matrix in tumour-free bowel specimen was investigated in comparison with non-infected bowel specimen from patients operated on for colonic diverticulosis. The following matrix parameters with known associations to tumour formation, cell proliferation, invasion and metastasis were analysed by immunohistochemistry and quantified by a scoring system: VEGF, TGF-beta, ESDN, CD117, c-erb-2, cyclin D1, p53, p27, COX-2, YB-1, collagen I/III, MMP-13, PAI and uPAR. Expression profiles and correlations were calculated. The comparison of the two groups revealed a significantly decreased immunostaining for CD117 and TGF-beta in the cancer group (8.5+/-2.6 vs 10.3+/-2,1 and 4.9+/-1.5 vs 8.1+/-3, respectively), whereas PAI scores were significantly higher than in patients with diverticular disease (8.1+/-1.6 vs 6.2+/-0.9). Overall correlation patterns of matrix parameters indicated pronounced differences between tumour-free tissue in cancer patients compared with patients with diverticular disease. Our results indicate distinct differences in the colonic tissue architecture between cancer patients and patients with diverticulitis that support the notion of an altered matrix composition predisposing to the development of colon cancer.

Discriminant Validity of the WISC-IV Culture-Language Interpretive Matrix

ERIC Educational Resources Information Center

Styck, Kara M.; Watkins, Marley W.

2014-01-01

The Culture-Language Interpretive Matrix (C-LIM) was developed to help practitioners determine the validity of test scores obtained from students who are culturally and linguistically different from the normative group of a test. The present study used an idiographic approach to investigate the diagnostic utility of the C-LIM for the Wechsler…

Cognitive performance and aphasia recovery.

PubMed

Fonseca, José; Raposo, Ana; Martins, Isabel Pavão

2018-03-01

Objectives This study assessed cognitive performance of subjects with aphasia during the acute stage of stroke and evaluated how such performance relates to recovery at 3 months. Materials & methods Patients with aphasia following a left hemisphere stroke were evaluated during the first (baseline) and the fourth-month post onset. Assessment comprised non-verbal tests of attention/processing speed (Symbol Search, Cancelation Task), executive functioning (Matrix Reasoning, Tower of Hanoi, Clock Drawing, Motor Initiative), semantic (Camel and Cactus Test), episodic and immediate memory (Memory for Faces Test, 5 Objects Memory Test, and Spatial Span. Recovery was measured by the Token Test score at 3 months. The impact of baseline performance on recovery was evaluated by logistic regression adjusting for age, education, severity of aphasia and the Alberta Stroke Program Early CT (ASPECT) score. Results Thirty-nine subjects (with a mean of 66.5 ± 10.6 years of age, 17 men) were included. Average baseline cognitive performance was within normal range in all tests except in memory tests (semantic, episodic and immediate memory) for which scores were ≤-1.5sd. Subjects with poor aphasia recovery (N = 27) were older and had fewer years of formal education but had identical ASPECT score compared to those with favorable recovery. Considering each test individually, the score obtained on the Matrix Reasoning test was the only one to predict aphasia recovery (Exp(B)=24.085 p = 0.038). Conclusions The Matrix Reasoning Test may contribute to predict aphasia recovery. Cognitive performance is a measure of network disruption but may also indicate the availability of recovery strategies.

A Metric-Based System for Evaluating the Productivity of Preclinical Faculty at an Academic Medical Center in the Era of Clinical and Translational Science.

PubMed

Wiegers, Susan E; Houser, Steven R; Pearson, Helen E; Untalan, Ann; Cheung, Joseph Y; Fisher, Susan G; Kaiser, Larry R; Feldman, Arthur M

2015-08-01

Academic medical centers are faced with increasing budgetary constraints due to a flat National Institutes of Health budget, lower reimbursements for clinical services, higher costs of technology including informatics and a changing competitive landscape. As such, institutional stakeholders are increasingly asking whether resources are allocated appropriately and whether there are objective methods for measuring faculty contributions and engagement. The complexities of translational research can be particularly challenging when trying to assess faculty contributions because of team science. For over a decade, we have used an objective scoring system called the Matrix to assess faculty productivity and engagement in four areas: research, education, scholarship, and administration or services. The Matrix was developed to be dynamic, quantitative, and able to insure that a fully engaged educator would have a Matrix score that was comparable to a fully engaged investigator. In this report, we present the Matrix in its current form in order to provide a well-tested objective system of performance evaluation for nonclinical faculty to help academic leaders in decision making. © 2015 Wiley Periodicals, Inc.

Environmental impact assessment of the industrial estate development plan with the geographical information system and matrix methods.

PubMed

Ghasemian, Mohammad; Poursafa, Parinaz; Amin, Mohammad Mehdi; Ziarati, Mohammad; Ghoddousi, Hamid; Momeni, Seyyed Alireza; Rezaei, Amir Hossein

2012-01-01

The purpose of this study is environmental impact assessment of the industrial estate development planning. This cross-sectional study was conducted in 2010 in Isfahan province, Iran. GIS and matrix methods were applied. Data analysis was done to identify the current situation of the region, zoning vulnerable areas, and scoping the region. Quantitative evaluation was done by using matrix of Wooten and Rau. The net score for impact of industrial units operation on air quality of the project area was (-3). According to the transition of industrial estate pollutants, residential places located in the radius of 2500 meters of the city were expected to be affected more. The net score for impact of construction of industrial units on plant species of the project area was (-2). Environmental protected areas were not affected by the air and soil pollutants because of their distance from industrial estate. Positive effects of project activities outweigh the drawbacks and the sum scores allocated to the project activities on environmental factor was (+37). Totally it does not have detrimental effects on the environment and residential neighborhood. EIA should be considered as an anticipatory, participatory environmental management tool before determining a plan application.

Novel use of a flowable collagen-glycosaminoglycan matrix (Integra™ Flowable Wound Matrix) combined with percutaneous cannula scar tissue release in treatment of post-burn malfunction of the hand--A preliminary 6 month follow-up.

PubMed

Hirche, C; Senghaas, A; Fischer, S; Hollenbeck, S T; Kremer, T; Kneser, U

2016-02-01

Long-term function following severe burns to the hand may be poor secondary to scar adhesions to the underlying tendons, webspaces, and joints. In this pilot study, we report the feasibility of applying a pasty dermal matrix combined with percutaneous cannula teno- and adhesiolysis. In this 6 month follow-up pilot study, we included eight hands in five patients with hand burns undergoing minimal-invasive, percutaneous cannula adhesiolysis and injection of INTEGRA™ Flowable Wound Matrix for a pilot study of this new concept. The flowable collagen-glycosaminoglycan wound matrix (FCGWM) was applied with a buttoned 2mm cannula to induce formation of a neo-gliding plane. Post treatment follow-up was performed to assess active range of motion (AROM), grip strength, Disabilities of the Arm, Shoulder and Hand (DASH) score, Vancouver Scar Scale (VSS) and quality of life Short-Form (SF)-36 questionnaire. No complications were detected associated with the treatment of FCGWM injection. The mean improvement (AROM) at 6 months was 30.6° for digits 2-5. The improvement in the DASH score was a mean of 9 points out of 100. The VSS improved by a mean of 2 points out of 14. The study demonstrates the feasibility and safety of percutaneous FCGWM for dermal augmentation after burn. Results from this pilot study show improvements in AROM for digits 2-5, functional scores from the patient's perspective (DASH) and scar quality (VSS). The flowable form of established INTEGRA™ wound matrix offers the advantage of minimal-invasive injection after scar release in the post-burned hand with a reduction in the risk of postsurgical re-scarring. Copyright © 2015 Elsevier Ltd and ISBI. All rights reserved.

IS THE PREFRONTAL CORTEX IMPORTANT FOR FLUID INTELLIGENCE? A NEUROPSYCHOLOGICAL STUDY USING MATRIX REASONING

PubMed Central

Tranel, Daniel; Manzel, Kenneth; Anderson, Steven W.

2008-01-01

Patients with prefrontal damage and severe defects in decision making and emotional regulation often have a remarkable absence of intellectual impairment, as measured by conventional IQ tests such as the WAIS/WAIS-R. This enigma might be explained by shortcomings in the tests, which tend to emphasize measures of “crystallized” (e.g., vocabulary, fund of information) more than “fluid” (e.g., novel problem solving) intelligence. The WAIS-III added the Matrix Reasoning subtest to enhance measurement of fluid reasoning. In a set of four studies, we investigated Matrix Reasoning performances in 80 patients with damage to various sectors of the prefrontal cortex, and contrasted these with the performances of 80 demographically matched patients with damage outside the frontal lobes. The results failed to support the hypothesis that prefrontal damage would disproportionately impair fluid intelligence, and every prefrontal subgroup we studied (dorsolateral, ventromedial, dorsolateral + ventromedial) had Matrix Reasoning scores (as well as IQ scores more generally) that were indistinguishable from those of the brain-damaged comparison groups. Our findings do not support a connection between fluid intelligence and the frontal lobes, although a viable alternative interpretation is that the Matrix Reasoning subtest lacks construct validity as a measure of fluid intelligence. PMID:17853146

Electroacupuncture Exerts Neuroprotection through Caveolin-1 Mediated Molecular Pathway in Intracerebral Hemorrhage of Rats.

PubMed

Li, Hui-Qin; Li, Yan; Chen, Zi-Xian; Zhang, Xiao-Guang; Zheng, Xia-Wei; Yang, Wen-Ting; Chen, Shuang; Zheng, Guo-Qing

2016-01-01

Spontaneous intracerebral hemorrhage (ICH) is one of the most devastating types of stroke. Here, we aim to demonstrate that electroacupuncture on Baihui (GV20) exerts neuroprotection for acute ICH possibly via the caveolin-1/matrix metalloproteinase/blood-brain barrier permeability pathway. The model of ICH was established by using collagenase VII. Rats were randomly divided into three groups: Sham-operation group, Sham electroacupuncture group, and electroacupuncture group. Each group was further divided into 4 subgroups according to the time points of 6 h, 1 d, 3 d, and 7 d after ICH. The methods were used including examination of neurological deficit scores according to Longa's scale, measurement of blood-brain barrier permeability through Evans Blue content, in situ immunofluorescent detection of caveolin-1 in brains, western blot analysis of caveolin-1 in brains, and in situ zymography for measuring matrix metalloproteinase-2/9 activity in brains. Compared with Sham electroacupuncture group, electroacupuncture group has resulted in a significant improvement in neurological deficit scores and in a reduction in Evans Blue content, expression of caveolin-1, and activity of matrix metalloproteinase-2/9 at 6 h, 1 d, 3 d, and 7 d after ICH ( P < 0.05). In conclusion, the present results suggested that electroacupuncture on GV20 can improve neurological deficit scores and reduce blood-brain barrier permeability after ICH, and the mechanism possibly targets caveolin-1/matrix metalloproteinase/blood-brain barrier permeability pathway.

High rate of improvement in serum matrix metalloproteinase-3 levels at 4 weeks predicts remission at 52 weeks in RA patients treated with adalimumab.

PubMed

Hattori, Yosuke; Kojima, Toshihisa; Kaneko, Atsushi; Kida, Daihei; Hirano, Yuji; Fujibayashi, Takayoshi; Yabe, Yuichiro; Oguchi, Takeshi; Kanayama, Yasuhide; Miyake, Hiroyuki; Kato, Takefumi; Takagi, Hideki; Hayashi, Masatoshi; Ito, Takayasu; Shioura, Tomone; Takahashi, Nobunori; Ishikawa, Hisato; Funahashi, Koji; Ishiguro, Naoki

2018-01-01

This study aimed to determine whether serum matrix metalloproteinase-3 (MMP-3) levels can predict remission in rheumatoid arthritis (RA) patients treated with adalimumab (ADA). Subjects were 114 RA patients continuously treated with ADA for 52 weeks. Predictive factors at baseline and 4 weeks after initiation of ADA therapy for the achievement of remission (28-point count Disease Activity Score-CRP (DAS28-CRP) < 2.3) at 52 weeks were evaluated by multivariate logistic regression analysis. DAS28-CRP at 4 weeks (odds ratio (OR) 0.614, 95% confidence interval (CI) 0.382-0.988) and improvement in serum MMP-3 levels at 4 weeks (OR 1.057, 95% CI 1.002-1.032) were independent predictors of remission at 52 weeks. The best cut-off level of DAS28-CRP and improvement in serum MMP-3 levels at 4 weeks for predicting remission at 52 weeks was 3.73 (sensitivity: 90%, specificity: 50%, area under the receiver operating characteristic curve (AUC): 62%) and 39.93% (sensitivity: 47%, specificity: 83%, AUC: 64%), respectively. Our findings suggest that a high rate of improvement in serum MMP-3 levels at 4 weeks after initiation of ADA therapy can predict remission at 52 weeks in RA patients.

Effect of Matrix Size on the Image Quality of Ultra-high-resolution CT of the Lung: Comparison of 512 × 512, 1024 × 1024, and 2048 × 2048.

PubMed

Hata, Akinori; Yanagawa, Masahiro; Honda, Osamu; Kikuchi, Noriko; Miyata, Tomo; Tsukagoshi, Shinsuke; Uranishi, Ayumi; Tomiyama, Noriyuki

2018-01-16

This study aimed to assess the effect of matrix size on the spatial resolution and image quality of ultra-high-resolution computed tomography (U-HRCT). Slit phantoms and 11 cadaveric lungs were scanned on U-HRCT. Slit phantom scans were reconstructed using a 20-mm field of view (FOV) with 1024 matrix size and a 320-mm FOV with 512, 1024, and 2048 matrix sizes. Cadaveric lung scans were reconstructed using 512, 1024, and 2048 matrix sizes. Three observers subjectively scored the images on a three-point scale (1 = worst, 3 = best), in terms of overall image quality, noise, streak artifact, vessel, bronchi, and image findings. The median score of the three observers was evaluated by Wilcoxon signed-rank test with Bonferroni correction. Noise was measured quantitatively and evaluated with the Tukey test. A P value of <.05 was considered significant. The maximum spatial resolution was 0.14 mm; among the 320-mm FOV images, the 2048 matrix had the highest resolution and was significantly better than the 1024 matrix in terms of overall quality, solid nodule, ground-glass opacity, emphysema, intralobular reticulation, honeycombing, and clarity of vessels (P < .05). Both the 2048 and 1024 matrices performed significantly better than the 512 matrix (P < .001), except for noise and streak artifact. The visual and quantitative noise decreased significantly in the order of 512, 1024, and 2048 (P < .001). In U-HRCT scans, a large matrix size maintained the spatial resolution and improved the image quality and assessment of lung diseases, despite an increase in image noise, when compared to a 512 matrix size. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Parallel protein secondary structure prediction based on neural networks.

PubMed

Zhong, Wei; Altun, Gulsah; Tian, Xinmin; Harrison, Robert; Tai, Phang C; Pan, Yi

2004-01-01

Protein secondary structure prediction has a fundamental influence on today's bioinformatics research. In this work, binary and tertiary classifiers of protein secondary structure prediction are implemented on Denoeux belief neural network (DBNN) architecture. Hydrophobicity matrix, orthogonal matrix, BLOSUM62 and PSSM (position specific scoring matrix) are experimented separately as the encoding schemes for DBNN. The experimental results contribute to the design of new encoding schemes. New binary classifier for Helix versus not Helix ( approximately H) for DBNN produces prediction accuracy of 87% when PSSM is used for the input profile. The performance of DBNN binary classifier is comparable to other best prediction methods. The good test results for binary classifiers open a new approach for protein structure prediction with neural networks. Due to the time consuming task of training the neural networks, Pthread and OpenMP are employed to parallelize DBNN in the hyperthreading enabled Intel architecture. Speedup for 16 Pthreads is 4.9 and speedup for 16 OpenMP threads is 4 in the 4 processors shared memory architecture. Both speedup performance of OpenMP and Pthread is superior to that of other research. With the new parallel training algorithm, thousands of amino acids can be processed in reasonable amount of time. Our research also shows that hyperthreading technology for Intel architecture is efficient for parallel biological algorithms.

Compressive Detection of Highly Overlapped Spectra Using Walsh-Hadamard-Based Filter Functions.

PubMed

Corcoran, Timothy C

2018-03-01

In the chemometric context in which spectral loadings of the analytes are already known, spectral filter functions may be constructed which allow the scores of mixtures of analytes to be determined in on-the-fly fashion directly, by applying a compressive detection strategy. Rather than collecting the entire spectrum over the relevant region for the mixture, a filter function may be applied within the spectrometer itself so that only the scores are recorded. Consequently, compressive detection shrinks data sets tremendously. The Walsh functions, the binary basis used in Walsh-Hadamard transform spectroscopy, form a complete orthonormal set well suited to compressive detection. A method for constructing filter functions using binary fourfold linear combinations of Walsh functions is detailed using mathematics borrowed from genetic algorithm work, as a means of optimizing said functions for a specific set of analytes. These filter functions can be constructed to automatically strip the baseline from analysis. Monte Carlo simulations were performed with a mixture of four highly overlapped Raman loadings and with ten excitation-emission matrix loadings; both sets showed a very high degree of spectral overlap. Reasonable estimates of the true scores were obtained in both simulations using noisy data sets, proving the linearity of the method.

Diagnostic performance of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry in blood bacterial infections: a systematic review and meta-analysis.

PubMed

Scott, Jamie S; Sterling, Sarah A; To, Harrison; Seals, Samantha R; Jones, Alan E

2016-07-01

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has shown promise in decreasing time to identification of causative organisms compared to traditional methods; however, the utility of MALDI-TOF MS in a heterogeneous clinical setting is uncertain. To perform a systematic review on the operational performance of the Bruker MALDI-TOF MS system and evaluate published cut-off values compared to traditional blood cultures. A comprehensive literature search was performed. Studies were included if they performed direct MALDI-TOF MS analysis of blood culture specimens in human patients with suspected bacterial infections using the Bruker Biotyper software. Sensitivities and specificities of the combined studies were estimated using a hierarchical random effects linear model (REML) incorporating cut-off scores of ≥1.7 and ≥2.0. Fifty publications were identified, with 11 studies included after final review. The estimated sensitivity utilising a cut-off of ≥2.0 from the combined studies was 74.6% (95% CI = 67.9-89.3%), with an estimated specificity of 88.0% (95% CI = 74.8-94.7%). When assessing a cut-off of ≥1.7, the combined sensitivity increases to 92.8% (95% CI = 87.4-96.0%), but the estimated specificity decreased to 81.2% (95% CI = 61.9-96.6%). In this analysis, MALDI-TOF MS showed acceptable sensitivity and specificity in bacterial speciation with the current recommended cut-off point compared to blood cultures; however, lowering the cut-off point from ≥2.0 to ≥1.7 would increase the sensitivity of the test without significant detrimental effect on the specificity, which could improve clinician confidence in their results.

Treatment of multiple adjacent Miller Class I and II gingival recessions with collagen matrix and the modified coronally advanced tunnel technique.

PubMed

Molnár, Bálint; Aroca, Sofia; Keglevich, Tibor; Gera, István; Windisch, Péter; Stavropoulos, Andreas; Sculean, Anton

2013-01-01

To clinically evaluate the treatment of Miller Class I and II multiple adjacent gingival recessions using the modified coronally advanced tunnel technique combined with a newly developed bioresorbable collagen matrix of porcine origin. Eight healthy patients exhibiting at least three multiple Miller Class I and II multiple adjacent gingival recessions (a total of 42 recessions) were consecutively treated by means of the modified coronally advanced tunnel technique and collagen matrix. The following clinical parameters were assessed at baseline and 12 months postoperatively: full mouth plaque score (FMPS), full mouth bleeding score (FMBS), probing depth (PD), recession depth (RD), recession width (RW), keratinized tissue thickness (KTT), and keratinized tissue width (KTW). The primary outcome variable was complete root coverage. Neither allergic reactions nor soft tissue irritations or matrix exfoliations occurred. Postoperative pain and discomfort were reported to be low, and patient acceptance was generally high. At 12 months, complete root coverage was obtained in 2 out of the 8 patients and 30 of the 42 recessions (71%). Within their limits, the present results indicate that treatment of Miller Class I and II multiple adjacent gingival recessions by means of the modified coronally advanced tunnel technique and collagen matrix may result in statistically and clinically significant complete root coverage. Further studies are warranted to evaluate the performance of collagen matrix compared with connective tissue grafts and other soft tissue grafts.

Understanding Antipsychotic Drug Treatment Effects: A Novel Method to Reduce Pseudospecificity of the Positive and Negative Syndrome Scale (PANSS) Factors.

PubMed

Hopkins, Seth C; Ogirala, Ajay; Loebel, Antony; Koblan, Kenneth S

2017-12-01

The Positive and Negative Syndrome Scale (PANSS) is the most widely used efficacy measure in acute treatment studies of schizophrenia. However, interpretation of the efficacy of antipsychotics in improving specific symptom domains is confounded by moderate-to-high correlations among standard (Marder) PANSS factors. The authors review the results of an uncorrelated PANSS score matrix (UPSM) transform designed to reduce pseudospecificity in assessment of symptom change in patients with schizophrenia. Based on a factor analysis of five pooled, placebo-controlled lurasidone clinical trials (N=1,710 patients), a UPSM transform was identified that generated PANSS factors with high face validity (good correlation with standard Marder PANSS factors), and high specificity/orthogonality (low levels of between-factor correlation measuring change during treatment). Between-factor correlations were low at baseline for both standard (Marder) PANSS factors and transformed PANSS factors. However, when measured change in symptom severity was measured during treatment (in a pooled 5-study analysis), there was a notable difference for standard PANSS factors, where changes across factors were found to be highly correlated (factors exhibited pseudospecificity), compared to transformed PANSS factors, where factor change scores exhibited the same low levels of between-factor correlation observed at baseline. At Week 6-endpoint, correlations among PANSS factor severity scores were moderate-to-high for standard factors (0.34-0.68), but continued to be low for the transformed factors (-0.22-0.20). As an additional validity check, we analyzed data from one of the original five pooled clinical trials that included other well-validated assessment scales (MADRS, Negative Symptom Assessment scale [NSA]). In this baseline analysis, UPSM-transformed PANSS factor severity scores (negative and depression factors) were found to correlate well with the MADRS and NSA. The availability of transformed PANSS factors with a high degree of orthogonality/specificity, but which retain a high degree of concurrent and face validity, can reduce pseudospecificity as a measurement confound, and should facilitate the drug development process, permitting a more accurate characterization of the efficacy of putative new agents in targeting specific symptom domains in patients with psychotic illness.

Separating temporal and topological effects in walk-based network centrality.

PubMed

Colman, Ewan R; Charlton, Nathaniel

2016-07-01

The recently introduced concept of dynamic communicability is a valuable tool for ranking the importance of nodes in a temporal network. Two metrics, broadcast score and receive score, were introduced to measure the centrality of a node with respect to a model of contagion based on time-respecting walks. This article examines the temporal and structural factors influencing these metrics by considering a versatile stochastic temporal network model. We analytically derive formulas to accurately predict the expectation of the broadcast and receive scores when one or more columns in a temporal edge-list are shuffled. These methods are then applied to two publicly available data sets and we quantify how much the centrality of each individual depends on structural or temporal influences. From our analysis, we highlight two practical contributions: a way to control for temporal variation when computing dynamic communicability and the conclusion that the broadcast and receive scores can, under a range of circumstances, be replaced by the row and column sums of the matrix exponential of a weighted adjacency matrix given by the data.

Separating temporal and topological effects in walk-based network centrality

NASA Astrophysics Data System (ADS)

Colman, Ewan R.; Charlton, Nathaniel

2016-07-01

The recently introduced concept of dynamic communicability is a valuable tool for ranking the importance of nodes in a temporal network. Two metrics, broadcast score and receive score, were introduced to measure the centrality of a node with respect to a model of contagion based on time-respecting walks. This article examines the temporal and structural factors influencing these metrics by considering a versatile stochastic temporal network model. We analytically derive formulas to accurately predict the expectation of the broadcast and receive scores when one or more columns in a temporal edge-list are shuffled. These methods are then applied to two publicly available data sets and we quantify how much the centrality of each individual depends on structural or temporal influences. From our analysis, we highlight two practical contributions: a way to control for temporal variation when computing dynamic communicability and the conclusion that the broadcast and receive scores can, under a range of circumstances, be replaced by the row and column sums of the matrix exponential of a weighted adjacency matrix given by the data.

Environmental Impact Assessment of the Industrial Estate Development Plan with the Geographical Information System and Matrix Methods

PubMed Central

Ghasemian, Mohammad; Poursafa, Parinaz; Amin, Mohammad Mehdi; Ziarati, Mohammad; Ghoddousi, Hamid; Momeni, Seyyed Alireza; Rezaei, Amir Hossein

2012-01-01

Background. The purpose of this study is environmental impact assessment of the industrial estate development planning. Methods. This cross-sectional study was conducted in 2010 in Isfahan province, Iran. GIS and matrix methods were applied. Data analysis was done to identify the current situation of the region, zoning vulnerable areas, and scoping the region. Quantitative evaluation was done by using matrix of Wooten and Rau. Results. The net score for impact of industrial units operation on air quality of the project area was (−3). According to the transition of industrial estate pollutants, residential places located in the radius of 2500 meters of the city were expected to be affected more. The net score for impact of construction of industrial units on plant species of the project area was (−2). Environmental protected areas were not affected by the air and soil pollutants because of their distance from industrial estate. Conclusion. Positive effects of project activities outweigh the drawbacks and the sum scores allocated to the project activities on environmental factor was (+37). Totally it does not have detrimental effects on the environment and residential neighborhood. EIA should be considered as an anticipatory, participatory environmental management tool before determining a plan application. PMID:22272210

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.

PubMed

Turatsinze, Jean-Valery; Thomas-Chollier, Morgane; Defrance, Matthieu; van Helden, Jacques

2008-01-01

This protocol shows how to detect putative cis-regulatory elements and regions enriched in such elements with the regulatory sequence analysis tools (RSAT) web server (http://rsat.ulb.ac.be/rsat/). The approach applies to known transcription factors, whose binding specificity is represented by position-specific scoring matrices, using the program matrix-scan. The detection of individual binding sites is known to return many false predictions. However, results can be strongly improved by estimating P value, and by searching for combinations of sites (homotypic and heterotypic models). We illustrate the detection of sites and enriched regions with a study case, the upstream sequence of the Drosophila melanogaster gene even-skipped. This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour.

Design and efficacy of an Ecohealth competency-based course on the prevention and control of vector diseases in Latin America.

PubMed

Magaña-Valladares, Laura; Rodríguez, Mario Henry; Betanzos-Reyes, Ángel Francisco; Riojas-Rodríguez, Horacio; Quezada-Jiménez, María Laura; Suárez-Conejero, Juana Elvira; Lamadrid-Figueroa, Héctor

2018-01-01

To design and analyze the efficacy of an Ecohealth competency-based course on the prevention and control of vector-borne-diseases for specific stakeholders. Multiple stakeholders and sectors of the region were consulted to identify Ecohealth group-specific competencies using an adjusted analysis matrix. Eight courses based on the competencies were implemented to train EA tutors. The effectiveness of the course was evaluated through the use of paired- t-tests by intervention group. Strategic, tactical, academia and community stakeholder groups and their competencies were identified. An overall gain of 43 percentage points (p<0.001) was observed in terms of competencies score in trained tutors, which further trained 1 033 people. The identification of the stakeholders and their competencies proved to be useful to guide training courses to significantly improve the initial competencies and create a critical mass to further advance the EA in the region.

Altered Associations between Pain Symptoms and Brain Morphometry in the Pain Matrix of HIV-Seropositive Individuals.

PubMed

Castillo, Deborrah; Ernst, Thomas; Cunningham, Eric; Chang, Linda

2018-03-01

Pain remains highly prevalent in HIV-seropositive (HIV+) patients despite their well-suppressed viremia with combined antiretroviral therapy. Investigating brain abnormalities within the pain matrix, and in relation to pain symptoms, in HIV+ participants may provide objective biomarkers and insights regarding their pain symptoms. We used Patient-Reported Outcome Measurement Information System (PROMIS®) pain questionnaire to evaluate pain symptoms (pain intensity, pain interference and pain behavior), and structural MRI to assess brain morphometry using FreeSurfer (cortical area, cortical thickness and subcortical volumes were evaluated in 12 regions within the pain matrix). Compared to seronegative (SN) controls, HIV+ participants had smaller surface areas in prefrontal pars triangularis (right: p = 0.04, left: p = 0.007) and right anterior cingulate cortex (p = 0.03) and smaller subcortical regions (thalamus: p ≤ 0.003 bilaterally; right putamen: p = 0.01), as well as higher pain scores (pain intensity-p = 0.005; pain interference-p = 0.008; pain-behavior-p = 0.04). Furthermore, higher pain scores were associated with larger cortical areas, thinner cortices and larger subcortical volumes in HIV+ participants; but smaller cortical areas, thicker cortices and smaller subcortical volumes in SN controls (interaction-p = 0.009 to p = 0.04). These group differences in the pain-associated brain abnormalities suggest that HIV+ individuals have abnormal pain responses. Since these abnormal pain-associated brain regions belong to the affective component of the pain matrix, affective symptoms may influence pain perception in HIV+ patients and should be treated along with their physical pain symptoms. Lastly, associations of lower pain scores with better physical or mental health scores, regardless of HIV-serostatus (p < 0.001), suggest adequate pain treatment would lead to better quality of life in all participants.

What is the effect of matrices on cartilage repair? A systematic review.

PubMed

Wylie, James D; Hartley, Melissa K; Kapron, Ashley L; Aoki, Stephen K; Maak, Travis G

2015-05-01

Articular cartilage has minimal endogenous ability to undergo repair. Multiple chondral restoration strategies have been attempted with varied results. The purpose of our review was to determine: (1) Does articular chondrocyte transplantation or matrix-assisted articular chondrocyte transplantation provide better patient-reported outcomes scores, MRI morphologic measurements, or histologic quality of repair tissue compared with microfracture in prospective comparative studies of articular cartilage repair; and (2) which available matrices for matrix-assisted articular chondrocyte transplantation show the best patient-reported outcomes scores, MRI morphologic measurements, or histologic quality of repair tissue? We conducted a systematic review of PubMed, CINAHL, and MEDLINE from March 2004 to February 2014 using keywords determined to be important for articular cartilage repair, including "cartilage", "chondral", "cell source", "chondrocyte", "matrix", "augment", "articular", "joint", "repair", "treatment", "regeneration", and "restoration" to find articles related to cell-based articular cartilage repair of the knee. The articles were reviewed by two authors (JDW, MKH), our study exclusion criteria were applied, and articles were determined to be relevant (or not) to the research questions. The Methodological Index for Nonrandomized Studies (MINORS) scale was used to judge the quality of nonrandomized manuscripts used in this review and the Jadad score was used to judge the quality of randomized trials. Seventeen articles were reviewed for the first research question and 83 articles were reviewed in the second research question from 301 articles identified in the original systematic search. The average MINORS score was 9.9 (62%) for noncomparative studies and 16.1 (67%) for comparative studies. The average Jadad score was 2.3 for the randomized studies. Articular chondrocyte transplantation shows better patient-reported outcomes at 5 years in patients without chronic symptoms preoperatively compared with microfracture (p = 0.026). Matrix-assisted articular chondrocyte transplantation consistently showed improved patient-reported functional outcomes compared with microfracture (p values ranging from < 0.001 to 0.029). Hyalograft C(®) (Anika Therapeutics Inc, Bedford, MA, USA) and Chondro-gide(®) (Genzyme Biosurgery, Kastrup, Denmark) are the matrices with the most published evidence in the literature, but no studies comparing different matrices met our inclusion criteria, because the literature consists only of uncontrolled case series. Matrix-assisted articular chondrocyte transplantation leads to better patient-reported outcomes in cartilage repair compared with microfracture; however, future prospective research is needed comparing different matrices to determine which products optimize cartilage repair. Level IV, therapeutic study.

A knowledge-based theory of rising scores on "culture-free" tests.

PubMed

Fox, Mark C; Mitchum, Ainsley L

2013-08-01

Secular gains in intelligence test scores have perplexed researchers since they were documented by Flynn (1984, 1987). Gains are most pronounced on abstract, so-called culture-free tests, prompting Flynn (2007) to attribute them to problem-solving skills availed by scientifically advanced cultures. We propose that recent-born individuals have adopted an approach to analogy that enables them to infer higher level relations requiring roles that are not intrinsic to the objects that constitute initial representations of items. This proposal is translated into item-specific predictions about differences between cohorts in pass rates and item-response patterns on the Raven's Matrices (Flynn, 1987), a seemingly culture-free test that registers the largest Flynn effect. Consistent with predictions, archival data reveal that individuals born around 1940 are less able to map objects at higher levels of relational abstraction than individuals born around 1990. Polytomous Rasch models verify predicted violations of measurement invariance, as raw scores are found to underestimate the number of analogical rules inferred by members of the earlier cohort relative to members of the later cohort who achieve the same overall score. The work provides a plausible cognitive account of the Flynn effect, furthers understanding of the cognition of matrix reasoning, and underscores the need to consider how test-takers select item responses. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Alteration of matrix metalloproteinase-3 O-glycan structure as a biomarker for disease activity of rheumatoid arthritis.

PubMed

Takeshita, Masaru; Kuno, Atsushi; Suzuki, Katsuya; Matsuda, Atsushi; Shimazaki, Hiroko; Nakagawa, Tomomi; Otomo, Yuki; Kabe, Yasuaki; Suematsu, Makoto; Narimatsu, Hisashi; Takeuchi, Tsutomu

2016-05-21

Nearly all secreted proteins are glycosylated, and serum glycoproteins that exhibit disease-associated glycosylation changes have potential to be biomarkers. In rheumatoid arthritis (RA), C-reactive protein (CRP), and matrix metalloproteinase-3 (MMP-3) are widely used as serologic biomarkers, but they lack sufficient specificity or precision. We performed comparative glycosylation profiling of MMP-3 using a recently developed antibody-overlay lectin microarray technology that allows semicomprehensive and quantitative analysis of specific protein glycosylation to develop an RA-specific disease activity biomarker. Serum was taken from patients with RA (n = 24) whose disease activity was scored using composite measures, and MMP-3 was immunoprecipitated and subjected to lectin microarray analysis. A disease activity index (DAI) based on lectin signal was developed and validated using another cohort (n = 60). Synovial fluid MMP-3 in patients with RA and patients with osteoarthritis (OA) was also analyzed. Intense signals were observed on a sialic acid-binding lectin (Agrocybe cylindracea galectin [ACG]) and O-glycan-binding lectins (Jacalin, Agaricus bisporus agglutinin [ABA], and Amaranthus caudatus agglutinin [ACA]) by applying subnanogram levels of serum MMP-3. ACG, ABA, and ACA revealed differences in MMP-3 quantity, and Jacalin revealed differences in MMP-3 quality. The resultant index, ACG/Jacalin, correlated well with disease activity. Further validation using another cohort confirmed that this index correlated well with several DAIs and their components, and reflected DAI changes following RA treatment, with correlations greater than those for MMP-3 and CRP. Furthermore, MMP-3, which generated a high ACG/Jacalin score, accumulated in synovial fluid of patients with RA but not in that of patients with OA. Sialidase digestion revealed that the difference in quality was derived from O-glycan α-2,6-sialylation. This is the first report of a glycoprotein biomarker using glycan change at a local lesion to assess disease activity in autoimmune diseases. Differences in the degree of serum MMP-3 α-2,6-sialylation may be a useful index for estimating disease activity.

Optimization of microfabricated nanoliter-scale solid-phase extraction device for detection of gel-separated proteins in low abundance by matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Chen, Wenzhang; Shen, Jing; Yin, Xuefeng; Yu, Yingnian

2007-01-01

A nano-scale solid-phase extraction (SPE) device was developed for the detection of gel-separated proteins in low abundance by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) with a simplified microfabrication technology. By using SU-8 photoresist instead of epoxy glue to connect the microchannel and transfer capillary, polymeric contaminant signals in MS analysis were significantly reduced. Micro SPE columns with different capacities and geometric characteristics were investigated in order to increase the detection sensitivity and decrease spot size for MALDI-TOF-MS analysis. It is shown that enhancements in sensitivities for the detection of proteins in low abundance were correlated with the reduction in column capacity and increase in column aspect ratio. Fifty nanoliters of matrix solution were sufficient to elute the sample completely from the optimized micro SPE column with 3.5 nL capacity. The mass spectrum of a 5 fmol in-gel tryptic digest of bovine serum albumin (BSA), processed by the micro SPE column, demonstrated that 29 peptides matched the protein giving a sequence coverage of 51%, which was better than that obtained from analysis of 25 fmol of the same sample prepared by the dried-droplet method. With the micro SPE column treatment of 2 microL of digestion supernatant of a gel spot of the IQGAP1 protein, 15 peptides were detected from the mass spectrum with the highest individual score of 111, while, with a ZipTip procedure, only nine peaks were detected with the highest individual score of 71. Analytical results demonstrated that this approach greatly improved the sequence coverage and identification specificity for the tested protein. It can serve as a very useful tool in proteomics studies, especially for low abundance proteins. Copyright (c) 2006 John Wiley & Sons, Ltd.

Some Results on Mean Square Error for Factor Score Prediction

ERIC Educational Resources Information Center

Krijnen, Wim P.

2006-01-01

For the confirmatory factor model a series of inequalities is given with respect to the mean square error (MSE) of three main factor score predictors. The eigenvalues of these MSE matrices are a monotonic function of the eigenvalues of the matrix gamma[subscript rho] = theta[superscript 1/2] lambda[subscript rho] 'psi[subscript rho] [superscript…

Improvement of identification of Capnocytophaga canimorsus by matrix-assisted laser desorption ionization-time of flight mass spectrometry using enriched database.

PubMed

Magnette, Amandine; Huang, Te-Din; Renzi, Francesco; Bogaerts, Pierre; Cornelis, Guy R; Glupczynski, Youri

2016-01-01

Capnocytophaga canimorsus and Capnocytophaga cynodegmi can be transmitted from dogs or cats and cause serious human infections. We aimed to evaluate the ability of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to identify these two Capnocytophaga species. Ninety-four C. canimorsus and 10 C. cynodegmi isolates identified by 16S rRNA gene sequencing were analyzed. Using the MALDI BioTyper database, correct identification was achieved for only 16 of 94 (17%) C. canimorsus and all 10 C. cynodegmi strains, according to the manufacturer's log score specifications. Following the establishment of a complementary homemade reference database by addition of 51 C. canimorsus and 8 C. cynodegmi mass spectra, MALDI-TOF MS provided reliable identification to the species level for 100% of the 45 blind-coded Capnocytophaga isolates tested. MALDI-TOF MS can accurately identify C. canimorsus and C. cynodegmi using an enriched database and thus constitutes a valuable diagnostic tool in the clinical laboratory. Copyright © 2016 Elsevier Inc. All rights reserved.

Correlation of pretreatment 18F-FDG PET tumor textural features with gene expression in pharyngeal cancer and implications for radiotherapy-based treatment outcomes.

PubMed

Chen, Shang-Wen; Shen, Wei-Chih; Lin, Ying-Chun; Chen, Rui-Yun; Hsieh, Te-Chun; Yen, Kuo-Yang; Kao, Chia-Hung

2017-04-01

This study investigated the correlation of the matrix heterogeneity of tumors on 18 F-fluorodeoxyglucose positron emission tomography-computed tomography (PET-CT) with gene-expression profiling in patients with pharyngeal cancer and determined the prognostic factors for radiotherapy-based treatment outcomes. We retrospectively reviewed the records of 57 patients with stage III-IV oropharyngeal or hypopharyngeal cancer who had completed definitive therapy. Four groups of the textural features as well as 31 indices were studied in addition to maximum standard uptake value, metastatic tumor volume, and total lesion glycolysis. Immunohistochemical data from pretreatment biopsy specimens (Glut1, CAIX, VEGF, HIF-1α, EGFR, Ki-67, Bcl-2, CLAUDIN-4, YAP-1, c-Met, and p16) were analyzed. The relationships between the indices and genomic expression were studied, and the robustness of various textural features relative to cause-specific survival and primary relapse-free survival was analyzed. The overexpression of VEGF was positively associated with the increased values of the matrix heterogeneity obtained using gray-level nonuniformity for zone (GLNUz) and run-length nonuniformity (RLNU). Advanced T stage (p = 0.01, hazard ratio [HR] = 3.38), a VEGF immunoreactive score of >2 (p = 0.03, HR = 2.79), and a higher GLNUz value (p = 0.04, HR = 2.51) were prognostic factors for low cause-specific survival, whereas advanced T stage, a HIF-1α staining percentage of ≥80%, and a higher GLNUz value were prognostic factors for low primary-relapse free survival. The overexpression of VEGF was associated with the increased matrix index of GLNUz and RLNU. For patients with pharyngeal cancer requiring radiotherapy, the treatment outcome can be stratified according to the textural features, T stage, and biomarkers.

Determination of Flavonol Aglycones in Ginkgo biloba Dietary Supplement Crude Materials and Finished Products by High-Performance Liquid Chromatography: Single Laboratory Validation

PubMed Central

Gray, Dean; LeVanseler, Kerri; Pan, Meide

2008-01-01

A single laboratory validation (SLV) was completed for a method to determine the flavonol aglycones quercetin, kaempferol, and isorhamnetin in Ginkgo biloba products. The method calculates total glycosides based on these aglycones formed following acid hydrolysis. Nine matrixes were chosen for the study, including crude leaf material, standardized dry powder extract, single and multiple entity finished products, and ethanol and glycerol tinctures. For the 9 matrixes evaluated as part of this SLV, the method appeared to be selective and specific, with no observed interferences. The simplified 60 min oven heating hydrolysis procedure was effective for each of the matrixes studied, with no apparent or consistent differences between 60, 75, and 90 min at 90°C. A Youden ruggedness trial testing 7 factors with the potential to affect quantitative results showed that 2 factors (volume hydrolyzed and test sample extraction/hydrolysis weight) were the most important parameters for control during sample preparation. The method performed well in terms of precision, with 4 matrixes tested in triplicate over a 3-day period showing an overall repeatability (relative standard deviation, RSD) of 2.3%. Analysis of variance testing at α = 0.05 showed no significant differences among the within- or between-group sources of variation, although comparisons of within-day (Sw), between-day (Sb), and total (St) precision showed that a majority of the standard deviation came from within-day determinations for all matrixes. Accuracy testing at 2 levels (approximately 30 and 90% of the determined concentrations in standardized dry powder extract) from 2 complex negative control matrixes showed an overall 96% recovery and RSD of 1.0% for the high spike, and 94% recovery and RSD of 2.5% for the low spike. HorRat scores were within the limits for performance acceptability, ranging from 0.4 to 1.3. Based on the performance results presented herein, it is recommended that this method progress to the collaborative laboratory trial. PMID:16001841

Optical matrix-matrix multiplication method demonstrated by the use of a multifocus hololens

NASA Technical Reports Server (NTRS)

Liu, H. K.; Liang, Y.-Z.

1984-01-01

A method of optical matrix-matrix multiplication is presented. The feasibility of the method is also experimentally demonstrated by the use of a dichromated-gelatin multifocus holographic lens (hololens). With the specific values of matrices chosen, the average percentage error between the theoretical and experimental data of the elements of the output matrix of the multiplication of some specific pairs of 3 x 3 matrices is 0.4 percent, which corresponds to an 8-bit accuracy.

Validity of the KABC-II Culture-Language Interpretive Matrix: A Comparison of Native English Speakers and Spanish-Speaking English Language Learners

ERIC Educational Resources Information Center

Van Deth, Leah M.

2013-01-01

The purpose of the present study was to investigate the validity of the Culture-Language Interpretive Matrix (C-LIM; Flanagan, Ortiz, & Alfonso, 2013) when applied to scores from the Kaufman Assessment Battery for Children, 2nd Edition (KABC-II; Kaufman & Kaufman, 2004). Data were analyzed from the KABC-II standardization sample as well as…

The creation, management, and use of data quality information for life cycle assessment.

PubMed

Edelen, Ashley; Ingwersen, Wesley W

2018-04-01

Despite growing access to data, questions of "best fit" data and the appropriate use of results in supporting decision making still plague the life cycle assessment (LCA) community. This discussion paper addresses revisions to assessing data quality captured in a new US Environmental Protection Agency guidance document as well as additional recommendations on data quality creation, management, and use in LCA databases and studies. Existing data quality systems and approaches in LCA were reviewed and tested. The evaluations resulted in a revision to a commonly used pedigree matrix, for which flow and process level data quality indicators are described, more clarity for scoring criteria, and further guidance on interpretation are given. Increased training for practitioners on data quality application and its limits are recommended. A multi-faceted approach to data quality assessment utilizing the pedigree method alongside uncertainty analysis in result interpretation is recommended. A method of data quality score aggregation is proposed and recommendations for usage of data quality scores in existing data are made to enable improved use of data quality scores in LCA results interpretation. Roles for data generators, data repositories, and data users are described in LCA data quality management. Guidance is provided on using data with data quality scores from other systems alongside data with scores from the new system. The new pedigree matrix and recommended data quality aggregation procedure can now be implemented in openLCA software. Additional ways in which data quality assessment might be improved and expanded are described. Interoperability efforts in LCA data should focus on descriptors to enable user scoring of data quality rather than translation of existing scores. Developing and using data quality indicators for additional dimensions of LCA data, and automation of data quality scoring through metadata extraction and comparison to goal and scope are needed.

The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains.

PubMed

Ren, Siyuan; Yang, Guang; He, Youyu; Wang, Yiguo; Li, Yixue; Chen, Zhengjun

2008-10-01

Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains. Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains.

The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains

PubMed Central

Ren, Siyuan; Yang, Guang; He, Youyu; Wang, Yiguo; Li, Yixue; Chen, Zhengjun

2008-01-01

Background Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains. Results Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. Conclusion The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains. PMID:18828911

The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Based Typing: Employment of Bioinformatics in a Multicenter Study

PubMed Central

Oberle, Michael; Wohlwend, Nadia; Jonas, Daniel; Maurer, Florian P.; Jost, Geraldine; Tschudin-Sutter, Sarah; Vranckx, Katleen; Egli, Adrian

2016-01-01

Background The technical, biological, and inter-center reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) typing data has not yet been explored. The aim of this study is to compare typing data from multiple centers employing bioinformatics using bacterial strains from two past outbreaks and non-related strains. Material/Methods Participants received twelve extended spectrum betalactamase-producing E. coli isolates and followed the same standard operating procedure (SOP) including a full-protein extraction protocol. All laboratories provided visually read spectra via flexAnalysis (Bruker, Germany). Raw data from each laboratory allowed calculating the technical and biological reproducibility between centers using BioNumerics (Applied Maths NV, Belgium). Results Technical and biological reproducibility ranged between 96.8–99.4% and 47.6–94.4%, respectively. The inter-center reproducibility showed a comparable clustering among identical isolates. Principal component analysis indicated a higher tendency to cluster within the same center. Therefore, we used a discriminant analysis, which completely separated the clusters. Next, we defined a reference center and performed a statistical analysis to identify specific peaks to identify the outbreak clusters. Finally, we used a classifier algorithm and a linear support vector machine on the determined peaks as classifier. A validation showed that within the set of the reference center, the identification of the cluster was 100% correct with a large contrast between the score with the correct cluster and the next best scoring cluster. Conclusions Based on the sufficient technical and biological reproducibility of MALDI-TOF MS based spectra, detection of specific clusters is possible from spectra obtained from different centers. However, we believe that a shared SOP and a bioinformatics approach are required to make the analysis robust and reliable. PMID:27798637

Single-stage cartilage repair in the knee with microfracture covered with a resorbable polymer-based matrix and autologous bone marrow concentrate.

PubMed

Enea, D; Cecconi, S; Calcagno, S; Busilacchi, A; Manzotti, S; Kaps, C; Gigante, A

2013-12-01

Different single-stage surgical approaches are currently under evaluation to repair focal cartilage lesions. This study aims to analyze the clinical and histological results after treatment of focal condylar articular lesions of the knee with microfracture and subsequent covering with a resorbable polyglycolic acid/hyaluronan (PGA -HA) matrix augmented with autologous bone marrow concentrate (BMC). Nine patients with focal lesions of the condylar articular cartilage were consecutively treated with arthroscopic PGA -HA-covered microfracture and bone marrow concentrate (PGA -HA-CMBMC). Patients were retrospectively assessed using standardized assessment tools and magnetic resonance imaging (MRI). Five patients consented to undergo second look arthroscopy and 2 consented biopsy harvest. All the patients but one showed improvement in clinical scoring from the pre-operative situation to the latest follow-up (average 22±2months). The mean IKDC subjective score, Lysholm score, VAS and the median Tegner score significantly increased from baseline to the latest follow-up. Cartilage macroscopic assessment at 12months revealed that one repair appeared normal, three almost normal and one appeared abnormal. Histological analysis proofed hyaline-like cartilage repair tissue formation in one case. MRI at 8 to 12months follow-up showed complete defect filling. The first clinical experience with single-stage treatment of focal cartilage defects of the knee with microfracture and covering with the PGA -HA matrix augmented with autologous BMC (PGA -HA-CMBMC) suggests that it is safe, it improves knee function and has the potential to regenerate hyaline-like cartilage. IV, case series. Copyright © 2013 Elsevier B.V. All rights reserved.

A comparison of likelihood ratio tests and Rao's score test for three separable covariance matrix structures.

PubMed

Filipiak, Katarzyna; Klein, Daniel; Roy, Anuradha

2017-01-01

The problem of testing the separability of a covariance matrix against an unstructured variance-covariance matrix is studied in the context of multivariate repeated measures data using Rao's score test (RST). The RST statistic is developed with the first component of the separable structure as a first-order autoregressive (AR(1)) correlation matrix or an unstructured (UN) covariance matrix under the assumption of multivariate normality. It is shown that the distribution of the RST statistic under the null hypothesis of any separability does not depend on the true values of the mean or the unstructured components of the separable structure. A significant advantage of the RST is that it can be performed for small samples, even smaller than the dimension of the data, where the likelihood ratio test (LRT) cannot be used, and it outperforms the standard LRT in a number of contexts. Monte Carlo simulations are then used to study the comparative behavior of the null distribution of the RST statistic, as well as that of the LRT statistic, in terms of sample size considerations, and for the estimation of the empirical percentiles. Our findings are compared with existing results where the first component of the separable structure is a compound symmetry (CS) correlation matrix. It is also shown by simulations that the empirical null distribution of the RST statistic converges faster than the empirical null distribution of the LRT statistic to the limiting χ 2 distribution. The tests are implemented on a real dataset from medical studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Semantic representation in the white matter pathway

PubMed Central

Fang, Yuxing; Wang, Xiaosha; Zhong, Suyu; Song, Luping; Han, Zaizhu; Gong, Gaolang

2018-01-01

Object conceptual processing has been localized to distributed cortical regions that represent specific attributes. A challenging question is how object semantic space is formed. We tested a novel framework of representing semantic space in the pattern of white matter (WM) connections by extending the representational similarity analysis (RSA) to structural lesion pattern and behavioral data in 80 brain-damaged patients. For each WM connection, a neural representational dissimilarity matrix (RDM) was computed by first building machine-learning models with the voxel-wise WM lesion patterns as features to predict naming performance of a particular item and then computing the correlation between the predicted naming score and the actual naming score of another item in the testing patients. This correlation was used to build the neural RDM based on the assumption that if the connection pattern contains certain aspects of information shared by the naming processes of these two items, models trained with one item should also predict naming accuracy of the other. Correlating the neural RDM with various cognitive RDMs revealed that neural patterns in several WM connections that connect left occipital/middle temporal regions and anterior temporal regions associated with the object semantic space. Such associations were not attributable to modality-specific attributes (shape, manipulation, color, and motion), to peripheral picture-naming processes (picture visual similarity, phonological similarity), to broad semantic categories, or to the properties of the cortical regions that they connected, which tended to represent multiple modality-specific attributes. That is, the semantic space could be represented through WM connection patterns across cortical regions representing modality-specific attributes. PMID:29624578

Matrix Metalloproteinases as a Therapeutic Target to Improve Neurologic Recovery After Spinal Cord Injury

DTIC Science & Technology

2013-10-01

the BMS scale where a score of 0 indicates hindlimb paralysis and a score of 9 reflects normal hindlimb locomotor function. The more mildly injured...graded levels of injury severity based upon the BMS scale . Urologic status shows injury severity-dependent changes with UICs being most pronounced...BMS scale . Exclusion criteria were as follows: any animal showing an average score of > 0.5 at 8 hours post- injury or morbidity as defined in UCSF

FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications.

PubMed

Backenroth, Daniel; He, Zihuai; Kiryluk, Krzysztof; Boeva, Valentina; Pethukova, Lynn; Khurana, Ekta; Christiano, Angela; Buxbaum, Joseph D; Ionita-Laza, Iuliana

2018-05-03

We describe a method based on a latent Dirichlet allocation model for predicting functional effects of noncoding genetic variants in a cell-type- and/or tissue-specific way (FUN-LDA). Using this unsupervised approach, we predict tissue-specific functional effects for every position in the human genome in 127 different tissues and cell types. We demonstrate the usefulness of our predictions by using several validation experiments. Using eQTL data from several sources, including the GTEx project, Geuvadis project, and TwinsUK cohort, we show that eQTLs in specific tissues tend to be most enriched among the predicted functional variants in relevant tissues in Roadmap. We further show how these integrated functional scores can be used for (1) deriving the most likely cell or tissue type causally implicated for a complex trait by using summary statistics from genome-wide association studies and (2) estimating a tissue-based correlation matrix of various complex traits. We found large enrichment of heritability in functional components of relevant tissues for various complex traits, and FUN-LDA yielded higher enrichment estimates than existing methods. Finally, using experimentally validated functional variants from the literature and variants possibly implicated in disease by previous studies, we rigorously compare FUN-LDA with state-of-the-art functional annotation methods and show that FUN-LDA has better prediction accuracy and higher resolution than these methods. In particular, our results suggest that tissue- and cell-type-specific functional prediction methods tend to have substantially better prediction accuracy than organism-level prediction methods. Scores for each position in the human genome and for each ENCODE and Roadmap tissue are available online (see Web Resources). Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Estimating Time to Event From Longitudinal Categorical Data: An Analysis of Multiple Sclerosis Progression.

PubMed

Mandel, Micha; Gauthier, Susan A; Guttmann, Charles R G; Weiner, Howard L; Betensky, Rebecca A

2007-12-01

The expanded disability status scale (EDSS) is an ordinal score that measures progression in multiple sclerosis (MS). Progression is defined as reaching EDSS of a certain level (absolute progression) or increasing of one point of EDSS (relative progression). Survival methods for time to progression are not adequate for such data since they do not exploit the EDSS level at the end of follow-up. Instead, we suggest a Markov transitional model applicable for repeated categorical or ordinal data. This approach enables derivation of covariate-specific survival curves, obtained after estimation of the regression coefficients and manipulations of the resulting transition matrix. Large sample theory and resampling methods are employed to derive pointwise confidence intervals, which perform well in simulation. Methods for generating survival curves for time to EDSS of a certain level, time to increase of EDSS of at least one point, and time to two consecutive visits with EDSS greater than three are described explicitly. The regression models described are easily implemented using standard software packages. Survival curves are obtained from the regression results using packages that support simple matrix calculation. We present and demonstrate our method on data collected at the Partners MS center in Boston, MA. We apply our approach to progression defined by time to two consecutive visits with EDSS greater than three, and calculate crude (without covariates) and covariate-specific curves.

A pragmatic approach for mortality prediction after surgery in infective endocarditis: optimizing and refining EuroSCORE.

PubMed

Fernández-Hidalgo, N; Ferreria-González, I; Marsal, J R; Ribera, A; Aznar, M L; de Alarcón, A; García-Cabrera, E; Gálvez-Acebal, J; Sánchez-Espín, G; Reguera-Iglesias, J M; De La Torre-Lima, J; Lomas, J M; Hidalgo-Tenorio, C; Vallejo, N; Miranda, B; Santos-Ortega, A; Castro, M A; Tornos, P; García-Dorado, D; Almirante, B

2018-03-03

To simplify and optimize the ability of EuroSCORE I and II to predict early mortality after surgery for infective endocarditis (IE). Multicentre retrospective study (n = 775). Simplified scores, eliminating irrelevant variables, and new specific scores, adding specific IE variables, were created. The performance of the original, recalibrated and specific EuroSCOREs was assessed by Brier score, C-statistic and calibration plot in bootstrap samples. The Net Reclassification Index was quantified. Recalibrated scores including age, previous cardiac surgery, critical preoperative state, New York Heart Association >I, and emergent surgery (EuroSCORE I and II); renal failure and pulmonary hypertension (EuroSCORE I); and urgent surgery (EuroSCORE II) performed better than the original EuroSCOREs (Brier original and recalibrated: EuroSCORE I: 0.1770 and 0.1667; EuroSCORE II: 0.2307 and 0.1680). Performance improved with the addition of fistula, staphylococci and mitral location (EuroSCORE I and II) (Brier specific: EuroSCORE I 0.1587, EuroSCORE II 0.1592). Discrimination improved in specific models (C-statistic original, recalibrated and specific: EuroSCORE I: 0.7340, 0.7471 and 0.7728; EuroSCORE II: 0.7442, 0.7423 and 0.7700). Calibration improved in both EuroSCORE I models (intercept 0.295, slope 0.829 (original); intercept -0.094, slope 0.888 (recalibrated); intercept -0.059, slope 0.925 (specific)) but only in specific EuroSCORE II model (intercept 2.554, slope 1.114 (original); intercept -0.260, slope 0.703 (recalibrated); intercept -0.053, slope 0.930 (specific)). Net Reclassification Index was 5.1% and 20.3% for the specific EuroSCORE I and II CONCLUSIONS: The use of simplified EuroSCORE I and EuroSCORE II models in IE with the addition of specific variables may lead to simpler and more accurate models. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Transformed PANSS Factors Intended to Reduce Pseudospecificity Among Symptom Domains and Enhance Understanding of Symptom Change in Antipsychotic-Treated Patients With Schizophrenia

PubMed Central

Hopkins, Seth C; Ogirala, Ajay; Loebel, Antony; Koblan, Kenneth S

2018-01-01

Abstract Positive and Negative Syndrome Scale (PANSS) total score is the standard primary efficacy measure in acute treatment studies of schizophrenia. However, PANSS factors that have been derived from factor analytic approaches over the past several decades have uncertain clinical and regulatory status as they are, to varying degrees, intercorrelated. As a consequence of cross-factor correlations, the apparent improvement in key clinical domains (eg, negative symptoms, disorganized thinking/behavior) may largely be attributable to improvement in a related clinical domain, such as positive symptoms, a problem often referred to as pseudospecificity. Here, we analyzed correlations among PANSS items, at baseline and change post-baseline, in a pooled sample of 5 placebo-controlled clinical trials (N = 1710 patients), using clustering and factor analysis to identify an uncorrelated PANSS score matrix (UPSM) that minimized the degree of correlation between each resulting transformed PANSS factor. The transformed PANSS factors corresponded well with discrete symptom domains described by prior factor analyses, but between-factor change-scores correlations were markedly lower. We then used the UPSM to transform PANSS in data from 4657 unique schizophrenia patients included in 12 additional lurasidone clinical trials. The results confirmed that transformed PANSS factors retained a high degree of specificity, thus validating that low between-factor correlations are a reliable property of the USPM when transforming PANSS data from a variety of clinical trial data sets. These results provide a more robust understanding of the structure of symptom change in schizophrenia and suggest a means to evaluate the specificity of antipsychotic treatment effects. PMID:28981857

Clinical validation of the General Ability Index--Estimate (GAI-E): estimating premorbid GAI.

PubMed

Schoenberg, Mike R; Lange, Rael T; Iverson, Grant L; Chelune, Gordon J; Scott, James G; Adams, Russell L

2006-09-01

The clinical utility of the General Ability Index--Estimate (GAI-E; Lange, Schoenberg, Chelune, Scott, & Adams, 2005) for estimating premorbid GAI scores was investigated using the WAIS-III standardization clinical trials sample (The Psychological Corporation, 1997). The GAI-E algorithms combine Vocabulary, Information, Matrix Reasoning, and Picture Completion subtest raw scores with demographic variables to predict GAI. Ten GAI-E algorithms were developed combining demographic variables with single subtest scaled scores and with two subtests. Estimated GAI are presented for participants diagnosed with dementia (n = 50), traumatic brain injury (n = 20), Huntington's disease (n = 15), Korsakoff's disease (n = 12), chronic alcohol abuse (n = 32), temporal lobectomy (n = 17), and schizophrenia (n = 44). In addition, a small sample of participants without dementia and diagnosed with depression (n = 32) was used as a clinical comparison group. The GAI-E algorithms provided estimates of GAI that closely approximated scores expected for a healthy adult population. The greatest differences between estimated GAI and obtained GAI were observed for the single subtest GAI-E algorithms using the Vocabulary, Information, and Matrix Reasoning subtests. Based on these data, recommendations for the use of the GAI-E algorithms are presented.

New insights into the roles of matrix metalloproteinases in colorectal cancer development and progression.

PubMed

Leeman, Matthew F; Curran, Stephanie; Murray, Graeme I

2003-12-01

This review outlines new concepts that are emerging for the functions of matrix metalloproteinases in colorectal cancer development and progression. The two main concepts that will be discussed are the role of matrix metalloproteinases in the early stages of colorectal tumour development and the functional mechanisms by which matrix metalloproteinases contribute to colorectal tumour invasion and metastasis. The matrix metalloproteinases are a group of enzymes, which have been best characterized for their ability to degrade extracellular matrix proteins and thus they have been extensively studied in tumour invasion. It is now becoming recognized that the matrix metalloproteinases have key roles in a variety of biological processes that are distinct from their well-defined role in matrix degradation. This group of enzymes has been shown to interact with a broad range of non-matrix proteins including growth factors and their receptors, mediators of apoptosis, and cell adhesion molecules. The elucidation of novel biological roles for the matrix metalloproteinases also challenges the current predominant concept of matrix metalloproteinases as enzymes only involved in matrix degradation. Recent studies have shown that several matrix metalloproteinases, especially matrilysin (MMP-7), interact with the specific molecular genetic and signalling pathways involved in colorectal cancer development. In particular, matrilysin is activated at an early stage of colorectal tumourigenesis by the beta-catenin signalling pathway. Furthermore, studies are now elucidating specific mechanisms by which individual matrix metalloproteinases, especially membrane-type matrix metalloproteinases, interact with specific cell adhesion molecules and cytoskeletal proteins and thus contribute dynamically to colorectal tumour invasion. Copyright 2003 John Wiley & Sons, Ltd.

Retest Effects in Matrix Test Performance: Differential Impact of Predictors at Different Hierarchy Levels in an Educational Setting

ERIC Educational Resources Information Center

Freund, Philipp Alexander; Holling, Heinz

2011-01-01

If tests of cognitive ability are repeatedly taken, test scores rise. Such retest effects have been observed for a long time and for a variety of tasks. This study investigates retest effects on figural matrix items in an educational context. A short term effect is assumed for the direct retest administration in the same test session, and a long…

Multispectral Palmprint Recognition Using a Quaternion Matrix

PubMed Central

Xu, Xingpeng; Guo, Zhenhua; Song, Changjiang; Li, Yafeng

2012-01-01

Palmprints have been widely studied for biometric recognition for many years. Traditionally, a white light source is used for illumination. Recently, multispectral imaging has drawn attention because of its high recognition accuracy. Multispectral palmprint systems can provide more discriminant information under different illuminations in a short time, thus they can achieve better recognition accuracy. Previously, multispectral palmprint images were taken as a kind of multi-modal biometrics, and the fusion scheme on the image level or matching score level was used. However, some spectral information will be lost during image level or matching score level fusion. In this study, we propose a new method for multispectral images based on a quaternion model which could fully utilize the multispectral information. Firstly, multispectral palmprint images captured under red, green, blue and near-infrared (NIR) illuminations were represented by a quaternion matrix, then principal component analysis (PCA) and discrete wavelet transform (DWT) were applied respectively on the matrix to extract palmprint features. After that, Euclidean distance was used to measure the dissimilarity between different features. Finally, the sum of two distances and the nearest neighborhood classifier were employed for recognition decision. Experimental results showed that using the quaternion matrix can achieve a higher recognition rate. Given 3000 test samples from 500 palms, the recognition rate can be as high as 98.83%. PMID:22666049

Multispectral palmprint recognition using a quaternion matrix.

PubMed

Xu, Xingpeng; Guo, Zhenhua; Song, Changjiang; Li, Yafeng

2012-01-01

Palmprints have been widely studied for biometric recognition for many years. Traditionally, a white light source is used for illumination. Recently, multispectral imaging has drawn attention because of its high recognition accuracy. Multispectral palmprint systems can provide more discriminant information under different illuminations in a short time, thus they can achieve better recognition accuracy. Previously, multispectral palmprint images were taken as a kind of multi-modal biometrics, and the fusion scheme on the image level or matching score level was used. However, some spectral information will be lost during image level or matching score level fusion. In this study, we propose a new method for multispectral images based on a quaternion model which could fully utilize the multispectral information. Firstly, multispectral palmprint images captured under red, green, blue and near-infrared (NIR) illuminations were represented by a quaternion matrix, then principal component analysis (PCA) and discrete wavelet transform (DWT) were applied respectively on the matrix to extract palmprint features. After that, Euclidean distance was used to measure the dissimilarity between different features. Finally, the sum of two distances and the nearest neighborhood classifier were employed for recognition decision. Experimental results showed that using the quaternion matrix can achieve a higher recognition rate. Given 3000 test samples from 500 palms, the recognition rate can be as high as 98.83%.

Lung tissue remodelling in MCT-induced pulmonary hypertension: a proposal for a novel scoring system and changes in extracellular matrix and fibrosis associated gene expression.

PubMed

Franz, Marcus; Grün, Katja; Betge, Stefan; Rohm, Ilonka; Ndongson-Dongmo, Bernadin; Bauer, Reinhard; Schulze, P Christian; Lichtenauer, Michael; Petersen, Iver; Neri, Dario; Berndt, Alexander; Jung, Christian

2016-12-06

Pulmonary hypertension (PH) is associated with vasoconstriction and remodelling. We studied lung tissue remodelling in a rat model of PH with special focus on histology and extracellular matrix (ECM) remodelling. After induction of PH by monocrotaline, lung tissue was analysed histologically, by gene expression analysis and immunofluorescence labelling of ED-A domain containing fibronectin (ED-A+ Fn), B domain containing tenascin-C (B+ Tn-C) as well as alpha-smooth muscle actin (α-SMA). Serum concentrations of ED-A+ Fn were determined by ELISA. Systolic right ventricular pressure (RVPsys) values were significantly elevated in PH (n = 18; 75 ± 26.4 mmHg) compared to controls (n = 10; 29 ± 19.3 mmHg; p = 0.015). The histological sum-score was significantly increased in PH (8.0 ± 2.2) compared to controls (2.5 ± 1.6; p < 0.001). Gene expression analysis revealed relevant induction of several key genes of extracellular matrix remodelling. Increased protein deposition of ED-A+ Fn but not of B+ Tn-C and α-SMA in lung tissue was found in PH (2.88 ± 3.19 area%) compared to controls (1.32 ± 0.16 area%; p = 0.030). Serum levels of ED-A+ Fn were significantly higher in PH (p = 0.007) positively correlating with RVPsys (r = 0.618, p = 0.019). We here present a novel histological scoring system to assess lung tissue remodelling in PH. Gene expression analysis revealed induction of candidate genes involved in collagen matrix turnover, fibrosis and vascular remodelling. The stable increased tissue deposition of ED-A+ Fn in PH as well as its dynamics in serum suggests a role as a promising novel biomarker and potential therapeutic target.

Exploring Environmental Variation in Residential Care Facilities for Older People.

PubMed

Nordin, Susanna; McKee, Kevin; Wijk, Helle; Elf, Marie

2017-01-01

The aim of this study was to explore variation in environmental quality in Swedish residential care facilities (RCFs) using the Swedish version of the Sheffield Care Environment Assessment Matrix (S-SCEAM). Well-designed physical environments can positively impact on health and well-being among older persons with frail health living in RCFs and are essential for supporting person-centered care. However, the evidence base for informing the design of RCFs is weak, partly due to a lack of valid and reliable instruments that could provide important information on the environmental quality. Twenty RCFs were purposively sampled from several regions, varying in their building design, year of construction, size, and geographic location. The RCFs were assessed using S-SCEAM and the data were analyzed to examine variation in environmental quality between and within facilities. There was substantial variation in the quality of the physical environment between and within RCFs, reflected in S-SCEAM scores related to specific facility locations and with regard to domains reflecting residents' needs. In general, private apartments and dining areas had high S-SCEAM scores, while gardens had lower scores. Scores on the safety domain were high in the majority of RCFs, whereas scores for cognitive support and privacy were relatively low. Despite high building standard requirements, the substantial variations regarding environmental quality between and within RCFs indicate the potential for improvements to support the needs of older persons. We conclude that S-SCEAM is a sensitive and unique instrument representing a valuable contribution to evidence-based design that can support person-centered care.

Muscle Biopsy Findings in Combination With Myositis‐Specific Autoantibodies Aid Prediction of Outcomes in Juvenile Dermatomyositis

PubMed Central

Deakin, Claire T.; Yasin, Shireena A.; Simou, Stefania; Arnold, Katie A.; Tansley, Sarah L.; Betteridge, Zoe E.; McHugh, Neil J.; Varsani, Hemlata; Holton, Janice L.; Jacques, Thomas S.; Pilkington, Clarissa A.; Nistala, Kiran; Armon, Kate; Ellis‐Gage, Joe; Roper, Holly; Briggs, Vanja; Watts, Joanna; McCann, Liza; Roberts, Ian; Baildam, Eileen; Hanna, Louise; Lloyd, Olivia; Wadeson, Susan; Riley, Phil; McGovern, Ann; Ryder, Clive; Scott, Janis; Thomas, Beverley; Southwood, Taunton; Al‐Abadi, Eslam; Wyatt, Sue; Jackson, Gillian; Amin, Tania; Wood, Mark; VanRooyen, Vanessa; Burton, Deborah; Davidson, Joyce; Gardner‐Medwin, Janet; Martin, Neil; Ferguson, Sue; Waxman, Liz; Browne, Michael; Friswell, Mark; Swift, Alison; Jandial, Sharmila; Stevenson, Vicky; Wade, Debbie; Sen, Ethan; Smith, Eve; Qiao, Lisa; Watson, Stuart; Duong, Claire; Venning, Helen; Satyapal, Rangaraj; Stretton, Elizabeth; Jordan, Mary; Mosley, Ellen; Frost, Anna; Crate, Lindsay; Warrier, Kishore; Stafford, Stefanie; Hasson, Nathan; Maillard, Sue; Halkon, Elizabeth; Brown, Virginia; Juggins, Audrey; Smith, Sally; Lunt, Sian; Enayat, Elli; Kassoumeri, Laura; Beard, Laura; Glackin, Yvonne; Almeida, Beverley; Marques, Raquel; Dowle, Stefanie; Papadopoulou, Charis; Murray, Kevin; Ioannou, John; Suffield, Linda; Al‐Obaidi, Muthana; Lee, Helen; Leach, Sam; Smith, Helen; McMahon, Anne‐Marie; Chisem, Heather; Kingshott, Ruth; Wilkinson, Nick; Inness, Emma; Kendall, Eunice; Mayers, David; Etherton, Ruth; Bailey, Kathryn; Clinch, Jacqui; Fineman, Natalie; Pluess‐Hall, Helen; Vallance, Lindsay; Akeroyd, Louise; Leahy, Alice; Collier, Amy; Cutts, Rebecca; De Graaf, Hans; Davidson, Brian; Hartfree, Sarah; Pratt, Danny

2016-01-01

Objective Juvenile dermatomyositis (DM) is a rare and severe autoimmune condition characterized by rash and proximal muscle weakness. While some patients respond to standard treatment, others do not. This study was carried out to investigate whether histopathologic findings and myositis‐specific autoantibodies (MSAs) have prognostic significance in juvenile DM. Methods Muscle biopsy samples (n = 101) from patients in the UK Juvenile Dermatomyositis Cohort and Biomarker Study were stained, analyzed, and scored for severity of histopathologic features. In addition, autoantibodies were measured in the serum or plasma of patients (n = 90) and longitudinal clinical data were collected (median duration of follow‐up 4.9 years). Long‐term treatment status (on or off medication over time) was modeled using generalized estimating equations. Results Muscle biopsy scores differed according to MSA subgroup. When the effects of MSA subgroup were accounted for, increased severity of muscle histopathologic features was predictive of an increased risk of remaining on treatment over time: for the global pathology score (histopathologist's visual analog scale [hVAS] score), 1.48‐fold higher odds (95% confidence interval [95% CI] 1.12–1.96; P = 0.0058), and for the total biopsy score (determined with the standardized score tool), 1.10‐fold higher odds (95% CI 1.01–1.21; P = 0.038). A protective effect was identified in patients with anti–Mi‐2 autoantibodies, in whom the odds of remaining on treatment were 7.06‐fold lower (95% CI 1.41–35.36; P = 0.018) despite muscle biopsy scores indicating more severe disease. In patients with anti–nuclear matrix protein 2 autoantibodies, anti–transcription intermediary factor 1γ autoantibodies, or no detectable autoantibody, increased histopathologic severity alone, without adjustment for the effect of MSA subtype, was predictive of the risk of remaining on treatment: for the hVAS global pathology score, 1.61‐fold higher odds (95% CI 1.16–2.22; P = 0.004), and for the total biopsy score, 1.13‐fold higher odds (95% CI 1.03–1.24; P = 0.013). Conclusion Histopathologic severity, in combination with MSA subtype, is predictive of the risk of remaining on treatment in patients with juvenile DM and may be useful for discussing probable treatment length with parents and patients. Understanding these associations may identify patients at greater risk of severe disease. PMID:27214289

Single-stage cell-based cartilage regeneration using a combination of chondrons and mesenchymal stromal cells: comparison with microfracture.

PubMed

Bekkers, Joris E J; Tsuchida, Anika I; van Rijen, Mattie H P; Vonk, Lucienne A; Dhert, Wouter J A; Creemers, Laura B; Saris, Daniel B F

2013-09-01

Autologous chondrocyte implantation (ACI) is traditionally a 2-step procedure used to repair focal articular cartilage lesions. With use of a combination of chondrons (chondrocytes in their own territorial matrix) and mesenchymal stromal cells (MSCs), ACI could be innovated and performed in a single step, as sufficient cells would be available to fill the defect within a 1-step surgical procedure. Chondrons have been shown to have higher regenerative capacities than chondrocytes without such a pericellular matrix. To evaluate cartilage formation by a combination of chondrons and MSCs in vitro and in both small and large animal models. Controlled laboratory study. Chondrons and MSCs were cultured at different ratios in vitro containing 0%, 5%, 10%, 20%, 50%, or 100% chondrons (n = 3); embedded in injectable fibrin glue (Beriplast); and implanted subcutaneously in nude mice (n = 10; ratios of 0%, 5%, 10%, and 20% chondrons). Also, in a 1-step procedure, a combination of chondrons and MSCs was implanted in a freshly created focal articular cartilage lesion (10% chondrons) in goats (n = 8) and compared with microfracture. The effect of both treatments, after 6-month follow-up, was evaluated using biochemical glycosaminoglycan (GAG) and GAG/DNA analysis and scored using validated scoring systems for macroscopic and microscopic defect repairs. The addition of MSCs to chondron cultures enhanced cartilage-specific matrix production as reflected by a higher GAG production (P < .03), both in absolute levels and normalized to DNA content, compared with chondrocyte and 100% chondron cultures. Similar results were observed after 4 weeks of subcutaneous implantation in nude mice. Treatment of freshly created cartilage defects in goats using a combination of chondrons and MSCs in Beriplast resulted in better microscopic, macroscopic, and biochemical cartilage regeneration (P ≤ .02) compared with microfracture treatment. The combination of chondrons and MSCs increased cartilage matrix formation, and this combination of cells was safely applied in a goat model for focal cartilage lesions, outperforming microfracture. This study describes the bench-to-preclinical development of a new cell-based regenerative treatment for focal articular cartilage defects that outperforms microfracture in goats. In addition, it is a single-step procedure, thereby making the expensive cell expansion and reimplantation of dedifferentiated cells, as in ACI, redundant.

Language of administration and neuropsychological test performance in neurologically intact Hispanic American bilingual adults.

PubMed

Gasquoine, Philip Gerard; Croyle, Kristin L; Cavazos-Gonzalez, Cynthia; Sandoval, Omar

2007-11-01

This study compared the performance of Hispanic American bilingual adults on Spanish and English language versions of a neuropsychological test battery. Language achievement test scores were used to divide 36 bilingual, neurologically intact, Hispanic Americans from south Texas into Spanish-dominant, balanced, and English-dominant bilingual groups. They were administered the eight subtests of the Bateria Neuropsicologica and the Matrix Reasoning subtest of the WAIS-III in Spanish and English. Half the participants were tested in Spanish first. Balanced bilinguals showed no significant differences in test scores between Spanish and English language administrations. Spanish and/or English dominant bilinguals showed significant effects of language of administration on tests with higher language compared to visual perceptual weighting (Woodcock-Munoz Language Survey-Revised, Letter Fluency, Story Memory, and Stroop Color and Word Test). Scores on tests with higher visual-perceptual weighting (Matrix Reasoning, Figure Memory, Wisconsin Card Sorting Test, and Spatial Span), were not significantly affected by language of administration, nor were scores on the Spanish/California Verbal Learning Test, and Digit Span. A problem was encountered in comparing false positive rates in each language, as Spanish norms fell below English norms, resulting in a much higher false positive rate in English across all bilingual groupings. Use of a comparison standard (picture vocabulary score) reduced false positive rates in both languages, but the higher false positive rate in English persisted.

How to Get Really Smart: Modeling Retest and Training Effects in Ability Testing using Computer-Generated Figural Matrix Items

ERIC Educational Resources Information Center

Freund, Philipp Alexander; Holling, Heinz

2011-01-01

The interpretation of retest scores is problematic because they are potentially affected by measurement and predictive bias, which impact construct validity, and because their size differs as a function of various factors. This paper investigates the construct stability of scores on a figural matrices test and models retest effects at the level of…

A Technical Description of the Procedures Used in Calculating School-Level Scaled Scores for the "Survey of Basic Skills: Grade 6."

ERIC Educational Resources Information Center

Mislevy, Robert J.; Bock, R. Darrell

New legislation in 1972 shifted the emphasis of the California Assessment Program (CAP) from traditional every pupil achievement testing to a more efficient multiple-matrix testing design, under which a broad spectrum of skills could be surveyed without undue expenditure of educational resources. Scale score reporting was introduced to the grade 6…

Physiological Ranges of Matrix Rigidity Modulate Primary Mouse Hepatocyte Function In Part Through Hepatocyte Nuclear Factor 4 Alpha

PubMed Central

Desai, Seema S.; Tung, Jason C.; Zhou, Vivian X.; Grenert, James P.; Malato, Yann; Rezvani, Milad; Español-Suñer, Regina; Willenbring, Holger; Weaver, Valerie M.; Chang, Tammy T.

2016-01-01

Matrix rigidity has important effects on cell behavior and is increased during liver fibrosis; however, its effect on primary hepatocyte function is unknown. We hypothesized that increased matrix rigidity in fibrotic livers would activate mechanotransduction in hepatocytes and lead to inhibition of hepatic-specific functions. To determine the physiologically relevant ranges of matrix stiffness at the cellular level, we performed detailed atomic force microscopy analysis across liver lobules from normal and fibrotic livers. We determined that normal liver matrix stiffness was around 150Pa and increased to 1–6kPa in areas near fibrillar collagen deposition in fibrotic livers. In vitro culture of primary hepatocytes on collagen matrix of tunable rigidity demonstrated that fibrotic levels of matrix stiffness had profound effects on cytoskeletal tension and significantly inhibited hepatocyte-specific functions. Normal liver stiffness maintained functional gene regulation by hepatocyte nuclear factor 4 alpha (HNF4α) whereas fibrotic matrix stiffness inhibited the HNF4α transcriptional network. Fibrotic levels of matrix stiffness activated mechanotransduction in primary hepatocytes through focal adhesion kinase (FAK). In addition, blockade of the Rho/Rho-associated protein kinase (ROCK) pathway rescued HNF4α expression from hepatocytes cultured on stiff matrix. Conclusion Fibrotic levels of matrix stiffness significantly inhibit hepatocyte-specific functions in part by inhibiting the HNF4α transcriptional network mediated through the Rho/ROCK pathway. Increased appreciation of the role of matrix rigidity in modulating hepatocyte function will advance our understanding of the mechanisms of hepatocyte dysfunction in liver cirrhosis and spur development of novel treatments for chronic liver disease. PMID:26755329

Does a regular Wessex Head Injury Matrix assessment identify early signs of infections in people with Prolonged Disorders of Consciousness?

PubMed

Dhamapurkar, Samira Kashinath; Wilson, Barbara A; Rose, Anita; Florschutz, Gerhard; Watson, Peter; Shiel, Agnes

2018-06-12

Patients with brain injury are at high risk for infections. Although infection and cognitive deterioration are established for people with dementia, this has not been shown for patients with a prolonged disorder of consciousness (PDOC). This study determines whether regular Wessex Head Injury Matrix (WHIM) assessments can identify early signs of infections in patients with PDOC. Retrospective and prospective approaches were used to assess the WHIM scores of patients with a PDOC (N = 21 in the retrospective study and 22 in the prospective study). The WHIM total scores decreased due to infections in 17 of the 21 cases of infection (p < 0.001) in the retrospective study and 15 (p = 0.001) of the 22 prospective cases of infection. Patients in a minimally conscious state (MCS) showed a bigger proportion of change between their baseline score and the scores taken in the pre-infection stage in both the retrospective and prospective studies when compared to patients in a vegetative state (VS). The findings suggest the importance of serial WHIM assessments throughout the period of recovery, not only to measure cognitive changes but also to highlight underlying physical changes such as infections that will impact the response to rehabilitation and recovery.

Metal- and intermetallic-matrix composites for aerospace propulsion and power systems

NASA Astrophysics Data System (ADS)

Doychak, J.

1992-06-01

Successful development and deployment of metal-matrix composites and intermetallic- matrix composites are critical to reaching the goals of many advanced aerospace propulsion and power development programs. The material requirements are based on the aerospace propulsion and power system requirements, economics, and other factors. Advanced military and civilian aircraft engines will require higher specific strength materials that operate at higher temperatures, and the civilian engines will also require long lifetimes. The specific space propulsion and power applications require hightemperature, high-thermal-conductivity, and high-strength materials. Metal-matrix composites and intermetallic-matrix composites either fulfill or have the potential of fulfilling these requirements.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry for direct bacterial identification from positive blood culture pellets.

PubMed

Prod'hom, Guy; Bizzini, Alain; Durussel, Christian; Bille, Jacques; Greub, Gilbert

2010-04-01

An ammonium chloride erythrocyte-lysing procedure was used to prepare a bacterial pellet from positive blood cultures for direct matrix-assisted laser desorption-ionization time of flight (MALDI-TOF) mass spectrometry analysis. Identification was obtained for 78.7% of the pellets tested. Moreover, 99% of the MALDI-TOF identifications were congruent at the species level when considering valid scores. This fast and accurate method is promising.

Comparison of a New Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Platform, ASTA MicroIDSys, With Bruker Biotyper for Species Identification.

PubMed

Lee, Yangsoon; Sung, Ji Yeon; Kim, Hyunsoo; Yong, Dongeun; Lee, Kyungwon

2017-11-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, with its accuracy and speed, is widely used for bacterial identification. The ASTA MicroIDSys system (ASTA, Korea) was recently developed for species identification. We compared its performance with that of Bruker Biotyper (Bruker Daltonics, Germany). Microbes were recovered from sputum, urine, and pus samples from patients admitted to a tertiary care hospital in Korea from January to April 2016. Matrix solution (α-cyano-4-hydroxycinnamic acid) was used, and the peptide profiles acquired from the Microflex LT (Bruker Daltonics) and Tinkerbell LT (ASTA) were analyzed by using their respective software. From 5,322 isolates, Bruker Biotyper identified 163 species; fifty species from 4,919 isolates were identified more than 10 times, including Klebsiella pneumoniae (n=571), Acinetobacter baumannii (n=436), Pseudomonas aeruginosa (n=358), Escherichia coli (n=372), Staphylococcus aureus (n=511), S. epidermidis (n=444), Enterococcus faecium (n=262), E. faecalis (n=220), and Candida albicans (n=248). Identical results, confidence scores (≥ 2.0 for Bruker Biotyper), and acceptable scores (≥140 for ASTA MicroIDSys) were obtained for 86.1% of isolates. Of 4,267 isolates, 99.2% showed acceptable scores in both systems. Results from the ASTA MicroIDSys showed good agreement with those from the Bruker Biotyper. The ASTA MicroIDSys could reliably identify clinically important microorganisms. © The Korean Society for Laboratory Medicine.

Quality of information about success rates provided on assisted reproductive technology clinic websites in Australia and New Zealand.

PubMed

Hammarberg, Karin; Prentice, Tess; Purcell, Isabelle; Johnson, Louise

2018-06-01

Many factors influence the chance of having a baby with assisted reproductive technologies (ART). A 2016 Australian Competition and Consumer Commission (ACCC) investigation concluded that ART clinics needed to improve the quality of information they provide about chance of ART success. To evaluate changes in the quality of information about success rates provided on the websites of ART clinics in Australia and New Zealand before and after the ACCC investigation. Desktop audits of websites of ART clinics in Australia and New Zealand were conducted in 2016 and 2017 and available information about success rates was scored using a matrix with eight variables and a possible range of scores of 0-9. Of the 54 clinic websites identified in 2016, 32 had unique information and were eligible to be audited. Of these, 29 were also eligible to be audited in 2017. While there was a slight improvement in the mean score from 2016 to 2017 (4.93-5.28), this was not statistically significantly different. Of the 29 clinics, 14 had the same score on both occasions, 10 had a higher and five a lower information quality score in 2017. To allow people who consider ART to make informed decisions about treatment they need comprehensive and accurate information about what treatment entails and what the likely outcomes are. As measured by a scoring matrix, most ART clinics had not improved the quality of the information about success rates following the ACCC investigation. © 2017 The Royal Australian and New Zealand College of Obstetricians and Gynaecologists.

Infrared fiber optic probe evaluation of degenerative cartilage correlates to histological grading.

PubMed

Hanifi, Arash; Bi, Xiaohong; Yang, Xu; Kavukcuoglu, Beril; Lin, Ping Chang; DiCarlo, Edward; Spencer, Richard G; Bostrom, Mathias P G; Pleshko, Nancy

2012-12-01

Osteoarthritis (OA), a degenerative cartilage disease, results in alterations of the chemical and structural properties of tissue. Arthroscopic evaluation of full-depth tissue composition is limited and would require tissue harvesting, which is inappropriate in daily routine. Fourier transform infrared (FT-IR) spectroscopy is a modality based on molecular vibrations of matrix components that can be used in conjunction with fiber optics to acquire quantitative compositional data from the cartilage matrix. To develop a model based on infrared spectra of articular cartilage to predict the histological Mankin score as an indicator of tissue quality. Comparative laboratory study. Infrared fiber optic probe (IFOP) spectra were collected from nearly normal and more degraded regions of tibial plateau articular cartilage harvested during knee arthroplasty (N = 61). Each region was graded using a modified Mankin score. A multivariate partial least squares algorithm using second-derivative spectra was developed to predict the histological modified Mankin score. The partial least squares model derived from IFOP spectra predicted the modified Mankin score with a prediction error of approximately 1.4, which resulted in approximately 72% of the Mankin-scored tissues being predicted correctly and 96% being predicted within 1 grade of their true score. These data demonstrate that IFOP spectral parameters correlate with histological tissue grade and can be used to provide information on tissue composition. Infrared fiber optic probe studies have significant potential for the evaluation of cartilage tissue quality without the need for tissue harvest. Combined with arthroscopy, IFOP analysis could facilitate the definition of tissue margins in debridement procedures.

Practical, transparent prospective risk analysis for the clinical laboratory.

PubMed

Janssens, Pim Mw

2014-11-01

Prospective risk analysis (PRA) is an essential element in quality assurance for clinical laboratories. Practical approaches to conducting PRA in laboratories, however, are scarce. On the basis of the classical Failure Mode and Effect Analysis method, an approach to PRA was developed for application to key laboratory processes. First, the separate, major steps of the process under investigation are identified. Scores are then given for the Probability (P) and Consequence (C) of predefined types of failures and the chances of Detecting (D) these failures. Based on the P and C scores (on a 10-point scale), an overall Risk score (R) is calculated. The scores for each process were recorded in a matrix table. Based on predetermined criteria for R and D, it was determined whether a more detailed analysis was required for potential failures and, ultimately, where risk-reducing measures were necessary, if any. As an illustration, this paper presents the results of the application of PRA to our pre-analytical and analytical activities. The highest R scores were obtained in the stat processes, the most common failure type in the collective process steps was 'delayed processing or analysis', the failure type with the highest mean R score was 'inappropriate analysis' and the failure type most frequently rated as suboptimal was 'identification error'. The PRA designed is a useful semi-objective tool to identify process steps with potential failures rated as risky. Its systematic design and convenient output in matrix tables makes it easy to perform, practical and transparent. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Development and modification of a single overhead camshaft 4-valve 4-stroke 135 cc formula varsity race car engine

NASA Astrophysics Data System (ADS)

Abdullah, M. A.; Tamaldin, N.; Rusnandi, H.; Manoharan, T.; Samsir, M. A.

2013-12-01

The engine that was chosen to be developed and modified is Yamaha LC 135 Single Overhead Camshaft (SOHC) 4-valve 4-stroke 135cc liquid-cooled engine. The engine selection is based on the specification, rule and regulation in UTeM Formula Varsity 2012 (FV 2012). The engine performance is determined by engine operating characteristics. The engine air flow affects the filtration, intake and exhaust systems. The heat from the engine rejected to the surrounding through the active cooling system which has radiator and fan. The selection of the engine is based on weighted decision matrix which consists of reliability, operating and maintenance cost, fuel consumption and weight. The score of the matrix is formulated based on relative weighted factor among the selections. It been compared between Yamaha LC 135 Single Overhead Camshaft (SOHC) 4-valve 4-stroke 135cc liquid-cooled engine, Honda Wave 125 X Air Cooled, 4 Cycle Engine Overhead Camshaft (OHC) and Suzuki Shogun RR 4 stroke air cooled Single Overhead Camshaft (SOHC). The modification is applied to the engine through the simulation and tuning of Capacitor Discharge Ignition (CDI).

Platelet-rich fibrin matrix in the management of arthroscopic repair of the rotator cuff: a prospective, randomized, double-blinded study.

PubMed

Weber, Stephen C; Kauffman, Jeffrey I; Parise, Carol; Weber, Sophia J; Katz, Stephen D

2013-02-01

Arthroscopic rotator cuff repair has a high rate of patient satisfaction. However, multiple studies have shown significant rates of anatomic failure. Biological augmentation would seem to be a reasonable technique to improve clinical outcomes and healing rates. To represent a prospective, double-blinded, randomized study to assess the use of platelet-rich fibrin matrix (PRFM) in rotator cuff surgery. Randomized controlled trial; level of evidence, 1. Prestudy power analysis demonstrated that a sample size of 30 patients in each group (PRFM vs control) would allow recognition of a 20% difference in perioperative pain scores. Sixty consecutive patients were randomized to either receive a commercially available PRFM product or not. Preoperative and postoperative range of motion (ROM), University of California-Los Angeles (UCLA), and simple shoulder test (SST) scores were recorded. Surgery was performed using an arthroscopic single-row technique. Visual analog scale (VAS) pain scores were obtained upon arrival to the recovery room and 1 hour postoperatively, and narcotic consumption was recorded and converted to standard narcotic equivalents. The SST and ROM measurements were taken at 3, 6, 9, and 12 weeks postoperatively, and final (1 year) American shoulder and elbow surgeons (ASES) shoulder and UCLA shoulder scores were assessed. There were no complications. Randomization created comparable groups except that the PRFM group was younger than the control group (mean ± SD, 59.67 ± 8.16 y vs 64.50 ± 8.59 y, respectively; P < .05). Mean surgery time was longer for the PRFM group than for the control group (83.28 ± 17.13 min vs 73.28 ± 17.18 min, respectively; P < .02). There was no significant difference in VAS scores or narcotic use between groups and no statistically significant differences in recovery of motion, SST, or ASES scores. Mean ASES scores were 82.48 ± 8.77 (PRFM group) and 82.52 ± 12.45 (controls) (F(1,56) = 0.00, P > .98). Mean UCLA shoulder scores were 27.94 ± 4.98 for the PRFM group versus 29.59 ± 1.68 for the controls (P < .046). Structural results correlated with age and size of the tear and did not differ between the groups. Platelet-rich fibrin matrix was not shown to significantly improve perioperative morbidity, clinical outcomes, or structural integrity. While longer term follow-up or different platelet-rich plasma formulations may show differences, early follow-up does not show significant improvement in perioperative morbidity, structural integrity, or clinical outcome.

Attempting to validate the overtriage/undertriage matrix at a Level I trauma center

PubMed Central

Davis, James W.; Dirks, Rachel C.; Sue, Lawrence P.; Kaups, Krista L.

2017-01-01

BACKGROUND The Optimal Resources Document mandates trauma activation based on injury mechanism, physiologic and anatomic criteria and recommends using the overtriage/undertriage matrix (Matrix) to evaluate the appropriateness of trauma team activation. The purpose of this study was to assess the effectiveness of the Matrix method by comparing patients appropriately triaged with those undertriaged. We hypothesized that these two groups are different, and Matrix does not discriminate the needs or outcomes of these different groups of patients. METHODS Trauma registry data, from January 2013 to December 2015, at a Level I trauma center, were reviewed. Overtriage and undertriage rates were calculated by Matrix. Patients with Injury Severity Score (ISS) of 16 or greater were classified by activation level (full, limited, consultation), and triage category by Matrix. Patients in the limited activation and consultation groups were compared with patients with full activation by demographics, injuries, initial vital signs, procedures, delays to procedure, intensive care unit admission, length of stay, and mortality. RESULTS Seven thousand thirty-one patients met activation criteria. Compliance with American College of Surgeons tiered activation criteria was 99%. The Matrix overtriage rate was 45% and undertriage was 24%. Of 2,282 patients with an ISS of 16 or greater, 1,026 were appropriately triaged (full activation), and 1,256 were undertriaged. Undertriaged patients had better Glasgow Coma Scale score, blood pressure, and base deficit than patients with full activation. Intensive care unit admission, hospital stays, and mortality were lower in the undertriaged group. The undertriaged group required fewer operative interventions with fewer delays to procedure. CONCLUSION Despite having an ISS of 16 or greater, patients with limited activations were dissimilar to patients with full activation. Level of activation and triage are not equivalent. The American College of Surgeons Committee on Trauma full and tiered activation criteria are a robust means to have the appropriate personnel present based on the available prehospital information. Evaluation of the process of care, regardless of level of activation, should be used to evaluate trauma center performance. LEVEL OF EVIDENCE Therapeutic and care management, level III. PMID:29189678

Matrix Metalloproteinase-7 Is a Urinary Biomarker and Pathogenic Mediator of Kidney Fibrosis

PubMed Central

Zhou, Dong; Tian, Yuan; Sun, Ling; Zhou, Lili; Xiao, Liangxiang; Tan, Roderick J.; Tian, Jianwei; Fu, Haiyan

2017-01-01

Matrix metalloproteinase-7 (MMP-7), a secreted zinc– and calcium–dependent endopeptidase, is a transcriptional target of canonical Wnt/β-catenin signaling. Because Wnt/β-catenin is activated in diseased kidney, we hypothesized that urinary MMP-7 level may be used as a noninvasive surrogate biomarker for fibrotic lesions. To test this hypothesis, we conducted a cross-sectional study, measuring urinary MMP-7 levels in a cohort of 102 patients with CKD. Compared with normal subjects, patients with various kidney disorders had markedly elevated urinary levels of MMP-7. Furthermore, urinary MMP-7 levels closely correlated with renal fibrosis scores in patients. In mice, knockout of MMP-7 ameliorated the fibrotic lesions and expression of matrix genes induced by obstructive injury. Genetic ablation of MMP-7 also preserved E-cadherin protein expression and substantially reduced the expression of total and dephosphorylated β-catenin and the de novo expression of vimentin and fibroblast-specific protein 1 in renal tubules of obstructed kidneys. In vitro, MMP-7 proteolytically degraded E-cadherin in proximal tubular cells, leading to β-catenin liberation and nuclear translocation and induction of β-catenin target genes by a mechanism independent of Wnt ligands. Finally, pharmacologic inhibition of MMP-7 immediately after obstructive injury reduced renal fibrosis in vivo. These results suggest that MMP-7 not only can serve as a noninvasive biomarker but also is an important pathogenic mediator of kidney fibrosis. PMID:27624489

Spaceflight has compartment- and gene-specific effects on mRNA levels for bone matrix proteins in rat femur

NASA Technical Reports Server (NTRS)

Evans, G. L.; Morey-Holton, E.; Turner, R. T.

1998-01-01

In the present study, we evaluated the possibility that the abnormal bone matrix produced during spaceflight may be associated with reduced expression of bone matrix protein genes. To test this possibility, we investigated the effects of a 14-day spaceflight (SLS-2 experiment) on steady-state mRNA levels for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), osteocalcin, osteonectin, and prepro-alpha(1) subunit of type I collagen in the major bone compartments of rat femur. There were pronounced site-specific differences in the steady-state levels of expression of the mRNAs for the three bone matrix proteins and GAPDH in normal weight-bearing rats, and these relationships were altered after spaceflight. Specifically, spaceflight resulted in decreases in mRNA levels for GAPDH (decreased in proximal metaphysis), osteocalcin (decreased in proximal metaphysis), osteonectin (decreased in proximal and distal metaphysis), and collagen (decreased in proximal and distal metaphysis) compared with ground controls. There were no changes in mRNA levels for matrix proteins or GAPDH in the shaft and distal epiphysis. These results demonstrate that spaceflight leads to site- and gene-specific decreases in mRNA levels for bone matrix proteins. These findings are consistent with the hypothesis that spaceflight-induced decreases in bone formation are caused by concomitant decreases in expression of genes for bone matrix proteins.

Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity.

PubMed

Linnemann, Amelia K; Krawetz, Stephen A

2009-05-01

DNA loop organization by nuclear scaffold/matrix attachment is a key regulator of gene expression that may provide a means to modulate phenotype. We have previously shown that attachment of genes to the NaCl-isolated nuclear matrix correlates with their silencing in HeLa cells. In contrast, expressed genes were associated with the lithium 3,5-diiodosalicylate (LIS)-isolated nuclear scaffold. To define their role in determining phenotype matrix attached regions (MARs) on human chromosomes 14-18 were identified as a function of expression in a primary cell line. The locations of MARs in aortic adventitial fibroblast (AoAF) cells were very stable (r = 0.909) and 96% of genes attached at MARs are silent (P < 0.001). Approximately one-third of the genes uniquely expressed in AoAF cells were associated with the HeLa cell nuclear matrix and silenced. Comparatively, 81% were associated with the AoAF cell nuclear scaffold (P < 0.001) and expressed. This suggests that nuclear scaffold/matrix association mediates a portion of cell type-specific gene expression thereby modulating phenotype. Interestingly, nuclear matrix attachment and thus silencing of specific genes that regulate proliferation and maintain the integrity of the HeLa cell genome suggests that transformation may at least in part be achieved through aberrant nuclear matrix attachment.

Does the Use of Platelet-Rich Plasma at the Time of Surgery Improve Clinical Outcomes in Arthroscopic Rotator Cuff Repair When Compared With Control Cohorts? A Systematic Review of Meta-analyses.

PubMed

Saltzman, Bryan M; Jain, Akshay; Campbell, Kirk A; Mascarenhas, Randy; Romeo, Anthony A; Verma, Nikhil N; Cole, Brian J

2016-05-01

The aims of the study were as follows: (1) to perform a systematic review of meta-analyses evaluating platelet-rich plasma (PRP) use at the time of arthroscopic rotator cuff repair surgery and to determine its effect on retear rates and clinical outcomes; (2) to provide a framework for the analysis and interpretation of the best currently available evidence; and (3) to identify gaps within the literature where suggestions for continued investigational efforts would be valid. Literature searches were performed to identify meta-analyses examining arthroscopic rotator cuff repairs augmented with PRP versus control (no PRP). Clinical data were extracted and meta-analysis quality was assessed using the Quality of Reporting of Meta-analyses and Oxman-Guyatt scales. Seven meta-analyses met inclusion and exclusion criteria. All were considered as being of similar quality with Quality of Reporting of Meta-analyses scores >15 and Oxman scores of 7. A total of 3,193 overlapping patients treated were included with mean follow-up from 12 to 31 months. When compared with control patients, use of PRP at the time of rotator cuff repair did not result in significantly lower overall retear rates or improved clinical outcome scores. The following postoperative functional scores comparing PRP versus control were reported: Constant (no significant difference demonstrated with PRP use in 5 of 6 reporting meta-analyses), University of California - Los Angeles (no difference, 6 of 6), American Shoulder and Elbow Society (no difference, 4 of 4), and Simple Shoulder Test (no difference, 3 of 5). Subgroup analysis performed by 3 meta-analyses showed evidence of improved outcomes with solid PRP matrix versus liquid, small- and/or medium-sized versus large and/or massive tears, PRP application at the tendon-bone interface versus over tendon, and in the setting of double-row versus single-row rotator cuff. The current highest level of evidence suggests that PRP use at the time of arthroscopic rotator cuff repair does not universally improve retear rates or affect clinical outcome scores. However, the effects of PRP use on retear rates trend toward beneficial outcomes if evaluated in the context of the following specific variables: use of a solid PRP matrix; application of PRP at the tendon-bone interface; in double-row repairs; and with small- and/or medium-sized rotator cuff tears. Level III, systematic review of Level II and III studies. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Predictive Value of Matrix Metalloproteinases and Their Inhibitors for Mortality in Septic Patients: A Cohort Study.

PubMed

Serrano-Gomez, Sergio; Burgos-Angulo, Gabriel; Niño-Vargas, Daniela Camila; Niño, María Eugenia; Cárdenas, María Eugenia; Chacón-Valenzuela, Estephania; McCosham, Diana Margarita; Peinado-Acevedo, Juan Sebastián; Lopez, M Marcos; Cunha, Fernando; Pazin-Filho, Antonio; Ilarraza, Ramses; Schulz, Richard; Torres-Dueñas, Diego

2017-01-01

Over 170 biomarkers are being investigated regarding their prognostic and diagnostic accuracy in sepsis in order to find new tools to reduce morbidity and mortality. Matrix metalloproteinases (MMPs) and their inhibitors have been recently studied as promising new prognostic biomarkers in patients with sepsis. This study is aimed at determining the utility of several cutoff points of these biomarkers to predict mortality in patients with sepsis. A multicenter, prospective, analytic cohort study was performed in the metropolitan area of Bucaramanga, Colombia. A total of 289 patients with sepsis and septic shock were included. MMP-9, MMP-2, tissue inhibitor of metalloproteinase 1 (TIMP-1), TIMP-2, TIMP-1/MMP-9 ratio, and TIMP-2/MMP-2 ratio were determined in blood samples. Value ranges were correlated with mortality to estimate sensitivity, specificity, positive predictive value, negative predictive value, and area under the receiving operating characteristic curve. Sensitivity ranged from 33.3% (MMP-9/TIMP-1 ratio) to 60.6% (TIMP-1) and specificity varied from 38.8% (MMP-2/TIMP-2 ratio) to 58.5% (TIMP-1). As for predictive values, positive predictive value range was from 17.5% (MMP-9/TIMP-1 ratio) to 70.4% (MMP-2/TIMP-2 ratio), whereas negative predictive values were between 23.2% (MMP-2/TIMP-2 ratio) and 80.9% (TIMP-1). Finally, area under the curve scores ranged from 0.31 (MMP-9/TIMP-1 ratio) to 0.623 (TIMP-1). Although TIMP-1 showed higher sensitivity, specificity, and negative predictive value, with a representative population sample, we conclude that none of the evaluated biomarkers had significant predictive value for mortality.

Physiological ranges of matrix rigidity modulate primary mouse hepatocyte function in part through hepatocyte nuclear factor 4 alpha.

PubMed

Desai, Seema S; Tung, Jason C; Zhou, Vivian X; Grenert, James P; Malato, Yann; Rezvani, Milad; Español-Suñer, Regina; Willenbring, Holger; Weaver, Valerie M; Chang, Tammy T

2016-07-01

Matrix rigidity has important effects on cell behavior and is increased during liver fibrosis; however, its effect on primary hepatocyte function is unknown. We hypothesized that increased matrix rigidity in fibrotic livers would activate mechanotransduction in hepatocytes and lead to inhibition of liver-specific functions. To determine the physiologically relevant ranges of matrix stiffness at the cellular level, we performed detailed atomic force microscopy analysis across liver lobules from normal and fibrotic livers. We determined that normal liver matrix stiffness was around 150 Pa and increased to 1-6 kPa in areas near fibrillar collagen deposition in fibrotic livers. In vitro culture of primary hepatocytes on collagen matrix of tunable rigidity demonstrated that fibrotic levels of matrix stiffness had profound effects on cytoskeletal tension and significantly inhibited hepatocyte-specific functions. Normal liver stiffness maintained functional gene regulation by hepatocyte nuclear factor 4 alpha (HNF4α), whereas fibrotic matrix stiffness inhibited the HNF4α transcriptional network. Fibrotic levels of matrix stiffness activated mechanotransduction in primary hepatocytes through focal adhesion kinase. In addition, blockade of the Rho/Rho-associated protein kinase pathway rescued HNF4α expression from hepatocytes cultured on stiff matrix. Fibrotic levels of matrix stiffness significantly inhibit hepatocyte-specific functions in part by inhibiting the HNF4α transcriptional network mediated through the Rho/Rho-associated protein kinase pathway. Increased appreciation of the role of matrix rigidity in modulating hepatocyte function will advance our understanding of the mechanisms of hepatocyte dysfunction in liver cirrhosis and spur development of novel treatments for chronic liver disease. (Hepatology 2016;64:261-275). © 2016 by the American Association for the Study of Liver Diseases.

Retroviral gene transfer of an antisense construct against membrane type 1 matrix metalloproteinase reduces the invasiveness of rheumatoid arthritis synovial fibroblasts.

PubMed

Rutkauskaite, Edita; Volkmer, Dagmar; Shigeyama, Yukio; Schedel, Jörg; Pap, Geza; Müller-Ladner, Ulf; Meinecke, Ingmar; Alexander, Dorothea; Gay, Renate E; Drynda, Susanne; Neumann, Wolfram; Michel, Beat A; Aicher, Wilhelm K; Gay, Steffen; Pap, Thomas

2005-07-01

Membrane type 1 matrix metalloproteinase (MT1-MMP) is expressed prominently in rheumatoid arthritis synovial fibroblasts (RASFs), but the specific contribution of MT1-MMP to fibroblast-mediated destruction of articular cartilage is incompletely understood. This study used gene transfer of an antisense expression construct to assess the effects of MT1-MMP inhibition on the invasiveness of RASFs. Retroviral gene transfer of a pLXIN vector-based antisense RNA expression construct (MT1-MMPalphaS) to MT1-MMP was used to stably transduce RASFs. Levels of MT1-MMP RNA and protein were determined by quantitative polymerase chain reaction, Western blotting, and immunocytochemistry in MT1-MMPalphaS-transduced RASFs as well as in control cells, with monitoring for 60 days. The effects of MT1-MMPalphaS on the invasiveness of RASFs were analyzed in the SCID mouse co-implantation model of RA. MT1-MMPalphaS-transduced RASFs produced high levels of antisense RNA that exceeded endogenous levels of MT1-MMP messenger RNA by 15-fold and resulted in a down-regulation of MT1-MMP at the protein level. Inhibition of MT1-MMP production was maintained for 60 days and significantly reduced the invasiveness of RASFs in the SCID mouse model. Whereas prominent invasion into cartilage by non-transduced and mock-transduced RASFs was observed (mean invasion scores 3.0 and 3.1, respectively), MT1-MMPalphaS-transduced cells showed only moderate invasiveness (mean invasion score 1.8; P < 0.05). The data demonstrate that an antisense RNA expression construct against MT1-MMP can be generated and expressed in RASFs for at least 60 days. Inhibition of MT1-MMP significantly reduces the cartilage degradation by RASFs.

Corrected score estimation in the proportional hazards model with misclassified discrete covariates

PubMed Central

Zucker, David M.; Spiegelman, Donna

2013-01-01

SUMMARY We consider Cox proportional hazards regression when the covariate vector includes error-prone discrete covariates along with error-free covariates, which may be discrete or continuous. The misclassification in the discrete error-prone covariates is allowed to be of any specified form. Building on the work of Nakamura and his colleagues, we present a corrected score method for this setting. The method can handle all three major study designs (internal validation design, external validation design, and replicate measures design), both functional and structural error models, and time-dependent covariates satisfying a certain ‘localized error’ condition. We derive the asymptotic properties of the method and indicate how to adjust the covariance matrix of the regression coefficient estimates to account for estimation of the misclassification matrix. We present the results of a finite-sample simulation study under Weibull survival with a single binary covariate having known misclassification rates. The performance of the method described here was similar to that of related methods we have examined in previous works. Specifically, our new estimator performed as well as or, in a few cases, better than the full Weibull maximum likelihood estimator. We also present simulation results for our method for the case where the misclassification probabilities are estimated from an external replicate measures study. Our method generally performed well in these simulations. The new estimator has a broader range of applicability than many other estimators proposed in the literature, including those described in our own earlier work, in that it can handle time-dependent covariates with an arbitrary misclassification structure. We illustrate the method on data from a study of the relationship between dietary calcium intake and distal colon cancer. PMID:18219700

The Hydra regeneration assay reveals ecological risks in running waters: a new proposal to detect environmental teratogenic threats.

PubMed

Traversetti, Lorenzo; Del Grosso, Floriano; Malafoglia, Valentina; Colasanti, Marco; Ceschin, Simona; Larsen, Stefano; Scalici, Massimiliano

2017-03-01

The regenerative ability of Hydra vulgaris was tested as potential biomarker for the development of a new eco-toxicological index. The test is based on the regeneration rate and the aberration frequency of the columna (body and adhesive foot) after separation from head and tentacles by a bistoury. Particularly, 45 columnae were submerged in the rearing solution (that is Hydra medium) to have control, and 285 in potential contaminated waters to have treatments, collected from 19 sites along 10 rivers in central Italy. ANCOVA and chi-square tests were used to compare values from each site to a laboratory control. Subsequently the values on regeneration rate and aberration frequency were inserted in a double entry matrix, where the match of the two entries in the matrix provides the score of the proposed Teratogenic Risk Index (TRI). Each score corresponded to one of the 5 teratogenic risk classes, to which a risk level was associated: from 1 (no risk) to 5 (very high risk). On the whole, 32% of the studied sites were classified as no teratogenic risk while the remaining showed a variable risk level from low to very high. This study proposed for the first time an early warning system to detect the presence of teratogens in running waters, providing a rapid and cost-effective evaluation method. Therefore, TRI may contribute to initiate adequate measures to manage riverine habitats, and to monitor the running water teratogenic status. Specifically, this index may provide the opportunity to identify the disturbance sources and then to drive the decisions, together with competent authorities, on the catchment and landscape management and on the possible use of waters for urban, agricultural, and industrial activities, since they may show significant effects on the human health.

Biomarkers of hepatic fibrosis, fibrogenesis and genetic pre-disposition pending between fiction and reality

PubMed Central

Gressner, OA; Weiskirchen, R; Gressner, AM

2007-01-01

Abstract Fibrosis is a frequent, life-threatening complication of most chronic liver diseases. Despite major achievements in the understanding of its pathogenesis, the translation of this knowledge into clinical practice is still limited. In particular, non-invasive and reliable (serum-) biomarkers indicating the activity of fibrogenesis are scarce. Class I biomarkers are defined as serum components having a direct relation to the mechanism of fibrogenesis, either as secreted matrix-related components of activated hepatic stellate cells and fibroblasts or as mediators of extracellular matrix (ECM) synthesis or turnover. They reflect primarily the activity of the fibrogenic process. Many of them, however, proved to be disappointing with regard to sensitivity and speci-ficity. Up to now hyaluronan turned out to be the relative best type I serum marker. Class II biomarkers comprise in general rather simple standard laboratory tests, which are grouped into panels. They fulfil most criteria for detection and staging of fibrosis and to a lesser extent grading of fibrogenic activity. More than 20 scores are currently available, among which Fibrotest™ is the most popular one. However, the diagnostic use of many of these scores is still limited and standardization of the assays is only partially realized. Combining of panel markers in sequential algorithms might increase their diagnostic validity. The translation of genetic pre-disposition biomarkers into clinical practice has not yet started, but some polymorphisms indicate a link to progression and outcome of fibrogenesis. Parallel to serum markers non-invasive physical techniques, for example, transient elastography, are developed, which can be combined with serum tests and profiling of serum proteins and glycans. PMID:17979881

Textural features of pretreatment 18F-FDG PET/CT images: prognostic significance in patients with advanced T-stage oropharyngeal squamous cell carcinoma.

PubMed

Cheng, Nai-Ming; Fang, Yu-Hua Dean; Chang, Joseph Tung-Chieh; Huang, Chung-Guei; Tsan, Din-Li; Ng, Shu-Hang; Wang, Hung-Ming; Lin, Chien-Yu; Liao, Chun-Ta; Yen, Tzu-Chen

2013-10-01

Previous studies have shown that total lesion glycolysis (TLG) may serve as a prognostic indicator in oropharyngeal squamous cell carcinoma (OPSCC). We sought to investigate whether the textural features of pretreatment (18)F-FDG PET/CT images can provide any additional prognostic information over TLG and clinical staging in patients with advanced T-stage OPSCC. We retrospectively analyzed the pretreatment (18)F-FDG PET/CT images of 70 patients with advanced T-stage OPSCC who had completed concurrent chemoradiotherapy, bioradiotherapy, or radiotherapy with curative intent. All of the patients had data on human papillomavirus (HPV) infection and were followed up for at least 24 mo or until death. A standardized uptake value (SUV) of 2.5 was taken as a cutoff for tumor boundary. The textural features of pretreatment (18)F-FDG PET/CT images were extracted from histogram analysis (SUV variance and SUV entropy), normalized gray-level cooccurrence matrix (uniformity, entropy, dissimilarity, contrast, homogeneity, inverse different moment, and correlation), and neighborhood gray-tone difference matrix (coarseness, contrast, busyness, complexity, and strength). Receiver-operating-characteristic curves were used to identify the optimal cutoff values for the textural features and TLG. Thirteen patients were HPV-positive. Multivariate Cox regression analysis showed that age, tumor TLG, and uniformity were independently associated with progression-free survival (PFS) and disease-specific survival (DSS). TLG, uniformity, and HPV positivity were significantly associated with overall survival (OS). A prognostic scoring system based on TLG and uniformity was derived. Patients who presented with TLG > 121.9 g and uniformity ≤ 0.138 experienced significantly worse PFS, DSS, and OS rates than those without (P < 0.001, < 0.001, and 0.002, respectively). Patients with TLG > 121.9 g or uniformity ≤ 0.138 were further divided according to age, and different PFS and DSS were observed. Uniformity extracted from the normalized gray-level cooccurrence matrix represents an independent prognostic predictor in patients with advanced T-stage OPSCC. A scoring system was developed and may serve as a risk-stratification strategy for guiding therapy.

Identification of Non-diphtheriae Corynebacterium by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Alatoom, Adnan A.; Cazanave, Charles J.; Cunningham, Scott A.; Ihde, Sherry M.

2012-01-01

We evaluated the Bruker Biotyper matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry for identification of 92 clinical isolates of Corynebacterium species in comparison to identification using rpoB or 16S rRNA gene sequencing. Eighty isolates (87%) yielded a score of ≥1.700, and all of these were correctly identified to the species level with the exception of Corynebacterium aurimucosum being misidentified as the closely related Corynebacterium minutissimum. PMID:22075579

A positive correlation between serum levels of mature brain-derived neurotrophic factor and negative symptoms in schizophrenia.

PubMed

Niitsu, Tomihisa; Ishima, Tamaki; Yoshida, Taisuke; Hashimoto, Tasuku; Matsuzawa, Daisuke; Shirayama, Yukihiko; Nakazato, Michiko; Shimizu, Eiji; Hashimoto, Kenji; Iyo, Masaomi

2014-02-28

A meta-analysis study reported serum brain-derived neurotrophic factor (BDNF) levels as a potential biomarker for schizophrenia. However, at the time, commercially available human ELISA kits were unable to distinguish between pro-BDNF (precursor BDNF) and mature BDNF, because of limited antibody specificity. Here, we used new ELISA kits, to examine serum levels of mature BDNF and matrix metalloproteinase-9 (MMP-9), which converts pro-BDNF to mature BDNF in schizophrenia. Sixty-three patients with chronic schizophrenia and 52 age- and sex-matched healthy controls were enrolled. Patients were evaluated using the Brief Psychiatry Rating Scale, the Scale for the Assessment of Negative Symptoms (SANS) and neuropsychological tests. Neither serum mature BDNF nor MMP-9 levels differed between patients and controls. In male subgroups, serum MMP-9 levels of smoking patients were higher than those of non-smoking patients, but this was not observed in male controls or the female subgroup. In patients, serum mature BDNF levels were associated with SANS total scores and the Information subtest scores of the Wechsler Adult Intelligence Scale Revised (WAIS-R), while serum MMP-9 levels were associated with smoking and category fluency scores. These findings suggest that neither mature BDNF nor MMP-9 is a suitable biomarker for schizophrenia, although further studies using large samples are needed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Matrix metalloproteinase-9, -10, and tissue inhibitor of matrix metalloproteinases-1 blood levels as biomarkers of severity and mortality in sepsis.

PubMed

Lorente, Leonardo; Martín, María M; Labarta, Lorenzo; Díaz, César; Solé-Violán, Jordi; Blanquer, José; Orbe, Josune; Rodríguez, José A; Jiménez, Alejandro; Borreguero-León, Juan M; Belmonte, Felipe; Medina, Juan C; Llimiñana, Maria C; Ferrer-Agüero, José M; Ferreres, José; Mora, María L; Lubillo, Santiago; Sánchez, Manuel; Barrios, Ysamar; Sierra, Antonio; Páramo, José A

2009-01-01

Matrix metalloproteinases (MMPs) play a role in infectious diseases through extracellular matrix (ECM) degradation, which favors the migration of immune cells from the bloodstream to sites of inflammation. Although higher levels of MMP-9 and tissue inhibitor of matrix metalloproteinases-1 (TIMP-1) have been found in small series of patients with sepsis, MMP-10 levels have not been studied in this setting. The objective of this study was to determine the predictive value of MMP-9, MMP-10, and TIMP-1 on clinical severity and mortality in a large series of patients with severe sepsis. This was a multicenter, observational, and prospective study carried out in six Spanish Intensive Care Units. We included 192 (125 surviving and 67 nonsurviving) patients with severe sepsis and 50 age- and sex-matched healthy controls in the study. Serum levels of MMP-9, MMP-10, TIMP-1, tumor necrosis factor (TNF)-alpha, and interleukin (IL)-10 were measured in patients with severe sepsis at the time of diagnosis and in healthy controls. Sepsis patients had higher levels of MMP-10 and TIMP-1, higher MMP-10/TIMP-1 ratios, and lower MMP-9/TIMP-1 ratios than did healthy controls (P < 0.001). An association was found between MMP-9, MMP-10, TIMP-1, and MMP-9/TIMP-1 ratios and parameters of sepsis severity, assessed by the SOFA score, the APACHE-II score, lactic acid, platelet count, and markers of coagulopathy. Nonsurviving sepsis patients had lower levels of MMP-9 (P = 0.037), higher levels of TIMP-1 (P < 0.001), lower MMP-9/TIMP-1 ratio (P = 0.003), higher levels of IL-10 (P < 0.001), and lower TNF-alpha/IL-10 ratio than did surviving patients. An association was found between MMP-9, MMP-10, and TIMP-1 levels, and TNF-alpha and IL-10 levels. The risk of death in sepsis patients with TIMP-1 values greater than 531 ng/ml was 80% higher than that in patients with lower values (RR = 1.80; 95% CI = 1.13 to 2.87;P = 0.01; sensitivity = 0.73; specificity = 0.45). The novel findings of our study on patients with severe sepsis (to our knowledge, the largest series reporting data about MMP levels in sepsis) are that reduced MMP-9/TIMP-1 ratios and increased MMP-10 levels may be of great pathophysiologic significance in terms of severity and mortality, and that TIMP-1 levels may represent a biomarker to predict the clinical outcome of patients with sepsis.

Matrix metalloproteinase-9, -10, and tissue inhibitor of matrix metalloproteinases-1 blood levels as biomarkers of severity and mortality in sepsis

PubMed Central

2009-01-01

Introduction Matrix metalloproteinases (MMPs) play a role in infectious diseases through extracellular matrix (ECM) degradation, which favors the migration of immune cells from the bloodstream to sites of inflammation. Although higher levels of MMP-9 and tissue inhibitor of matrix metalloproteinases-1 (TIMP-1) have been found in small series of patients with sepsis, MMP-10 levels have not been studied in this setting. The objective of this study was to determine the predictive value of MMP-9, MMP-10, and TIMP-1 on clinical severity and mortality in a large series of patients with severe sepsis. Methods This was a multicenter, observational, and prospective study carried out in six Spanish Intensive Care Units. We included 192 (125 surviving and 67 nonsurviving) patients with severe sepsis and 50 age- and sex-matched healthy controls in the study. Serum levels of MMP-9, MMP-10, TIMP-1, tumor necrosis factor (TNF)-alpha, and interleukin (IL)-10 were measured in patients with severe sepsis at the time of diagnosis and in healthy controls. Results Sepsis patients had higher levels of MMP-10 and TIMP-1, higher MMP-10/TIMP-1 ratios, and lower MMP-9/TIMP-1 ratios than did healthy controls (P < 0.001). An association was found between MMP-9, MMP-10, TIMP-1, and MMP-9/TIMP-1 ratios and parameters of sepsis severity, assessed by the SOFA score, the APACHE-II score, lactic acid, platelet count, and markers of coagulopathy. Nonsurviving sepsis patients had lower levels of MMP-9 (P = 0.037), higher levels of TIMP-1 (P < 0.001), lower MMP-9/TIMP-1 ratio (P = 0.003), higher levels of IL-10 (P < 0.001), and lower TNF-α/IL-10 ratio than did surviving patients. An association was found between MMP-9, MMP-10, and TIMP-1 levels, and TNF-α and IL-10 levels. The risk of death in sepsis patients with TIMP-1 values greater than 531 ng/ml was 80% higher than that in patients with lower values (RR = 1.80; 95% CI = 1.13 to 2.87;P = 0.01; sensitivity = 0.73; specificity = 0.45). Conclusions The novel findings of our study on patients with severe sepsis (to our knowledge, the largest series reporting data about MMP levels in sepsis) are that reduced MMP-9/TIMP-1 ratios and increased MMP-10 levels may be of great pathophysiologic significance in terms of severity and mortality, and that TIMP-1 levels may represent a biomarker to predict the clinical outcome of patients with sepsis. PMID:19799791

Interposition Dermal Matrix Xenografts: A Successful Alternative to Traditional Treatment of Massive Rotator Cuff Tears.

PubMed

Neumann, Julie A; Zgonis, Miltiadis H; Rickert, Kathleen D; Bradley, Kendall E; Kremen, Thomas J; Boggess, Blake R; Toth, Alison P

2017-05-01

Management of massive rotator cuff tears in shoulders without glenohumeral arthritis remains problematic for surgeons. Repairs of massive rotator cuff tears have failure rates of 20% to 94% at 1 to 2 years postoperatively as demonstrated with arthrography, ultrasound, and magnetic resonance imaging. Additionally, inconsistent outcomes have been reported with debridement alone of massive rotator cuff tears, and limitations have been seen with other current methods of operative intervention, including arthroplasty and tendon transfers. The use of interposition porcine acellular dermal matrix xenograft in patients with massive rotator cuff tears will result in improved subjective outcomes, postoperative pain, function, range of motion, and strength. Case series; Level of evidence, 4. Sixty patients (61 shoulders) were prospectively observed for a mean of 50.3 months (range, 24-63 months) after repair of massive rotator cuff tears with porcine acellular dermal matrix xenograft as an interposition graft. Subjective outcome data were obtained with visual analog scale for pain score (0-10, 0 = no pain) and Modified American Shoulder and Elbow Surgeons (MASES) score. Active range of motion in flexion, external rotation, and internal rotation were recorded. Strength in the supraspinatus and infraspinatus muscles was assessed manually on a 10-point scale and by handheld dynamometer. Ultrasound was used to assess the integrity of the repair during latest follow-up. Mean visual analog scale pain score decreased from 4.0 preoperatively to 1.0 postoperatively ( P < .001). Mean active forward flexion improved from 140.7° to 160.4° ( P < .001), external rotation at 0° of abduction from 55.6° to 70.1° ( P = .001), and internal rotation at 90° of abduction from 52.0° to 76.2° ( P < .001). Supraspinatus manual strength increased from 7.7 to 8.8 ( P < .001) and infraspinatus manual strength from 7.7 to 9.3 ( P < .001). Mean dynamometric strength in forward flexion was 77.7 N in nonoperative shoulders (shoulder that did not undergo surgery) and 67.8 N ( P < .001) in operative shoulders (shoulder that underwent rotator cuff repair with interposition porcine dermal matrix xenograft). Mean dynamometric strength in external rotation was 54.5 N in nonoperative shoulders and 50.1 N in operative shoulders ( P = .04). Average postoperative MASES score was 87.8. Musculoskeletal ultrasound showed that 91.8% (56 of 61) of repairs were fully intact; 3.3% (2 of 61), partially intact; and 4.9% (3 of 61), not intact. Patients who underwent repair of massive rotator cuff tears with interposition porcine acellular dermal matrix graft have good subjective function as assessed by the MASES score. Patients have significant improvement in pain, range of motion, and manual muscle strength. Postoperative ultrasound demonstrated that the repair was completely intact in 91.8% of patients, a vast improvement compared with results previously reported for primary repairs of massive rotator cuff tears.

Design Specification Issues in Time-Series Intervention Models.

ERIC Educational Resources Information Center

Huitema, Bradley E.; McKean, Joseph W.

2000-01-01

Presents examples of egregious errors of interpretation in time-series intervention models and makes recommendations regarding the correct specification of the design matrix. Discusses the profound effects of variants of the slope change variable in the design matrix. (SLD)

Analysis of morphological characteristics and expression levels of extracellular matrix proteins in skin wounds to determine wound age in living subjects in forensic medicine.

PubMed

Fronczek, Judith; Lulf, Ronald; Korkmaz, H Ibrahim; Witte, Birgit I; van de Goot, Franklin R W; Begieneman, Mark P V; Krijnen, Paul A J; Rozendaal, Lawrence; Niessen, Hans W M; Reijnders, Udo J L

2015-01-01

Wound age determination in living subjects is important in routine diagnostics in forensic medicine. Macroscopical description of a wound to determine wound age however is inadequate. The aim of this study was to assess whether it would be feasible to determine wound age via analysis of morphological characteristics and extracellular matrix proteins in skin biopsies of living subjects referred to a forensic outpatient clinic. Skin biopsies (n=101), representing the border area of the wound, were taken from skin injuries of known wound age (range: 4.5h-25 days) in living subjects. All biopsies were analyzed for 3 morphological features (ulceration, parakeratosis and hemorrhage) and 3 extracellular matrix markers (collagen III, collagen IV and α-SMA). For quantification, biopsies were subdivided in 4 different timeframes: 0.2-2 days, 2-4 days, 4-10 days and 10-25 days old wounds. Subsequently, a probability scoring system was developed. For hemorrhage, collagen III, collagen IV and α-SMA expression no relation with wound age was found. Ulceration was only found in wounds of 0.2-2, 2-4 and 4-10 days old, implying that the probability that a wound was more than 10 days old in case of ulceration is equal to 0%. Also parakeratosis was almost exclusively found in wounds of 0.2-2, 2-4 and 4-10 days old, except for one case with a wound age of 15 days old. The probability scoring system of all analyzed markers, as depicted above, however can be used to calculate individual wound age probabilities in biopsies of skin wounds of living subjects. We have developed a probability scoring system, analysing morphological characteristics and extracellular matrix proteins in superficial skin biopsies of wounds in living subjects that can be applied in forensic medicine for wound age determination. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Matrix metalloproteinase-9 and tissue inhibitor of metalloproteinase-1 in hypertension and their relationship to cardiovascular risk and treatment: a substudy of the Anglo-Scandinavian Cardiac Outcomes Trial (ASCOT).

PubMed

Tayebjee, Muzahir H; Nadar, Sunil; Blann, Andrew D; Gareth Beevers, D; MacFadyen, Robert J; Lip, Gregory Y H

2004-09-01

Hypertension results in structural changes to the cardiac and vascular extracellular matrix (ECM). Matrix metalloproteinases (MMP) and their inhibitors (TIMP) may play a central role in the modulation of this matrix. We hypothesized that both MMP-9 and TIMP-1 would be abnormal in hypertension, reflecting alterations in ECM turnover, and that their circulating levels should be linked to cardiovascular (CHD) and stroke (CVA) risk scores using the Framingham equation. Second, we hypothesized that treatment would result in changes in ECM indices. Plasma MMP-9 and TIMP-1 were measured before and after treatment (median 3 years) from 96 patients with uncontrolled hypertension participating in the Anglo-Scandinavian Cardiac Outcomes Trial (ASCOT). Pretreatment values were compared to circulating MMP-9 and TIMP-1 levels in 45 age- and sex-matched healthy controls. Circulating pretreatment MMP-9 and TIMP-1 levels were significantly higher in patients with hypertension than in the normotensive controls (P =.0041 and P =.0166, respectively). Plasma MMP-9 levels decreased, and TIMP-1 levels increased after treatment (P =.035 and P =.005, respectively). Levels of MMP-9 correlated with CHD risk (r = 0.317, P =.007) and HDL cholesterol (r = -0.237, P =.022), but not CVA risk. There were no significant correlations between TIMP-1 and CVA or CHD scores. Increased circulating MMP-9 and TIMP-1 at baseline in patients with hypertension could reflect an increased deposition and retention of type I collagen at the expense of other components of ECM within the cardiac and vascular ECM. After cardiovascular risk management, MMP-9 levels decreased and TIMP-1 levels increased. Elevated levels of MMP-9 also appeared to be associated with higher Framingham cardiovascular risk scores. Our observations suggest a possible role for these surrogate markers of tissue ECM composition and the prognosis of cardiovascular events in hypertension. Copyright 2004 American Journal of Hypertension, Ltd.

SU-F-J-209: Quantification of Image-Guidance Benefit in Image-Guided Radiotherapy of Cancers

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

Zhou, L; Department of Therapeutic Radiology, Yale University, New Haven, CT; Deng, J

Purpose: Image-guidance has been widely used in radiation oncology for accurate radiotherapy. The goal of this study is to quantify the benefit of image-guidance in image-guided radiotherapy (IGRT) of cancers. Methods: In this study, a new index termed image-guidance benefit (IGB), was proposed to quantify the benefit of image-guidance in cancer radiotherapy. It is calculated as a ratio of the square sum of dose differences between planning dose matrix and actual delivery dose matrix post image-guidance to the square sum of dose summation between the two matrixes, summing over all dose scoring voxels. Ranging from 0 to 1, larger IGBmore » values indicate larger benefit out of image-guidance. With IRB approval, the DICOM RT files and 3D couch shifts applied during IGRT of 2219 patients were collected, based on which patient-specific IGB values were calculated with an in-house MATLAB code. Results: In this study, the mean IGB value was found to be 0.0398 (0.000583–0.999) with a positive correlation between IGB value and 3D couch shift vector at 0.0435 per cm (P<0.0001). With 2 mm shift as a threshold above which an image-guidance is deemed clinically necessary, the corresponding mean IGB value was 0.00457, much less than 0.0398 (P<0.001). However, the IGB values of 56 cases based on couch shifts were less than those based on 2 mm shift. Conclusion: The IGB values were patient-specific and site-dependent. Using 2 mm shifts as criterion for applying image-guidance, the applied image-guidance procedures were found clinically necessary and highly beneficial in 97.5% of cancer patients. However, image-guidance procedures were found over-used in about 2.5% of cancer patients in our current practices of IGRT, which should be avoided as they added no benefit in improving delivery accuracy while increasing cancer risk.« less

Development and Validation of a Job Exposure Matrix for Physical Risk Factors in Low Back Pain

PubMed Central

Solovieva, Svetlana; Pehkonen, Irmeli; Kausto, Johanna; Miranda, Helena; Shiri, Rahman; Kauppinen, Timo; Heliövaara, Markku; Burdorf, Alex; Husgafvel-Pursiainen, Kirsti; Viikari-Juntura, Eira

2012-01-01

Objectives The aim was to construct and validate a gender-specific job exposure matrix (JEM) for physical exposures to be used in epidemiological studies of low back pain (LBP). Materials and Methods We utilized two large Finnish population surveys, one to construct the JEM and another to test matrix validity. The exposure axis of the matrix included exposures relevant to LBP (heavy physical work, heavy lifting, awkward trunk posture and whole body vibration) and exposures that increase the biomechanical load on the low back (arm elevation) or those that in combination with other known risk factors could be related to LBP (kneeling or squatting). Job titles with similar work tasks and exposures were grouped. Exposure information was based on face-to-face interviews. Validity of the matrix was explored by comparing the JEM (group-based) binary measures with individual-based measures. The predictive validity of the matrix against LBP was evaluated by comparing the associations of the group-based (JEM) exposures with those of individual-based exposures. Results The matrix includes 348 job titles, representing 81% of all Finnish job titles in the early 2000s. The specificity of the constructed matrix was good, especially in women. The validity measured with kappa-statistic ranged from good to poor, being fair for most exposures. In men, all group-based (JEM) exposures were statistically significantly associated with one-month prevalence of LBP. In women, four out of six group-based exposures showed an association with LBP. Conclusions The gender-specific JEM for physical exposures showed relatively high specificity without compromising sensitivity. The matrix can therefore be considered as a valid instrument for exposure assessment in large-scale epidemiological studies, when more precise but more labour-intensive methods are not feasible. Although the matrix was based on Finnish data we foresee that it could be applicable, with some modifications, in other countries with a similar level of technology. PMID:23152793

Clinical and Radiological Regeneration of Large and Deep Osteochondral Defects of the Knee by Bone Augmentation Combined With Matrix-Guided Autologous Chondrocyte Transplantation.

PubMed

Zellner, Johannes; Grechenig, Stephan; Pfeifer, Christian G; Krutsch, Werner; Koch, Matthias; Welsch, Goetz; Scherl, Madeleine; Seitz, Johannes; Zeman, Florian; Nerlich, Michael; Angele, Peter

2017-11-01

Large osteochondral defects of the knee are a challenge for regenerative treatment. While matrix-guided autologous chondrocyte transplantation (MACT) represents a successful treatment for chondral defects, the treatment potential in combination with bone grafting by cancellous bone or bone block augmentation for large and deep osteochondral defects has not been evaluated. To evaluate 1- to 3-year clinical outcomes and radiological results on magnetic resonance imaging (MRI) after the treatment of large osteochondral defects of the knee with bone augmentation and MACT. Special emphasis is placed on different methods of bone grafting (cancellous bone grafting or bone block augmentation). Case series; Level of evidence, 4. Fifty-one patients were included. Five patients were lost to follow-up. This left 46 patients (mean age, 28.2 years) with a median follow-up time of 2 years. The 46 patients had 47 deep, large osteochondral defects of the knee joint (1 patient with bilateral defects; mean defect size, 6.7 cm 2 ). The origin of the osteochondral defects was osteochondritis dissecans (n = 34), osteonecrosis (n = 8), or subchondral cysts (n = 5). Depending on the depth, all defects were treated by cancellous bone grafting (defect depth ≤10 mm; n = 16) or bone block augmentation (defect depth >10 mm; n = 31) combined with MACT. Clinical outcomes were followed at 3 months, 6 months, 1 year, 2 years, and 3 years and evaluated using the International Knee Documentation Committee (IKDC) score and Cincinnati score. A magnetic resonance imaging (MRI) evaluation was performed at 1 and 2 years, and the magnetic resonance observation of cartilage repair tissue (MOCART) score with additional specific subchondral bone parameters (bone regeneration, bone signal quality, osteophytes, sclerotic areas, and edema) was analyzed. The clinical outcome scores revealed a significant increase at follow-up (6 months to 3 years) compared with the preclinical results. The median IKDC score increased from 42.6 preoperatively to 75.3 at 1 year, 79.7 at 2 years, and 84.3 at 3 years. The median Cincinnati score significantly increased from 39.8 preoperatively to 72.0 at 1 year, 78.0 at 2 years, and 80.3 at 3 years. The MRI evaluation revealed a MOCART score of 82.6 at 1 year without a deterioration at the later follow-up time point. Especially, the subchondral bone analysis showed successful regeneration. All bone blocks and cancellous bone grafts were integrated in the bony defects, and no chondrocyte transplant failure could be detected throughout the follow-up. Large and deep osteochondral defects of the knee joint can be treated successfully with bone augmentation and MACT. The treatment of shallow bony defects with cancellous bone grafting and deep bony defects with bone block augmentation shows promising results.

Biologic resurfacing arthroplasty with acellular human dermal allograft and platelet-rich plasma (PRP) in young patients with glenohumeral arthritis-average of 60 months of at mid-term follow-up.

PubMed

Lo, Eddie Y; Flanagin, Brody A; Burkhead, Wayne Z

2016-07-01

The treatment of young patients with glenohumeral arthritis has been challenging. Alternative treatment options include activity modification, arthroscopic débridement, and arthroplasty. Addressing the glenoid during arthroplasty in this population of patients continues to be a significant challenge. In this study, we evaluated the midterm outcomes of hemiarthroplasty with biologic resurfacing of the glenoid with human dermal matrix allograft. Between 2004 and 2011, 55 patients underwent hemiarthroplasty and biologic resurfacing of the glenoid with human dermal matrix allograft. The average age was 50 ± 9 years. Subjective evaluation was performed with the Western Ontario Osteoarthritis of the Shoulder Index, American Shoulder and Elbow Surgeons score, visual analog scale, and Single Assessment Numeric Evaluation. Patients returned to the clinic for clinical examination and radiographic evaluation. The average follow-up was 60 months. The average postoperative American Shoulder and Elbow Surgeons score was 76 ± 22, and the Western Ontario Osteoarthritis of the Shoulder Index score was 76% ± 22%. The visual analog scale score was 2.4 ± 2.6. The average preoperative Single Assessment Numeric Evaluation score was 33% ± 22%, which significantly improved to 72% ± 22% postoperatively. Eighty-one percent of the patients were satisfied (10/47) or highly satisfied (28/47) with their result. With radiographic evaluation, the average joint space was 1 ± 1 mm preoperatively and 2 ± 1 mm postoperatively. A total of 5 cases (9.1%) were revised to anatomic total shoulder arthroplasty with implantation of a glenoid component. Hemiarthroplasty with biologic resurfacing of the glenoid using human dermal matrix allograft can lead to successful midterm outcomes with satisfactory complication and revision rates. Both patient satisfaction and clinical outcome remain high regardless of radiographic outcome. Copyright © 2016 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Serum Matrix Metalloproteinase-9 and Cognitive Impairment After Acute Ischemic Stroke.

PubMed

Zhong, Chongke; Bu, Xiaoqing; Xu, Tan; Guo, Libing; Wang, Xuemei; Zhang, Jintao; Cui, Yong; Li, Dong; Zhang, Jianhui; Ju, Zhong; Chen, Chung-Shiuan; Chen, Jing; Zhang, Yonghong; He, Jiang

2018-01-06

The impact of serum matrix metalloproteinases-9 (MMP-9) on cognitive impairment after ischemic stroke is unclear. We aimed to investigate the association between serum MMP-9 in the short-term acute phase of ischemic stroke and cognitive impairment at 3 months. Our study was based on a subsample from the CATIS (China Antihypertensive Trial in Acute Ischemic Stroke); a total of 558 patients with serum MMP-9 levels from 7 of 26 participating sites of the trial were included in this analysis. Cognitive impairment severity was categorized as severe, mild, or none (Mini-Mental State Examination score, <23, 23-26, or ≥27, respectively; Montreal Cognitive Assessment score, <20, 20-24, or ≥25, respectively). Cognitive impairment was defined as a score of <27 for Mini-Mental State Examination or <25 for Montreal Cognitive Assessment. According to Mini-Mental State Examination score, 143 participants (25.6%) had mild cognitive impairment and 153 (27.4%) had severe cognitive impairment at 3 months. After adjustment for age, National Institutes of Health stroke score, education, and other covariates, the odds ratio for the highest quartile of serum MMP-9 compared with the lowest quartile was 3.20 (95% confidence interval, 1.87-5.49) for cognitive impairment. Multiple-adjusted spline regression model showed a linear association between MMP-9 levels and cognitive impairment ( P <0.001 for linearity). Sensitivity and subgroup analyses further confirmed these results. Similar significant findings were observed when cognitive impairment was defined by Montreal Cognitive Assessment score. Increased serum MMP-9 levels in the short-term phase of ischemic stroke were associated with 3-month cognitive impairment, independently of established risk factors. © 2018 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity

PubMed Central

Linnemann, Amelia K.; Krawetz, Stephen A.

2009-01-01

DNA loop organization by nuclear scaffold/matrix attachment is a key regulator of gene expression that may provide a means to modulate phenotype. We have previously shown that attachment of genes to the NaCl-isolated nuclear matrix correlates with their silencing in HeLa cells. In contrast, expressed genes were associated with the lithium 3,5-diiodosalicylate (LIS)-isolated nuclear scaffold. To define their role in determining phenotype matrix attached regions (MARs) on human chromosomes 14–18 were identified as a function of expression in a primary cell line. The locations of MARs in aortic adventitial fibroblast (AoAF) cells were very stable (r = 0.909) and 96% of genes attached at MARs are silent (P < 0.001). Approximately one-third of the genes uniquely expressed in AoAF cells were associated with the HeLa cell nuclear matrix and silenced. Comparatively, 81% were associated with the AoAF cell nuclear scaffold (P < 0.001) and expressed. This suggests that nuclear scaffold/matrix association mediates a portion of cell type-specific gene expression thereby modulating phenotype. Interestingly, nuclear matrix attachment and thus silencing of specific genes that regulate proliferation and maintain the integrity of the HeLa cell genome suggests that transformation may at least in part be achieved through aberrant nuclear matrix attachment. PMID:19276204

An extracellular-matrix-specific GEF-GAP interaction regulates Rho GTPase crosstalk for 3D collagen migration.

PubMed

Kutys, Matthew L; Yamada, Kenneth M

2014-09-01

Rho-family GTPases govern distinct types of cell migration on different extracellular matrix proteins in tissue culture or three-dimensional (3D) matrices. We searched for mechanisms selectively regulating 3D cell migration in different matrix environments and discovered a form of Cdc42-RhoA crosstalk governing cell migration through a specific pair of GTPase activator and inhibitor molecules. We first identified βPix, a guanine nucleotide exchange factor (GEF), as a specific regulator of migration in 3D collagen using an affinity-precipitation-based GEF screen. Knockdown of βPix specifically blocks cell migration in fibrillar collagen microenvironments, leading to hyperactive cellular protrusion accompanied by increased collagen matrix contraction. Live FRET imaging and RNAi knockdown linked this βPix knockdown phenotype to loss of polarized Cdc42 but not Rac1 activity, accompanied by enhanced, de-localized RhoA activity. Mechanistically, collagen phospho-regulates βPix, leading to its association with srGAP1, a GTPase-activating protein (GAP), needed to suppress RhoA activity. Our results reveal a matrix-specific pathway controlling migration involving a GEF-GAP interaction of βPix with srGAP1 that is critical for maintaining suppressive crosstalk between Cdc42 and RhoA during 3D collagen migration.

Leukocyte-Reduced Platelet-Rich Plasma Normalizes Matrix Metabolism in Torn Human Rotator Cuff Tendons.

PubMed

Cross, Jessica A; Cole, Brian J; Spatny, Kaylan P; Sundman, Emily; Romeo, Anthony A; Nicholson, Greg P; Wagner, Bettina; Fortier, Lisa A

2015-12-01

The optimal platelet-rich plasma (PRP) for treatment of supraspinatus tendinopathy has not been determined. To evaluate the effect of low- versus high-leukocyte concentrated PRP products on catabolic and anabolic mediators of matrix metabolism in diseased rotator cuff tendons. Controlled laboratory study. Diseased supraspinatus tendons were treated with PRP made by use of 2 commercial systems: Arthrex Autologous Conditioned Plasma Double Syringe System (L(lo) PRP) and Biomet GPS III Mini Platelet Concentrate System (L(hi) PRP). Tendon explants were placed in 6-well plates and cultured in L(lo) PRP, L(hi) PRP, or control media (Dulbecco's Modified Eagle Medium + 10% fetal bovine serum) for 96 hours. Tendons were processed for hematoxylin-eosin histologic results and were scored with the modified Bonar scale. Group 1 tendons were defined as moderate tendinopathy (Bonar score <3); group 2 tendons were assessed as severely affected (Bonar score = 3). Transforming growth factor β-1 (TGFβ-1), interleukin-1β (IL-1β), interleukin-1 receptor antagonist (IL-1Ra), interleukin-6 (IL-6), interleukin-8 (IL-8), and matrix metalloproteinase-9 (MMP-9) concentrations in PRP media were measured by use of enzyme-linked immunosorbent assay after 96 hours of culture with diseased tendon. Tendon messenger RNA expression of collagen type I (COL1A1), collagen type III (COL3A1), cartilage oligomeric matrix protein (COMP), MMP-9, MMP-13, and IL-1β was measured with real-time quantitative polymerase chain reaction. Leukocytes and platelets were significantly more concentrated in L(hi) PRP compared with L(lo) PRP. Increased IL-1β was present in L(hi) PRP after culture with group 1 tendons. IL-6 was increased in L(hi) PRP after culture with group 2 tendons. Both TGFβ-1 and MMP-9 were increased in L(hi) PRP after culture with either tendon group. In L(lo) PRP cultures, IL-1Ra:IL-1β in PRP used as media and COL1A1:COL3A1 gene expression were increased for group 1 tendon cultures. Gene expression of MMP-9 and IL-1β was increased in group 2 tendons cultured in L(lo) PRP. There was no significant difference in the expression of MMP-13 or COMP in either group of tendons cultured in L(lo) PRP or L(hi) PRP. L(lo) PRP promotes normal collagen matrix synthesis and decreases cytokines associated with matrix degradation and inflammation to a greater extent than does L(hi) PRP in moderately degenerative tendons. In severely degenerative tendons, neither PRP preparation enhanced matrix synthesis. L(lo) PRP may promote healing in moderately degenerative rotator cuff tendons. © 2015 The Author(s).

Advanced age does not affect abdominal wall reconstruction outcomes using acellular dermal matrix: A comparative study using propensity score analysis.

PubMed

Giordano, Salvatore; Schaverien, Mark; Garvey, Patrick B; Baumann, Donald P; Liu, Jun; Butler, Charles E

2017-06-01

We hypothesized that elderly patients (≥65 years) experience worse outcomes following abdominal wall reconstruction (AWR) for hernia or oncologic resection. We included all consecutive patients who underwent complex AWR using acellular dermal matrix (ADM) between 2005 and 2015. Propensity score analysis was performed for risk adjustment in multivariable analysis and for one-to-one matching. The primary outcome was hernia recurrence; the secondary outcomes included surgical site occurrence (SSO) and bulging. Mean follow-up for the 511 patients was 31.4 months; 184 (36%) patients were elderly. The elderly and non-elderly groups had similar rates of hernia recurrence (7.6% vs 10.1%, respectively; p = 0.43) and SSO (24.5% vs 23.5%, respectively; p = 0.82). Bulging occurred significantly more often in elderly patients (6.5% vs 2.8%, respectively; p = 0.04). After adjustment through the propensity score, which included 130 pairs, these results persisted. Contrary to our hypothesis, elderly patients did not have worse outcomes in AWR with ADM. Surgeons should not deny elderly patients AWR solely because of their age. Copyright © 2016 Elsevier Inc. All rights reserved.

Treatment of a Focal Articular Cartilage Defect of the Talus with Polymer-Based Autologous Chondrocyte Implantation: A 12-Year Follow-Up Period.

PubMed

Kreuz, Peter Cornelius; Kalkreuth, Richard Horst; Niemeyer, Philipp; Uhl, Markus; Erggelet, Christoph

Autologous chondrocyte implantation (ACI) is a first-line treatment option for large articular cartilage defects. Although well-established for cartilage defects in the knee, studies of the long-term outcomes of matrix-assisted ACI to treat cartilage defects in the ankle are rare. In the present report, we describe for the first time the long-term clinical and radiologic results 12 years after polymer-based matrix-assisted ACI treat a full-thickness talar cartilage defect in a 25-year-old male patient. The clinical outcome was assessed using the visual analog scale and Freiburg ankle score, magnetic resonance imaging evaluation using the Henderson-Kreuz scoring system and T2 mapping. Clinical assessment revealed improved visual analog scale and Freiburg ankle scores. The radiologic analysis and T2 relaxation time values indicated the formation of hyaline-like repair tissue. Polymer-based autologous chondrocytes has been shown to be a safe and clinically effective long-term treatment of articular cartilage defects in the talus. Copyright © 2017 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Investigation into Text Classification With Kernel Based Schemes

DTIC Science & Technology

2010-03-01

Document Matrix TDMs Term-Document Matrices TMG Text to Matrix Generator TN True Negative TP True Positive VSM Vector Space Model xxii THIS PAGE...are represented as a term-document matrix, common evaluation metrics, and the software package Text to Matrix Generator ( TMG ). The classifier...AND METRICS This chapter introduces the indexing capabilities of the Text to Matrix Generator ( TMG ) Toolbox. Specific attention is placed on the

Faecal matrix metalloprotease-9 is a more sensitive marker for diagnosing pouchitis than faecal calprotectin: results from a pilot study.

PubMed

Farkas, Klaudia; Bálint, Anita; Bor, Renáta; Földesi, Imre; Szűcs, Mónika; Nagy, Ferenc; Szepes, Zoltán; Annaházi, Anita; Róka, Richárd; Molnár, Tamás

2015-03-01

Potential non-invasive markers of pouchitis would have a great deal of significance within clinical practice. This study is aimed at assessing the diagnostic accuracy of fecal calprotectin and matrix metalloprotease-9 as potential markers in patients both with and without pouchitis. Stool and blood samples were collected from 33 ileal pouch-anal anastomosis patients before a follow-up pouchoscopy. Biopsy samples were taken for histological purposes. The presence of cuffitis and stenosis was evaluated with an endoscopy. Calprotectin and matrix metalloprotease-9 were quantified with an enzyme-linked immunosorbent assay. Pouchitis was detected in 30.3% of the patients. The levels of fecal calprotectin and matrix metalloprotease-9 increased significantly in patients with pouchitis. The sensitivity and specificity of matrix metalloprotease-9 was higher than that of fecal calprotectin. Only matrix metalloprotease-9 correlated significantly with the severity of pouchitis. Fecal matrix metalloprotease-9 has a high specificity in the diagnosis of pouchitis.

On the Matrix Exponential Function

ERIC Educational Resources Information Center

Hou, Shui-Hung; Hou, Edwin; Pang, Wan-Kai

2006-01-01

A novel and simple formula for computing the matrix exponential function is presented. Specifically, it can be used to derive explicit formulas for the matrix exponential of a general matrix A satisfying p(A) = 0 for a polynomial p(s). It is ready for use in a classroom and suitable for both hand as well as symbolic computation.

Program For Analysis Of Metal-Matrix Composites

NASA Technical Reports Server (NTRS)

Murthy, P. L. N.; Mital, S. K.

1994-01-01

METCAN (METal matrix Composite ANalyzer) is computer program used to simulate computationally nonlinear behavior of high-temperature metal-matrix composite structural components in specific applications, providing comprehensive analyses of thermal and mechanical performances. Written in FORTRAN 77.

Acoustooptic linear algebra processors - Architectures, algorithms, and applications

NASA Technical Reports Server (NTRS)

Casasent, D.

1984-01-01

Architectures, algorithms, and applications for systolic processors are described with attention to the realization of parallel algorithms on various optical systolic array processors. Systolic processors for matrices with special structure and matrices of general structure, and the realization of matrix-vector, matrix-matrix, and triple-matrix products and such architectures are described. Parallel algorithms for direct and indirect solutions to systems of linear algebraic equations and their implementation on optical systolic processors are detailed with attention to the pipelining and flow of data and operations. Parallel algorithms and their optical realization for LU and QR matrix decomposition are specifically detailed. These represent the fundamental operations necessary in the implementation of least squares, eigenvalue, and SVD solutions. Specific applications (e.g., the solution of partial differential equations, adaptive noise cancellation, and optimal control) are described to typify the use of matrix processors in modern advanced signal processing.

Behavioural and Emotional Problems in Children and Educational Outcomes: A Dynamic Panel Data Analysis.

PubMed

Khanam, Rasheda; Nghiem, Son

2018-05-01

This study investigates the effects of behavioural and emotional problems in children on their educational outcomes using data from the Longitudinal Survey of Australian Children (LSAC). We contribute to the extant literature using a dynamic specification to test the hypothesis of knowledge accumulation. Further, we apply the system generalised method of moments (GMM) estimator to minimise biases due to unobserved factors. We find that mental disorders in children has a negative effect on the National Assessment Program-Literacy and Numeracy (NAPLAN) test scores. Among all mental disorders, having emotional problems is found to be the most influential with one standard deviation (SD) increase in emotional problems being associated with 0.05 SD reduction in NAPLAN reading, writing and spelling; 0.04 SD reduction in matrix reasoning and grammar; and 0.03 SD reduction in NAPLAN numeracy.

Extracting physicochemical features to predict protein secondary structure.

PubMed

Huang, Yin-Fu; Chen, Shu-Ying

2013-01-01

We propose a protein secondary structure prediction method based on position-specific scoring matrix (PSSM) profiles and four physicochemical features including conformation parameters, net charges, hydrophobic, and side chain mass. First, the SVM with the optimal window size and the optimal parameters of the kernel function is found. Then, we train the SVM using the PSSM profiles generated from PSI-BLAST and the physicochemical features extracted from the CB513 data set. Finally, we use the filter to refine the predicted results from the trained SVM. For all the performance measures of our method, Q 3 reaches 79.52, SOV94 reaches 86.10, and SOV99 reaches 74.60; all the measures are higher than those of the SVMpsi method and the SVMfreq method. This validates that considering these physicochemical features in predicting protein secondary structure would exhibit better performances.

Extracting Physicochemical Features to Predict Protein Secondary Structure

PubMed Central

Chen, Shu-Ying

2013-01-01

We propose a protein secondary structure prediction method based on position-specific scoring matrix (PSSM) profiles and four physicochemical features including conformation parameters, net charges, hydrophobic, and side chain mass. First, the SVM with the optimal window size and the optimal parameters of the kernel function is found. Then, we train the SVM using the PSSM profiles generated from PSI-BLAST and the physicochemical features extracted from the CB513 data set. Finally, we use the filter to refine the predicted results from the trained SVM. For all the performance measures of our method, Q 3 reaches 79.52, SOV94 reaches 86.10, and SOV99 reaches 74.60; all the measures are higher than those of the SVMpsi method and the SVMfreq method. This validates that considering these physicochemical features in predicting protein secondary structure would exhibit better performances. PMID:23766688

Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix

PubMed Central

2010-01-01

Background The sea urchin embryo has been an important model organism in developmental biology for more than a century. This is due to its relatively simple construction, translucent appearance, and the possibility to follow the fate of individual cells as development to the pluteus larva proceeds. Because the larvae contain tiny calcitic skeletal elements, the spicules, they are also important model organisms for biomineralization research. Similar to other biominerals the spicule contains an organic matrix, which is thought to play an important role in its formation. However, only few spicule matrix proteins were identified previously. Results Using mass spectrometry-based methods we have identified 231 proteins in the matrix of the S. purpuratus spicule matrix. Approximately two thirds of the identified proteins are either known or predicted to be extracellular proteins or transmembrane proteins with large ectodomains. The ectodomains may have been solubilized by partial proteolysis and subsequently integrated into the growing spicule. The most abundant protein of the spicule matrix is SM50. SM50-related proteins, SM30-related proteins, MSP130 and related proteins, matrix metalloproteases and carbonic anhydrase are among the most abundant components. Conclusions The spicule matrix is a relatively complex mixture of proteins not only containing matrix-specific proteins with a function in matrix assembly or mineralization, but also: 1) proteins possibly important for the formation of the continuous membrane delineating the mineralization space; 2) proteins for secretory processes delivering proteinaceous or non-proteinaceous precursors; 3) or proteins reflecting signaling events at the cell/matrix interface. Comparison of the proteomes of different skeletal matrices allows prediction of proteins of general importance for mineralization in sea urchins, such as SM50, SM30-E, SM29 or MSP130. The comparisons also help point out putative tissue-specific proteins, such as tooth phosphodontin or specific spicule matrix metalloproteases of the MMP18/19 group. Furthermore, the direct sequence analysis of peptides by MS/MS validates many predicted genes and confirms the existence of the corresponding proteins. PMID:20565753

A Feature-Based Approach to Modeling Protein–DNA Interactions

PubMed Central

Segal, Eran

2008-01-01

Transcription factor (TF) binding to its DNA target site is a fundamental regulatory interaction. The most common model used to represent TF binding specificities is a position specific scoring matrix (PSSM), which assumes independence between binding positions. However, in many cases, this simplifying assumption does not hold. Here, we present feature motif models (FMMs), a novel probabilistic method for modeling TF–DNA interactions, based on log-linear models. Our approach uses sequence features to represent TF binding specificities, where each feature may span multiple positions. We develop the mathematical formulation of our model and devise an algorithm for learning its structural features from binding site data. We also developed a discriminative motif finder, which discovers de novo FMMs that are enriched in target sets of sequences compared to background sets. We evaluate our approach on synthetic data and on the widely used TF chromatin immunoprecipitation (ChIP) dataset of Harbison et al. We then apply our algorithm to high-throughput TF ChIP data from mouse and human, reveal sequence features that are present in the binding specificities of mouse and human TFs, and show that FMMs explain TF binding significantly better than PSSMs. Our FMM learning and motif finder software are available at http://genie.weizmann.ac.il/. PMID:18725950

Teacher Ratings from Incomplete Student Ranking Data.

ERIC Educational Resources Information Center

Kaiser, Henry F.; Cerny, Barbara A.

1979-01-01

A method for obtaining teacher ratings from incomplete student ranking data is presented. The procedure involves finding the scores for the teachers on the first principal component of a student intercorrelation matrix, where the missing data are supplied by least squares. (Author)

Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast.

PubMed

Dhiman, Neelam; Hall, Leslie; Wohlfiel, Sherri L; Buckwalter, Seanne P; Wengenack, Nancy L

2011-04-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was compared to phenotypic testing for yeast identification. MALDI-TOF mass spectrometry yielded 96.3% and 84.5% accurate species level identifications (spectral scores, ≥ 1.8) for 138 common and 103 archived strains of yeast. MALDI-TOF mass spectrometry is accurate, rapid (5.1 min of hands-on time/identification), and cost-effective ($0.50/sample) for yeast identification in the clinical laboratory.

COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming.

PubMed

Zhang, Huiling; Huang, Qingsheng; Bei, Zhendong; Wei, Yanjie; Floudas, Christodoulos A

2016-03-01

In this article, we present COMSAT, a hybrid framework for residue contact prediction of transmembrane (TM) proteins, integrating a support vector machine (SVM) method and a mixed integer linear programming (MILP) method. COMSAT consists of two modules: COMSAT_SVM which is trained mainly on position-specific scoring matrix features, and COMSAT_MILP which is an ab initio method based on optimization models. Contacts predicted by the SVM model are ranked by SVM confidence scores, and a threshold is trained to improve the reliability of the predicted contacts. For TM proteins with no contacts above the threshold, COMSAT_MILP is used. The proposed hybrid contact prediction scheme was tested on two independent TM protein sets based on the contact definition of 14 Å between Cα-Cα atoms. First, using a rigorous leave-one-protein-out cross validation on the training set of 90 TM proteins, an accuracy of 66.8%, a coverage of 12.3%, a specificity of 99.3% and a Matthews' correlation coefficient (MCC) of 0.184 were obtained for residue pairs that are at least six amino acids apart. Second, when tested on a test set of 87 TM proteins, the proposed method showed a prediction accuracy of 64.5%, a coverage of 5.3%, a specificity of 99.4% and a MCC of 0.106. COMSAT shows satisfactory results when compared with 12 other state-of-the-art predictors, and is more robust in terms of prediction accuracy as the length and complexity of TM protein increase. COMSAT is freely accessible at http://hpcc.siat.ac.cn/COMSAT/. © 2016 Wiley Periodicals, Inc.

Grafton and local bone have comparable outcomes to iliac crest bone in instrumented single-level lumbar fusions.

PubMed

Kang, James; An, Howard; Hilibrand, Alan; Yoon, S Tim; Kavanagh, Eoin; Boden, Scott

2012-05-20

Prospective multicenter randomized clinical trail. The goal of our 2-year prospective study was to perform a randomized clinical trial comparing the outcomes of Grafton demineralized bone matrix (DBM) Matrix with local bone with that of iliac crest bone graft (ICBG) in a single-level instrumented posterior lumbar fusion. There has been extensive research and development in identifying a suitable substitute to replace autologous ICBG that is associated with known morbidities. DBMs are a class of commercially available grafting agents that are prepared from allograft bone. Many such products have been commercially available for clinical use; however, their efficacy for spine fusion has been mostly based on anecdotal evidence rather than randomized controlled clinical trials. Forty-six patients were randomly assigned (2:1) to receive Grafton DBM Matrix with local bone (30 patients) or autologous ICBG (16 patients). The mean age was 64 (females [F] = 21, males [M] = 9) in the DBM group and 65 (F = 9, M = 5) in the ICBG group. An independent radiologist evaluated plain radiographs and computed tomographic scans at 6-month, 1-year, and 2-year time points. Clinical outcomes were measured using Oswestry Disability Index (ODI) and Medical Outcomes Study 36-Item Short Form Health Survey. Forty-one patients (DBM = 28 and ICBG = 13) completed the 2-year follow-up. Final fusion rates were 86% (Grafton Matrix) versus 92% (ICBG) (P = 1.0 not significant). The Grafton group showed slightly better improvement in ODI score than the ICBG group at the final 2-year follow-up (Grafton [16.2] and ICBG [22.7]); however, the difference was not statistically significant (P = 0.2346 at 24 mo). Grafton showed consistently higher physical function scores at 24 months; however, differences were not statistically significant (P = 0.0823). Similar improvements in the physical component summary scores were seen in both the Grafton and ICBG groups. There was a statistically significant greater mean intraoperative blood loss in the ICBG group than in the Grafton group (P < 0.0031). At 2-year follow-up, subjects who were randomized to Grafton Matrix and local bone achieved an 86% overall fusion rate and improvements in clinical outcomes that were comparable with those in the ICBG group.

The diagnostic performance of the Mass Restricted (MR) score in the identification of microbial invasion of the amniotic cavity or intra-amniotic inflammation is not superior to amniotic fluid interleukin-6

PubMed Central

Romero, Roberto; Kadar, Nicholas; Miranda, Jezid; Korzeniewski, Steven J.; Schwartz, Alyse G.; Chaemsaithong, Piya; Rogers, Wade; Soto, Eleazar; Gotsch, Francesca; Yeo, Lami; Hassan, Sonia S.; Chaiworapongsa, Tinnakorn

2018-01-01

Objective Intra-amniotic infection/inflammation are major causes of spontaneous preterm labor and delivery. However, diagnosis of intra-amniotic infection is challenging because most are subclinical and amniotic fluid (AF) cultures take several days before results are available. Several tests have been proposed for the rapid diagnosis of microbial invasion of the amniotic cavity (MIAC) or intra-amniotic inflammation. The aim of this study was to examine the diagnostic performance of the AF Mass Restricted (MR) score in comparison with interleukin-6 (IL-6) and matrix metalloproteinase-8 (MMP-8) for the identification of MIAC or inflammation. Methods AF samples were collected from patients with singleton gestations and symptoms of preterm labor (n = 100). Intra-amniotic inflammation was defined as >100 white blood cells/mm3 (WBCs) in AF; MIAC was defined as a positive AF culture. AF IL-6 and MMP-8 were determined using ELISA. The MR score was obtained using the Surface-Enhanced Laser Desorption Ionization Time of Flight (SELDI-TOF) mass spectrometry. Sensitivity and specificity were calculated and logistic regression models were fit to construct receiver-operating characteristic (ROC) curves for the identification of each outcome. The McNemar’s test and paired sample non-parametric statistical techniques were used to test for differences in diagnostic performance metrics. Results (1) The prevalence of MIAC and intra-amniotic inflammation was 34% (34/100) and 40% (40/100), respectively; (2) there were no significant differences in sensitivity of the three tests under study (MR score, IL-6 or MMP-8) in the identification of either MIAC or intra-amniotic inflammation (using the following cutoffs: MR score >2, IL-6 >11.4 ng/mL, and MMP-8 >23 ng/mL); (3) there was no significant difference in the sensitivity among the three tests for the same outcomes when the false positive rate was fixed at 15%; (4) the specificity for IL-6 was not significantly different from that of the MR score in identifying either MIAC or intra-amniotic inflammation when using previously reported thresholds; and (5) there were no significant differences in the area under the ROC curve when comparing the MR score, IL-6 or MMP-8 in the identification of these outcomes. Conclusions IL-6 and the MR score have equivalent diagnostic performance in the identification of MIAC or intra-amniotic inflammation. Selection from among these three tests (MR score, IL-6 and MMP-8) for diagnostic purposes should be based on factors such as availability, reproducibility, and cost. The MR score requires a protein chip and a SELDI-TOF instrument which are not widely available or considered “state of the art”. In contrast, immunoassays for IL-6 can be performed in the majority of clinical laboratories. PMID:24028673

The diagnostic performance of the Mass Restricted (MR) score in the identification of microbial invasion of the amniotic cavity or intra-amniotic inflammation is not superior to amniotic fluid interleukin-6.

PubMed

Romero, Roberto; Kadar, Nicholas; Miranda, Jezid; Korzeniewski, Steven J; Schwartz, Alyse G; Chaemsaithong, Piya; Rogers, Wade; Soto, Eleazar; Gotsch, Francesca; Yeo, Lami; Hassan, Sonia S; Chaiworapongsa, Tinnakorn

2014-05-01

Intra-amniotic infection/inflammation are major causes of spontaneous preterm labor and delivery. However, diagnosis of intra-amniotic infection is challenging because most are subclinical and amniotic fluid (AF) cultures take several days before results are available. Several tests have been proposed for the rapid diagnosis of microbial invasion of the amniotic cavity (MIAC) or intra-amniotic inflammation. The aim of this study was to examine the diagnostic performance of the AF Mass Restricted (MR) score in comparison with interleukin-6 (IL-6) and matrix metalloproteinase-8 (MMP-8) for the identification of MIAC or inflammation. AF samples were collected from patients with singleton gestations and symptoms of preterm labor (n = 100). Intra-amniotic inflammation was defined as >100 white blood cells/mm(3) (WBCs) in AF; MIAC was defined as a positive AF culture. AF IL-6 and MMP-8 were determined using ELISA. The MR score was obtained using the Surface-Enhanced Laser Desorption Ionization Time of Flight (SELDI-TOF) mass spectrometry. Sensitivity and specificity were calculated and logistic regression models were fit to construct receiver-operating characteristic (ROC) curves for the identification of each outcome. The McNemar's test and paired sample non-parametric statistical techniques were used to test for differences in diagnostic performance metrics. (1) The prevalence of MIAC and intra-amniotic inflammation was 34% (34/100) and 40% (40/100), respectively; (2) there were no significant differences in sensitivity of the three tests under study (MR score, IL-6 or MMP-8) in the identification of either MIAC or intra-amniotic inflammation (using the following cutoffs: MR score >2, IL-6 >11.4 ng/mL, and MMP-8 >23 ng/mL); (3) there was no significant difference in the sensitivity among the three tests for the same outcomes when the false positive rate was fixed at 15%; (4) the specificity for IL-6 was not significantly different from that of the MR score in identifying either MIAC or intra-amniotic inflammation when using previously reported thresholds; and (5) there were no significant differences in the area under the ROC curve when comparing the MR score, IL-6 or MMP-8 in the identification of these outcomes. IL-6 and the MR score have equivalent diagnostic performance in the identification of MIAC or intra-amniotic inflammation. Selection from among these three tests (MR score, IL-6 and MMP-8) for diagnostic purposes should be based on factors such as availability, reproducibility, and cost. The MR score requires a protein chip and a SELDI-TOF instrument which are not widely available or considered "state of the art". In contrast, immunoassays for IL-6 can be performed in the majority of clinical laboratories.

Comparison of three-dimensional fluorescence analysis methods for predicting formation of trihalomethanes and haloacetic acids.

PubMed

Peleato, Nicolás M; Andrews, Robert C

2015-01-01

This work investigated the application of several fluorescence excitation-emission matrix analysis methods as natural organic matter (NOM) indicators for use in predicting the formation of trihalomethanes (THMs) and haloacetic acids (HAAs). Waters from four different sources (two rivers and two lakes) were subjected to jar testing followed by 24hr disinfection by-product formation tests using chlorine. NOM was quantified using three common measures: dissolved organic carbon, ultraviolet absorbance at 254 nm, and specific ultraviolet absorbance as well as by principal component analysis, peak picking, and parallel factor analysis of fluorescence spectra. Based on multi-linear modeling of THMs and HAAs, principle component (PC) scores resulted in the lowest mean squared prediction error of cross-folded test sets (THMs: 43.7 (μg/L)(2), HAAs: 233.3 (μg/L)(2)). Inclusion of principle components representative of protein-like material significantly decreased prediction error for both THMs and HAAs. Parallel factor analysis did not identify a protein-like component and resulted in prediction errors similar to traditional NOM surrogates as well as fluorescence peak picking. These results support the value of fluorescence excitation-emission matrix-principal component analysis as a suitable NOM indicator in predicting the formation of THMs and HAAs for the water sources studied. Copyright © 2014. Published by Elsevier B.V.

Nonnegative matrix factorization and sparse representation for the automated detection of periodic limb movements in sleep.

PubMed

Shokrollahi, Mehrnaz; Krishnan, Sridhar; Dopsa, Dustin D; Muir, Ryan T; Black, Sandra E; Swartz, Richard H; Murray, Brian J; Boulos, Mark I

2016-11-01

Stroke is a leading cause of death and disability in adults, and incurs a significant economic burden to society. Periodic limb movements (PLMs) in sleep are repetitive movements involving the great toe, ankle, and hip. Evolving evidence suggests that PLMs may be associated with high blood pressure and stroke, but this relationship remains underexplored. Several issues limit the study of PLMs including the need to manually score them, which is time-consuming and costly. For this reason, we developed a novel automated method for nocturnal PLM detection, which was shown to be correlated with (a) the manually scored PLM index on polysomnography, and (b) white matter hyperintensities on brain imaging, which have been demonstrated to be associated with PLMs. Our proposed algorithm consists of three main stages: (1) representing the signal in the time-frequency plane using time-frequency matrices (TFM), (2) applying K-nonnegative matrix factorization technique to decompose the TFM matrix into its significant components, and (3) applying kernel sparse representation for classification (KSRC) to the decomposed signal. Our approach was applied to a dataset that consisted of 65 subjects who underwent polysomnography. An overall classification of 97 % was achieved for discrimination of the aforementioned signals, demonstrating the potential of the presented method.

Face verification with balanced thresholds.

PubMed

Yan, Shuicheng; Xu, Dong; Tang, Xiaoou

2007-01-01

The process of face verification is guided by a pre-learned global threshold, which, however, is often inconsistent with class-specific optimal thresholds. It is, hence, beneficial to pursue a balance of the class-specific thresholds in the model-learning stage. In this paper, we present a new dimensionality reduction algorithm tailored to the verification task that ensures threshold balance. This is achieved by the following aspects. First, feasibility is guaranteed by employing an affine transformation matrix, instead of the conventional projection matrix, for dimensionality reduction, and, hence, we call the proposed algorithm threshold balanced transformation (TBT). Then, the affine transformation matrix, constrained as the product of an orthogonal matrix and a diagonal matrix, is optimized to improve the threshold balance and classification capability in an iterative manner. Unlike most algorithms for face verification which are directly transplanted from face identification literature, TBT is specifically designed for face verification and clarifies the intrinsic distinction between these two tasks. Experiments on three benchmark face databases demonstrate that TBT significantly outperforms the state-of-the-art subspace techniques for face verification.

Protein Sub-Nuclear Localization Based on Effective Fusion Representations and Dimension Reduction Algorithm LDA.

PubMed

Wang, Shunfang; Liu, Shuhui

2015-12-19

An effective representation of a protein sequence plays a crucial role in protein sub-nuclear localization. The existing representations, such as dipeptide composition (DipC), pseudo-amino acid composition (PseAAC) and position specific scoring matrix (PSSM), are insufficient to represent protein sequence due to their single perspectives. Thus, this paper proposes two fusion feature representations of DipPSSM and PseAAPSSM to integrate PSSM with DipC and PseAAC, respectively. When constructing each fusion representation, we introduce the balance factors to value the importance of its components. The optimal values of the balance factors are sought by genetic algorithm. Due to the high dimensionality of the proposed representations, linear discriminant analysis (LDA) is used to find its important low dimensional structure, which is essential for classification and location prediction. The numerical experiments on two public datasets with KNN classifier and cross-validation tests showed that in terms of the common indexes of sensitivity, specificity, accuracy and MCC, the proposed fusing representations outperform the traditional representations in protein sub-nuclear localization, and the representation treated by LDA outperforms the untreated one.

ADPROCLUS: a graphical user interface for fitting additive profile clustering models to object by variable data matrices.

PubMed

Wilderjans, Tom F; Ceulemans, Eva; Van Mechelen, Iven; Depril, Dirk

2011-03-01

In many areas of psychology, one is interested in disclosing the underlying structural mechanisms that generated an object by variable data set. Often, based on theoretical or empirical arguments, it may be expected that these underlying mechanisms imply that the objects are grouped into clusters that are allowed to overlap (i.e., an object may belong to more than one cluster). In such cases, analyzing the data with Mirkin's additive profile clustering model may be appropriate. In this model: (1) each object may belong to no, one or several clusters, (2) there is a specific variable profile associated with each cluster, and (3) the scores of the objects on the variables can be reconstructed by adding the cluster-specific variable profiles of the clusters the object in question belongs to. Until now, however, no software program has been publicly available to perform an additive profile clustering analysis. For this purpose, in this article, the ADPROCLUS program, steered by a graphical user interface, is presented. We further illustrate its use by means of the analysis of a patient by symptom data matrix.

Protein Sub-Nuclear Localization Based on Effective Fusion Representations and Dimension Reduction Algorithm LDA

PubMed Central

Wang, Shunfang; Liu, Shuhui

2015-01-01

An effective representation of a protein sequence plays a crucial role in protein sub-nuclear localization. The existing representations, such as dipeptide composition (DipC), pseudo-amino acid composition (PseAAC) and position specific scoring matrix (PSSM), are insufficient to represent protein sequence due to their single perspectives. Thus, this paper proposes two fusion feature representations of DipPSSM and PseAAPSSM to integrate PSSM with DipC and PseAAC, respectively. When constructing each fusion representation, we introduce the balance factors to value the importance of its components. The optimal values of the balance factors are sought by genetic algorithm. Due to the high dimensionality of the proposed representations, linear discriminant analysis (LDA) is used to find its important low dimensional structure, which is essential for classification and location prediction. The numerical experiments on two public datasets with KNN classifier and cross-validation tests showed that in terms of the common indexes of sensitivity, specificity, accuracy and MCC, the proposed fusing representations outperform the traditional representations in protein sub-nuclear localization, and the representation treated by LDA outperforms the untreated one. PMID:26703574

The high failure rate of biologic resurfacing of the glenoid in young patients with glenohumeral arthritis.

PubMed

Strauss, Eric J; Verma, Nikhil N; Salata, Michael J; McGill, Kevin C; Klifto, Christopher; Nicholson, Gregory P; Cole, Brian J; Romeo, Anthony A

2014-03-01

The current study evaluated the outcomes of biologic resurfacing of the glenoid using a lateral meniscus allograft or human acellular dermal tissue matrix at intermediate-term follow-up. Forty-five patients (mean age, 42.2 years) underwent biologic resurfacing of the glenoid, and 41 were available for follow-up at a mean of 2.8 years. Lateral meniscal allograft resurfacing was used in 31 patients and human acellular dermal tissue matrix interposition in 10. Postoperative range of motion and clinical outcomes were assessed at the final follow-up. The overall clinical failure rate was 51.2%. The lateral meniscal allograft cohort had a failure rate of 45.2%, with a mean time to failure of 3.4 years. Human acellular dermal tissue matrix interposition had a failure rate of 70.0%, with a mean time to failure of 2.2 years. Overall, significant improvements were seen compared with baseline with respect to the visual analog pain score (3.0 vs. 6.3), American Shoulder and Elbow Surgeons score (62.0 vs. 36.8), and Simple Shoulder Test score (7.0 vs. 4.0). Significant improvements were seen for forward elevation (106° to 138°) and external rotation (31° to 51°). Despite significant improvements compared with baseline values, biologic resurfacing of the glenoid resulted in a high rate of clinical failure at intermediate follow-up. Our results suggest that biologic resurfacing of the glenoid may have a minimal and as yet undefined role in the management of glenohumeral arthritis in the young active patient over more traditional methods of hemiarthroplasty or total shoulder arthroplasty. Copyright © 2014 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Mosby, Inc. All rights reserved.

Shared Dosimetry Error in Epidemiological Dose-Response Analyses

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

Stram, Daniel O.; Preston, Dale L.; Sokolnikov, Mikhail

2015-03-23

Radiation dose reconstruction systems for large-scale epidemiological studies are sophisticated both in providing estimates of dose and in representing dosimetry uncertainty. For example, a computer program was used by the Hanford Thyroid Disease Study to provide 100 realizations of possible dose to study participants. The variation in realizations reflected the range of possible dose for each cohort member consistent with the data on dose determinates in the cohort. Another example is the Mayak Worker Dosimetry System 2013 which estimates both external and internal exposures and provides multiple realizations of "possible" dose history to workers given dose determinants. This paper takesmore » up the problem of dealing with complex dosimetry systems that provide multiple realizations of dose in an epidemiologic analysis. In this paper we derive expected scores and the information matrix for a model used widely in radiation epidemiology, namely the linear excess relative risk (ERR) model that allows for a linear dose response (risk in relation to radiation) and distinguishes between modifiers of background rates and of the excess risk due to exposure. We show that treating the mean dose for each individual (calculated by averaging over the realizations) as if it was true dose (ignoring both shared and unshared dosimetry errors) gives asymptotically unbiased estimates (i.e. the score has expectation zero) and valid tests of the null hypothesis that the ERR slope β is zero. Although the score is unbiased the information matrix (and hence the standard errors of the estimate of β) is biased for β≠0 when ignoring errors in dose estimates, and we show how to adjust the information matrix to remove this bias, using the multiple realizations of dose. Use of these methods for several studies, including the Mayak Worker Cohort and the U.S. Atomic Veterans Study, is discussed.« less

An examination of the Wechsler Adult Intelligence Scales, Fourth Edition (WAIS-IV) in individuals with complicated mild, moderate and Severe traumatic brain injury (TBI).

PubMed

Carlozzi, Noelle E; Kirsch, Ned L; Kisala, Pamela A; Tulsky, David S

2015-01-01

This study examined the clinical utility of the Wechsler Adult Intelligence Scales-Fourth Edition (WAIS-IV) in individuals with complicated mild, moderate or severe TBI. One hundred individuals with TBI (n = 35 complicated mild or moderate TBI; n = 65 severe TBI) and 100 control participants matched on key demographic variables from the WAIS-IV normative dataset completed the WAIS-IV. Univariate analyses indicated that participants with severe TBI had poorer performance than matched controls on all index scores and subtests (except Matrix Reasoning). Individuals with complicated mild/moderate TBI performed more poorly than controls on the Working Memory Index (WMI), Processing Speed Index (PSI), and Full Scale IQ (FSIQ), and on four subtests: the two processing speed subtests (SS, CD), two working memory subtests (AR, LN), and a perceptual reasoning subtest (BD). Participants with severe TBI had significantly lower scores than the complicated mild/moderate TBI on PSI, and on three subtests: the two processing speed subtests (SS and CD), and the new visual puzzles test. Effect sizes for index and subtest scores were generally small-to-moderate for the group with complicated mild/moderate and moderate-to-large for the group with severe TBI. PSI also showed good sensitivity and specificity for classifying individuals with severe TBI versus controls. Findings provide support for the clinical utility of the WAIS-IV in individuals with complicated mild, moderate, and severe TBI.

High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations.

PubMed

Shirai, Hiroki; Ikeda, Kazuyoshi; Yamashita, Kazuo; Tsuchiya, Yuko; Sarmiento, Jamica; Liang, Shide; Morokata, Tatsuaki; Mizuguchi, Kenji; Higo, Junichi; Standley, Daron M; Nakamura, Haruki

2014-08-01

In the second antibody modeling assessment, we used a semiautomated template-based structure modeling approach for 11 blinded antibody variable region (Fv) targets. The structural modeling method involved several steps, including template selection for framework and canonical structures of complementary determining regions (CDRs), homology modeling, energy minimization, and expert inspection. The submitted models for Fv modeling in Stage 1 had the lowest average backbone root mean square deviation (RMSD) (1.06 Å). Comparison to crystal structures showed the most accurate Fv models were generated for 4 out of 11 targets. We found that the successful modeling in Stage 1 mainly was due to expert-guided template selection for CDRs, especially for CDR-H3, based on our previously proposed empirical method (H3-rules) and the use of position specific scoring matrix-based scoring. Loop refinement using fragment assembly and multicanonical molecular dynamics (McMD) was applied to CDR-H3 loop modeling in Stage 2. Fragment assembly and McMD produced putative structural ensembles with low free energy values that were scored based on the OSCAR all-atom force field and conformation density in principal component analysis space, respectively, as well as the degree of consensus between the two sampling methods. The quality of 8 out of 10 targets improved as compared with Stage 1. For 4 out of 10 Stage-2 targets, our method generated top-scoring models with RMSD values of less than 1 Å. In this article, we discuss the strengths and weaknesses of our approach as well as possible directions for improvement to generate better predictions in the future. © 2014 Wiley Periodicals, Inc.

A comparison of two prospective risk analysis methods: Traditional FMEA and a modified healthcare FMEA.

PubMed

Rah, Jeong-Eun; Manger, Ryan P; Yock, Adam D; Kim, Gwe-Ya

2016-12-01

To examine the abilities of a traditional failure mode and effects analysis (FMEA) and modified healthcare FMEA (m-HFMEA) scoring methods by comparing the degree of congruence in identifying high risk failures. The authors applied two prospective methods of the quality management to surface image guided, linac-based radiosurgery (SIG-RS). For the traditional FMEA, decisions on how to improve an operation were based on the risk priority number (RPN). The RPN is a product of three indices: occurrence, severity, and detectability. The m-HFMEA approach utilized two indices, severity and frequency. A risk inventory matrix was divided into four categories: very low, low, high, and very high. For high risk events, an additional evaluation was performed. Based upon the criticality of the process, it was decided if additional safety measures were needed and what they comprise. The two methods were independently compared to determine if the results and rated risks matched. The authors' results showed an agreement of 85% between FMEA and m-HFMEA approaches for top 20 risks of SIG-RS-specific failure modes. The main differences between the two approaches were the distribution of the values and the observation that failure modes (52, 54, 154) with high m-HFMEA scores do not necessarily have high FMEA-RPN scores. In the m-HFMEA analysis, when the risk score is determined, the basis of the established HFMEA Decision Tree™ or the failure mode should be more thoroughly investigated. m-HFMEA is inductive because it requires the identification of the consequences from causes, and semi-quantitative since it allows the prioritization of high risks and mitigation measures. It is therefore a useful tool for the prospective risk analysis method to radiotherapy.

Reversed headspace analysis for characterization, identification, and analysis of solid and liquid matrices: Part I.

PubMed

Markelov, M; Bershevits, O

2006-03-01

This paper offers a methodology of an experimentally simple reversed headspace (RHS) analysis for measuring of matrix effects and their use for identification and characterization of condensed matrices such as pharmaceuticals, polymers, chromatographic packing, etc. applicable for both quality control monitoring and research and development investigation. In RHS methods, the matrix is spiked and equilibrated with a mixture of volatile chemicals containing various functional groups (molecular sensor array or MSA mixture). Headspace chromatograms of the same spikes of a sample and an empty vial are compared. Examination of basic headspace theory shows that matrix specific constants (M), rather than partition coefficients (K), can be calculated from the headspace chromatograms and M=(K-1)xbeta, where beta is a degree of matrix volume change during equilibration. Matrix specific constants can be plotted against any property of chemicals (polarity, dielectric constant, solubility parameter, vapor pressure, etc.) or just against a set of consecutive numbers, each representing a chemical in MSA. This plot is, in a sense, a molecular affinity spectrum (MAS) specific for a given matrix at a given temperature and is independent of an instrument. Changes in MAS that correspond to chemicals with a particular functional group give an insight to the type of differences between matrices and may quantitatively define them.

A novel alignment-free method to classify protein folding types by combining spectral graph clustering with Chou's pseudo amino acid composition.

PubMed

Tripathi, Pooja; Pandey, Paras N

2017-07-07

The present work employs pseudo amino acid composition (PseAAC) for encoding the protein sequences in their numeric form. Later this will be arranged in the similarity matrix, which serves as input for spectral graph clustering method. Spectral methods are used previously also for clustering of protein sequences, but they uses pair wise alignment scores of protein sequences, in similarity matrix. The alignment score depends on the length of sequences, so clustering short and long sequences together may not good idea. Therefore the idea of introducing PseAAC with spectral clustering algorithm came into scene. We extensively tested our method and compared its performance with other existing machine learning methods. It is consistently observed that, the number of clusters that we obtained for a given set of proteins is close to the number of superfamilies in that set and PseAAC combined with spectral graph clustering shows the best classification results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Poor Auditory Task Scores in Children with Specific Reading and Language Difficulties: Some Poor Scores Are More Equal than Others

ERIC Educational Resources Information Center

McArthur, Genevieve M.; Hogben, John H.

2012-01-01

Children with specific reading disability (SRD) or specific language impairment (SLI), who scored poorly on an auditory discrimination task, did up to 140 runs on the failed task. Forty-one percent of the children produced widely fluctuating scores that did not improve across runs (untrainable errant performance), 23% produced widely fluctuating…

Combination of STOP-Bang Score with Mallampati Score fails to improve specificity in the prediction of sleep-disordered breathing.

PubMed

Dette, Frank G; Graf, Juergen; Cassel, Werner; Lloyd-Jones, Carla; Boehm, Stefan; Zoremba, Martin; Schramm, Patrick; Pestel, Gunther; Thal, Serge C

2016-06-01

Sleep-disordered breathing (SDB) is closely associated with perioperative complications. STOP-Bang score was validated for preoperative screening of SDB. However, STOP-Bang Score lacks adequately high specificity. We aimed to improve it by combining it with the Mallampati Score. The study included 347 patients, in which we assessed both STOP-Bang and Mallampati scores. Overnight oxygen saturation was measured to calculate ODI4%. We calculated the sensitivity and specificity for AHI and ODI4% of both scores separately and in combination. We found that STOP-Bang Score ≥3 was present in 71%, ODI≥5/h (AHI ≥5/h) in 42.6% (39.3%) and ODI≥15/h (AHI ≥15/h) in 13.5% (17.8%). For ODI4%≥5/h (AHI ≥5/h) we observed in men a response rate for sensitivity and specificity of STOP-Bang of 94.5% and 17.1% (90.9% and 12.5%) and in women 66% and 51% (57.8% and 46.9%). For ODI4%≥15/h (AHI≥15/h) it was 92% and 12% (84.6% and 10.3%) and 93% and 49% (75% and 49.2%). For ODI4%≥5 (AHI≥5) sensitivity and specificity of Mallampati score were in men 38.4% and 78.6% (27.3% and 68.2%) and in women 25% and 82.7% (21.9% and 81.3%), for ODI≥15 (AHI ≥15/h) 38.5% and 71.8% (26.9% and 69.2%) and 33.3% and 81.4% (17.9% and 79.6%). In combination, for ODI4%≥15/h, we found sensitivity in men to be 92.3% and in women 93.3%, specificity 10.3% and 41.4%. STOP-Bang Score combined with Mallampati Score fails to increase specificity. Low specificity should be considered when using both scores for preoperative screening of SDB.

Outcomes of arthroscopic revision rotator cuff repair with acellular human dermal matrix allograft augmentation.

PubMed

Hohn, Eric A; Gillette, Blake P; Burns, Joseph P

2018-05-01

The purpose was to assess the minimum 2-year patient-reported outcomes and failure rate of patients who underwent revision arthroscopic rotator cuff repair augmented with acellular human dermal matrix (AHDM) allograft for repairable retears. From 2008-2014, patients who underwent revision rotator cuff repair augmented with AHDM with greater than 2 years' follow-up by a single surgeon were retrospectively reviewed. Data regarding surgical history, demographic characteristics, and medical comorbidities were collected. Outcome data included American Shoulder and Elbow Surgeons (ASES) and Single Assessment Numeric Evaluation (SANE) scores, as well as rotator cuff healing on magnetic resonance imaging or ultrasound. Retears and subsequent surgical procedures were characterized. A total of 28 patients met our inclusion criteria, and 23 (82%) were available for follow-up at 2 years. The mean age was 60.1 ± 9.3 years (range, 43-79 years), with a mean follow-up period of 48 ± 23 months. All patients had at least 1 prior rotator cuff repair. Of the 23 patients, 13 (56%) underwent postoperative imaging, and 4 of these 13 (31%) had a retear. A reoperation was performed in 3 of 23 patients (13%). Among the 6 patients with both preoperative and postoperative outcome scores, we saw improvement in the ASES score from 56 to 85 (P = .03) and in the SANE score from 42 to 76 (P = .03). The full cohort's mean postoperative ASES and SANE scores were 77 and 69, respectively. AHDM allograft augmentation is a safe and effective treatment method for patients with full-thickness rotator cuff retears. Further research is needed with larger studies to confirm these findings from our small cohort of patients. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Baseline serum level of matrix metalloproteinase-3 as a biomarker of progressive joint damage in rheumatoid arthritis patients.

PubMed

Galil, Sahar Mahfouz Abdel; El-Shafey, Abeer Mohamed; Hagrass, Hoda A; Fawzy, Faten; Sammak, Ahmed El

2016-04-01

Matrix metalloproteinase-3 (MMP-3) plays a pivotal role in the destruction of bone and degradation of cartilage components in rheumatoid arthritis (RA). We aimed in this study to analyze the relation between baseline levels of MMP-3 and the progression of joint damage in RA. Eighty-one untreated RA patients with joint symptoms for <1 year were evaluated at baseline and after 12 months as regards erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), rheumatoid factor (RF), anti-cyclic citrullinated peptide (anti-CCP) and plain X-ray of both hands and wrists. Baseline levels of MMP-3 were measured by enzyme-linked immunosorbent assay and magnetic resonance imaging (MRI) of hands/wrists was performed. Disease Activity Score (DAS28) and Health Assessment Questionnaire (HAQ) were performed at baseline evaluation and after 12 months. The baseline MMP-3 levels were significantly higher in the high-progression group compared with the low-progression one (95.75 ± 42.84 vs. 50.45 ± 12.83, P < 0.001). There was a positive correlation between baseline levels of MMP-3 and MRI erosion score and other baseline clinical parameters, except for HAQ and the van der Heijde modification of the Sharp scoring system (SvdH) scores, while after 12 months, there were high positive correlations between MMP-3 and SvdH score, as well as all parameters except for ESR. Serum baseline levels of MMP-3 are strong prognostic markers of disease activity, and act well as an early predictor of progressive joint damage in recent-onset RA disease. © 2014 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

NASA Astrophysics Data System (ADS)

Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

2017-07-01

DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

A highly sensitive and specific combined clinical and sonographic score to diagnose appendicitis.

PubMed

Reddy, Swathi B; Kelleher, Michael; Bokhari, S A Jamal; Davis, Kimberly A; Schuster, Kevin M

2017-10-01

Computed tomography (CT) scanning reduces the negative appendectomy rate however it exposes the patient to ionizing radiation. Ultrasound (US) does not carry this risk but may be nondiagnostic. We hypothesized that a clinical-US scoring system would improve diagnostic accuracy. We conducted a retrospective review of all patients (age, >15 years) who presented through the emergency department with suspected appendicitis and underwent initial US. A US score was developed using odds ratios for appendicitis given appendiceal diameter, compressibility, hyperemia, free fluid, and focal or diffuse tenderness. The US score was then combined with the Alvarado score. Final diagnosis of appendicitis was assigned by pathology reports. Three hundred patients who underwent US as initial imaging were identified. Thirty-two patients with evident nonappendiceal pathology on US were excluded. In 114 (38%), the appendix was not visualized and partially visualized in 36 (12%). Fifty-seven (21.3%) had an appendectomy with 1 (1.7%) negative. Six nonvisualized appendicies underwent appendectomy, with no negative cases. Sensitivity and specificity for the sonographic score were 86% and 90%, respectively, at a score of 1.5. The combined score demonstrated 98% sensitivity and 82% specificity at 6.5, and 95% sensitivity, and 87% specificity at a score of 7.5. Sensitivity and specificity were confirmed by bootstrap resampling for validation. Area under receiver operating characteristic (ROC) curves for our new US score were similar to the ROC curve for the Alvarado score (91.9 and 91.1, p = 0.8). The combined US and Alvarado score yielded an area under the ROC curve of 97.1, significantly better than either score alone (p = 0.017 and p < 0.001, respectively). Our scoring system based entirely on US findings was highly sensitive and specific for appendicitis, and it significantly improved when combined with the Alvarado score. After prospective evaluation, the combined US-Alvarado score might replace the need for computed tomography imaging in a majority of patients. Diagnostic Test, Level III.

Statistical Analysis of Q-matrix Based Diagnostic Classification Models

PubMed Central

Chen, Yunxiao; Liu, Jingchen; Xu, Gongjun; Ying, Zhiliang

2014-01-01

Diagnostic classification models have recently gained prominence in educational assessment, psychiatric evaluation, and many other disciplines. Central to the model specification is the so-called Q-matrix that provides a qualitative specification of the item-attribute relationship. In this paper, we develop theories on the identifiability for the Q-matrix under the DINA and the DINO models. We further propose an estimation procedure for the Q-matrix through the regularized maximum likelihood. The applicability of this procedure is not limited to the DINA or the DINO model and it can be applied to essentially all Q-matrix based diagnostic classification models. Simulation studies are conducted to illustrate its performance. Furthermore, two case studies are presented. The first case is a data set on fraction subtraction (educational application) and the second case is a subsample of the National Epidemiological Survey on Alcohol and Related Conditions concerning the social anxiety disorder (psychiatric application). PMID:26294801

Improved method for predicting protein fold patterns with ensemble classifiers.

PubMed

Chen, W; Liu, X; Huang, Y; Jiang, Y; Zou, Q; Lin, C

2012-01-27

Protein folding is recognized as a critical problem in the field of biophysics in the 21st century. Predicting protein-folding patterns is challenging due to the complex structure of proteins. In an attempt to solve this problem, we employed ensemble classifiers to improve prediction accuracy. In our experiments, 188-dimensional features were extracted based on the composition and physical-chemical property of proteins and 20-dimensional features were selected using a coupled position-specific scoring matrix. Compared with traditional prediction methods, these methods were superior in terms of prediction accuracy. The 188-dimensional feature-based method achieved 71.2% accuracy in five cross-validations. The accuracy rose to 77% when we used a 20-dimensional feature vector. These methods were used on recent data, with 54.2% accuracy. Source codes and dataset, together with web server and software tools for prediction, are available at: http://datamining.xmu.edu.cn/main/~cwc/ProteinPredict.html.

Protein Composition of Trypanosoma brucei Mitochondrial Membranes

PubMed Central

Acestor, Nathalie; Panigrahi, Aswini K.; Ogata, Yuko; Anupama, Atashi; Stuart, Kenneth D.

2010-01-01

Mitochondria consist of four compartments, outer membrane, intermembrane space, inner membrane and matrix; each harboring specific functions and structures. In this study, we used mass spectrometry (LC-MS/MS) to characterize the protein composition of Trypanosoma brucei mitochondrial membranes, which were enriched by different biochemical fractionation techniques. The analyses identified 202 proteins that contain one or more transmembrane domain(s) and/or positive GRAVY scores. Of these, various criteria were used to assign 72 proteins to mitochondrial membranes with high confidence, and 106 with moderate to low confidence. The sub-cellular localization of a selected subset of 13 membrane assigned proteins was confirmed by tagging and immunofluorescence analysis. While most proteins assigned to mitochondrial membrane have putative roles in metabolic, energy generating, and transport processes, ~50% have no known function. These studies result in a comprehensive profile of the composition and sub-organellar location of proteins in the T. brucei mitochondrion thus, providing useful information on mitochondrial functions. PMID:19834910

Linkage of the gene that encodes the alpha 1 chain of type V collagen (COL5A1) to type II Ehlers-Danlos syndrome (EDS II).

PubMed

Loughlin, J; Irven, C; Hardwick, L J; Butcher, S; Walsh, S; Wordsworth, P; Sykes, B

1995-09-01

Ehlers-Danlos syndrome (EDS) is a group of heritable disorders of connective tissue with skin, ligaments and blood vessels being the main sites affected. The commonest variant (EDS II) exhibits an autosomal dominant mode of inheritance and is characterized by joint hypermobility, cigarette paper scars, lax skin and excessive bruising. As yet no gene has been linked to EDS II, nor has linkage been established to a specific region of the genome. However, several candidate genes encoding proteins of the extracellular matrix have been excluded. Using an intragenic simple sequence repeat polymorphism, we report linkage of the COL5A1 gene, which encodes the alpha 1(V) chain of type V collagen, to EDS II. A maximum LOD score (Zmax) for linkage of 8.3 at theta = 0.00 was generated for a single large pedigree.

Geary autocorrelation and DCCA coefficient: Application to predict apoptosis protein subcellular localization via PSSM

NASA Astrophysics Data System (ADS)

Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

2017-02-01

Apoptosis is a fundamental process controlling normal tissue homeostasis by regulating a balance between cell proliferation and death. Predicting subcellular location of apoptosis proteins is very helpful for understanding its mechanism of programmed cell death. Prediction of apoptosis protein subcellular location is still a challenging and complicated task, and existing methods mainly based on protein primary sequences. In this paper, we propose a new position-specific scoring matrix (PSSM)-based model by using Geary autocorrelation function and detrended cross-correlation coefficient (DCCA coefficient). Then a 270-dimensional (270D) feature vector is constructed on three widely used datasets: ZD98, ZW225 and CL317, and support vector machine is adopted as classifier. The overall prediction accuracies are significantly improved by rigorous jackknife test. The results show that our model offers a reliable and effective PSSM-based tool for prediction of apoptosis protein subcellular localization.

Detrended cross-correlation coefficient: Application to predict apoptosis protein subcellular localization.

PubMed

Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

2016-12-01

Apoptosis, or programed cell death, plays a central role in the development and homeostasis of an organism. Obtaining information on subcellular location of apoptosis proteins is very helpful for understanding the apoptosis mechanism. The prediction of subcellular localization of an apoptosis protein is still a challenging task, and existing methods mainly based on protein primary sequences. In this paper, we introduce a new position-specific scoring matrix (PSSM)-based method by using detrended cross-correlation (DCCA) coefficient of non-overlapping windows. Then a 190-dimensional (190D) feature vector is constructed on two widely used datasets: CL317 and ZD98, and support vector machine is adopted as classifier. To evaluate the proposed method, objective and rigorous jackknife cross-validation tests are performed on the two datasets. The results show that our approach offers a novel and reliable PSSM-based tool for prediction of apoptosis protein subcellular localization. Copyright © 2016 Elsevier Inc. All rights reserved.

What Impact Does Venous Thromboembolism and Bleeding Have on Cancer Patients' Quality of Life?

PubMed

Lloyd, Andrew J; Dewilde, Sarah; Noble, Simon; Reimer, Elisabeth; Lee, Agnes Y Y

2018-04-01

Venous thromboembolism (VTE) is common in cancer patients and its treatment is associated with a high risk of recurrent VTE (rVTE) and bleeding. To analyze data from the Comparison of Acute Treatments in Cancer Hemostasis (CATCH) trial to describe the impact of rVTE and bleeding events on health-related quality of life. The three-level EuroQol five-dimensional questionnaire (EQ-5D) data were collected monthly for up to 7 months in patients starting anticoagulation for newly diagnosed VTE. Analyses were designed to describe the impact of rVTE and bleeding on EQ-5D scores while controlling for effects of covariates such as background and clinical variables and longitudinal changes. A repeated-measures model with specification of the variance-covariance matrix to characterize the intrapatient correlation was used to estimate the utility values. The impact of an rVTE or a bleeding event was assumed to be reflected in the utility value when it occurred within 2 weeks from a planned data collection point. Data were available from 883 patients. A total of 76 rVTE and 159 bleeding events occurred during follow-up. rVTE had a significant impact on EQ-5D scores, with a decrement of -0.075 on the basis of our reference case (male, no metastasis, Eastern Cooperative Oncology Group score = 1, Western European), but different patients might have different decrements. Bleeding events had a smaller (nonstatistically significant) impact on EQ-5D scores. This data set study has quantified the decline in EQ-5D scores associated with experiencing rVTE or bleeding events in cancer patients. These results indicate the net gain in quality of life and impact on cost-effectiveness of secondary VTE prevention. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Improving performances of suboptimal greedy iterative biclustering heuristics via localization.

PubMed

Erten, Cesim; Sözdinler, Melih

2010-10-15

Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. Even the simplest versions of the problem are computationally hard. Most of the proposed solutions therefore employ greedy iterative heuristics that locally optimize a suitably assigned scoring function. We provide a fast and simple pre-processing algorithm called localization that reorders the rows and columns of the input data matrix in such a way as to group correlated entries in small local neighborhoods within the matrix. The proposed localization algorithm takes its roots from effective use of graph-theoretical methods applied to problems exhibiting a similar structure to that of biclustering. In order to evaluate the effectivenesss of the localization pre-processing algorithm, we focus on three representative greedy iterative heuristic methods. We show how the localization pre-processing can be incorporated into each representative algorithm to improve biclustering performance. Furthermore, we propose a simple biclustering algorithm, Random Extraction After Localization (REAL) that randomly extracts submatrices from the localization pre-processed data matrix, eliminates those with low similarity scores, and provides the rest as correlated structures representing biclusters. We compare the proposed localization pre-processing with another pre-processing alternative, non-negative matrix factorization. We show that our fast and simple localization procedure provides similar or even better results than the computationally heavy matrix factorization pre-processing with regards to H-value tests. We next demonstrate that the performances of the three representative greedy iterative heuristic methods improve with localization pre-processing when biological correlations in the form of functional enrichment and PPI verification constitute the main performance criteria. The fact that the random extraction method based on localization REAL performs better than the representative greedy heuristic methods under same criteria also confirms the effectiveness of the suggested pre-processing method. Supplementary material including code implementations in LEDA C++ library, experimental data, and the results are available at http://code.google.com/p/biclustering/ cesim@khas.edu.tr; melihsozdinler@boun.edu.tr Supplementary data are available at Bioinformatics online.

Combined Endoscopic/Sonographic-Based Risk Matrix Model for Predicting One-Year Risk of Surgery: A Prospective Observational Study of a Tertiary Center Severe/Refractory Crohn's Disease Cohort.

PubMed

Rispo, Antonio; Imperatore, Nicola; Testa, Anna; Bucci, Luigi; Luglio, Gaetano; De Palma, Giovanni Domenico; Rea, Matilde; Nardone, Olga Maria; Caporaso, Nicola; Castiglione, Fabiana

2018-03-08

In the management of Crohn's Disease (CD) patients, having a simple score combining clinical, endoscopic and imaging features to predict the risk of surgery could help to tailor treatment more effectively. AIMS: to prospectively evaluate the one-year risk factors for surgery in refractory/severe CD and to generate a risk matrix for predicting the probability of surgery at one year. CD patients needing a disease re-assessment at our tertiary IBD centre underwent clinical, laboratory, endoscopy and bowel sonography (BS) examinations within one week. The optimal cut-off values in predicting surgery were identified using ROC curves for Simple Endoscopic Score for CD (SES-CD), bowel wall thickness (BWT) at BS, and small bowel CD extension at BS. Binary logistic regression and Cox's regression were then carried out. Finally, the probabilities of surgery were calculated for selected baseline levels of covariates and results were arranged in a prediction matrix. Of 100 CD patients, 30 underwent surgery within one year. SES-CD©9 (OR 15.3; p<0.001), BWT©7 mm (OR 15.8; p<0.001), small bowel CD extension at BS©33 cm (OR 8.23; p<0.001) and stricturing/penetrating behavior (OR 4.3; p<0.001) were the only independent factors predictive of surgery at one-year based on binary logistic and Cox's regressions. Our matrix model combined these risk factors and the probability of surgery ranged from 0.48% to 87.5% (sixteen combinations). Our risk matrix combining clinical, endoscopic and ultrasonographic findings can accurately predict the one-year risk of surgery in patients with severe/refractory CD requiring a disease re-evaluation. This tool could be of value in clinical practice, serving as the basis for a tailored management of CD patients.

Remodeling characteristics and collagen distribution in synthetic mesh materials explanted from human subjects after abdominal wall reconstruction: an analysis of remodeling characteristics by patient risk factors and surgical site classifications

PubMed Central

Cavallo, Jaime A.; Roma, Andres A.; Jasielec, Mateusz S.; Ousley, Jenny; Creamer, Jennifer; Pichert, Matthew D.; Baalman, Sara; Frisella, Margaret M.; Matthews, Brent D.

2014-01-01

Background The purpose of this study was to evaluate the associations between patient characteristics or surgical site classifications and the histologic remodeling scores of synthetic meshes biopsied from their abdominal wall repair sites in the first attempt to generate a multivariable risk prediction model of non-constructive remodeling. Methods Biopsies of the synthetic meshes were obtained from the abdominal wall repair sites of 51 patients during a subsequent abdominal re-exploration. Biopsies were stained with hematoxylin and eosin, and evaluated according to a semi-quantitative scoring system for remodeling characteristics (cell infiltration, cell types, extracellular matrix deposition, inflammation, fibrous encapsulation, and neovascularization) and a mean composite score (CR). Biopsies were also stained with Sirius Red and Fast Green, and analyzed to determine the collagen I:III ratio. Based on univariate analyses between subject clinical characteristics or surgical site classification and the histologic remodeling scores, cohort variables were selected for multivariable regression models using a threshold p value of ≤0.200. Results The model selection process for the extracellular matrix score yielded two variables: subject age at time of mesh implantation, and mesh classification (c-statistic = 0.842). For CR score, the model selection process yielded two variables: subject age at time of mesh implantation and mesh classification (r2 = 0.464). The model selection process for the collagen III area yielded a model with two variables: subject body mass index at time of mesh explantation and pack-year history (r2 = 0.244). Conclusion Host characteristics and surgical site assessments may predict degree of remodeling for synthetic meshes used to reinforce abdominal wall repair sites. These preliminary results constitute the first steps in generating a risk prediction model that predicts the patients and clinical circumstances for which non-constructive remodeling of an abdominal wall repair site with synthetic mesh reinforcement is most likely to occur. PMID:24442681

Optimizing identification of clinically relevant Gram-positive organisms by use of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system.

PubMed

McElvania Tekippe, Erin; Shuey, Sunni; Winkler, David W; Butler, Meghan A; Burnham, Carey-Ann D

2013-05-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including "heavy" (H) and "light" (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or "score." We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS.

Optimizing Identification of Clinically Relevant Gram-Positive Organisms by Use of the Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System

PubMed Central

McElvania TeKippe, Erin; Shuey, Sunni; Winkler, David W.; Butler, Meghan A.

2013-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including “heavy” (H) and “light” (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or “score.” We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS. PMID:23426925

Sports Activity After Reconstruction of Osteochondral Lesions of the Talus With Autologous Spongiosa Grafts and Autologous Matrix-Induced Chondrogenesis.

PubMed

Wiewiorski, Martin; Werner, Lorenzo; Paul, Jochen; Anderson, Andrew E; Barg, Alexej; Valderrabano, Victor

2016-10-01

For the treatment of osteochondral lesions of the talus (OCLTs), autologous matrix-induced chondrogenesis (AMIC) is a safe 1-step procedure with good clinical and radiological results. However, data regarding postoperative sports activity after AMIC are limited. To identify significant factors influencing the rate of postoperative sports and recreational activities. Case series; Level of evidence, 4. The sports and recreational activities of 60 patients (mean age, 34.9 ± 11.5 years) undergoing the AMIC procedure were retrospectively analyzed at a mean of 46.9 ± 17.8 months (range, 24.5-87.0 months) postoperatively. The visual analog scale (VAS) for pain score, Tegner activity scale score, activity rating scale (ARS) score, and satisfaction with surgery outcomes were assessed. Corrective calcaneal osteotomy was performed in 38 of 60 (63.3%) patients. Ligament repair was performed in 41 of 60 (68.3%) patients. The mean VAS score improved significantly from 6.9 ± 1.6 points (range, 5-10 points) preoperatively to 2.3 ± 1.9 points (range, 0-6 points) at latest follow-up (P < .001). No significant change in the mean Tegner activity scale score (3.3 ± 2.0 preoperatively to 3.4 ± 2.2 postoperatively; P = .526) and the mean ARS score (2.6 ± 4.3 preoperatively to 2.3 ± 3.4 postoperatively; P = .874) was noted. The percentage of patients involved in sports activity before the onset of symptoms became significantly lower at the time of surgery (from 95.0% to 53.3%; P < .001); no significant difference was noted postoperatively (from 53.3% to 58.3%; P = .663). No significant difference of the weekly sports frequency and the duration of sports activity was found postoperatively. Patients undergoing AMIC repair of an OCLT participate at a similar low postoperative sports and recreational activity level compared with the preoperative level. © 2016 The Author(s).

Sensitivity and Specificity of Fenyö-Lindberg and Teicher Scores in the Diagnosis of Acute Appendicitis in Women

PubMed

Madžar, Zrinko; Kopljar, Mario; Madžar, Tomislav; Mesić, Marko; Mužina Mišić, Dubravka; Čiček, Slaven; Zovak, Mario

2016-12-01

The aim of the study was to assess diagnostic accuracy (sensitivity and specificity) of Fenyö-Lindberg and Teicher scores for distinguishing patients that need immediate surgical treatment from the others, in a female population from an urban setting. The study prospectively included 130 female patients admitted to the emergency department with abdominal pain indicating acute appendicitis. The scores and parameters of validity were calculated and compared to definitive diagnosis. For Fenyö-Lindberg score of -17 or less, 84.5% sensitivity, 55.6% specificity, 87.9% positive predictive value (PPV) and 48.4% negative predictive value (NPV) were recorded. For cut-off value greater or equal to -2, there was 59.2% sensitivity, 77.8% specificity, 91% PPV and 33.3% NPV. The Receiver Operating Characteristic (ROC) curve analysis of Fenyö-Lindberg score showed that the best single cut-off value for discriminating acute appendicitis in the study population was -15. For Teicher score, values greater than -3 yielded 89.3% sensitivity and 22.2% specificity, 81.4% PPV and 35.3% NPV. In conclusion, Fenyö-Lindberg score could be used as an additional tool to exclude appendicitis and avoid unnecessary appendectomies. Teicher score may help in recognizing patients with appendicitis. None of the two scores can indicate or decline appendectomy in all cases. Scoring systems may be useful for pointing to important clinical signs and symptoms in specific subpopulations.

Selective and Responsive Nanopore-Filled Membranes

DTIC Science & Technology

2011-03-14

Materials Science and Engineering Poster Competition 15. Chen, H.; Elabd, Y.A. Ionic Liquid Polymers: Electrospinning and Solution Properties. Fall...hydrophilic ionic polymer gels within a hydrophobic polymer host matrix. The specific tasks of this project include (1) synthesizing stimuli...on polymer-polymer nanocomposites of hydrophilic ionic polymer gels within a hydrophobic polymer host matrix. The specific tasks of this project

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

Peterson, R.C.; Garard, R.J.; Lokhandwala, K.K.

The crush behavior (specific energy absorption and crush load stability) of unidirectional fiber composite rods having tougher matrices than vinyl ester were investigated and compared with the crush behavior of similar specimens having a vinyl ester matrix. The matrices were a cyclic polyester and two rubber-toughened vinyl esters. The specific energy absorption with the cyclic polyester matrix, 180 MJ/m{sup 3}, was slightly lower than that with the vinyl ester matrix, 230 MJ/m{sup 3}. On the other hand, the crush stability was markedly better. The average deviation of the crush load about the mean was as small as 3.5% with themore » cyclic polyester matrix, in contrast to about 12% with the vinyl ester matrix. The higher ductility of the cyclic polyester and the good fiber-matrix bond strength together resulted in less fracturing of the matrix and more uniform kink-band formation across the composite cross section than occurred with the vinyl ester matrix. There was also a reduction in the tendency for fibers at the periphery of the rod to splay outward rather than being crushed. Of the two rubber-toughened vinyl ester matrices, a 30% reduction was found in the average deviation of the crush load about the mean with the matrix toughened with a core-shell material, although no improvement was found with the CTBN rubber-modified vinyl ester resin.« less

Evaluation of modified Alvarado scoring system and RIPASA scoring system as diagnostic tools of acute appendicitis.

PubMed

Shuaib, Abdullah; Shuaib, Ali; Fakhra, Zainab; Marafi, Bader; Alsharaf, Khalid; Behbehani, Abdullah

2017-01-01

Acute appendicitis is the most common surgical condition presented in emergency departments worldwide. Clinical scoring systems, such as the Alvarado and modified Alvarado scoring systems, were developed with the goal of reducing the negative appendectomy rate to 5%-10%. The Raja Isteri Pengiran Anak Saleha Appendicitis (RIPASA) scoring system was established in 2008 specifically for Asian populations. The aim of this study was to compare the modified Alvarado with the RIPASA scoring system in Kuwait population. This study included 180 patients who underwent appendectomies and were documented as having "acute appendicitis" or "abdominal pain" in the operating theatre logbook (unit B) from November 2014 to March 2016. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic accuracy, predicted negative appendectomy and receiver operating characteristic (ROC) curve of the modified Alvarado and RIPASA scoring systems were derived using SPSS statistical software. A total of 136 patients were included in this study according to our criteria. The cut-off threshold point of the modified Alvarado score was set at 7.0, which yielded a sensitivity of 82.8% and a specificity of 56%. The PPV was 89.3% and the NPV was 42.4%. The cut-off threshold point of the RIPASA score was set at 7.5, which yielded a 94.5% sensitivity and an 88% specificity. The PPV was 97.2% and the NPV was 78.5%. The predicted negative appendectomy rates were 10.7% and 2.2% for the modified Alvarado and RIPASA scoring systems, respectively. The negative appendectomy rate decreased significantly, from 18.4% to 10.7% for the modified Alvarado, and to 2.2% for the RIPASA scoring system, which was a significant difference (P<0.001) for both scoring systems. Based on the results of this study, the RIPASA score is a simple scoring system with better sensitivity and specificity than the modified Alvarado scoring system in Asian populations. It consists of 14 clinical parameters that can be obtained from a good patient history, clinical examination and laboratory investigations. The RIPASA scoring system is more accurate and specific than the modified Alvarado scoring system for Kuwait population.

Prediction of molecular mimicry candidates in human pathogenic bacteria.

PubMed

Doxey, Andrew C; McConkey, Brendan J

2013-08-15

Molecular mimicry of host proteins is a common strategy adopted by bacterial pathogens to interfere with and exploit host processes. Despite the availability of pathogen genomes, few studies have attempted to predict virulence-associated mimicry relationships directly from genomic sequences. Here, we analyzed the proteomes of 62 pathogenic and 66 non-pathogenic bacterial species, and screened for the top pathogen-specific or pathogen-enriched sequence similarities to human proteins. The screen identified approximately 100 potential mimicry relationships including well-characterized examples among the top-scoring hits (e.g., RalF, internalin, yopH, and others), with about 1/3 of predicted relationships supported by existing literature. Examination of homology to virulence factors, statistically enriched functions, and comparison with literature indicated that the detected mimics target key host structures (e.g., extracellular matrix, ECM) and pathways (e.g., cell adhesion, lipid metabolism, and immune signaling). The top-scoring and most widespread mimicry pattern detected among pathogens consisted of elevated sequence similarities to ECM proteins including collagens and leucine-rich repeat proteins. Unexpectedly, analysis of the pathogen counterparts of these proteins revealed that they have evolved independently in different species of bacterial pathogens from separate repeat amplifications. Thus, our analysis provides evidence for two classes of mimics: complex proteins such as enzymes that have been acquired by eukaryote-to-pathogen horizontal transfer, and simpler repeat proteins that have independently evolved to mimic the host ECM. Ultimately, computational detection of pathogen-specific and pathogen-enriched similarities to host proteins provides insights into potentially novel mimicry-mediated virulence mechanisms of pathogenic bacteria.

Prediction of molecular mimicry candidates in human pathogenic bacteria

PubMed Central

Doxey, Andrew C; McConkey, Brendan J

2013-01-01

Molecular mimicry of host proteins is a common strategy adopted by bacterial pathogens to interfere with and exploit host processes. Despite the availability of pathogen genomes, few studies have attempted to predict virulence-associated mimicry relationships directly from genomic sequences. Here, we analyzed the proteomes of 62 pathogenic and 66 non-pathogenic bacterial species, and screened for the top pathogen-specific or pathogen-enriched sequence similarities to human proteins. The screen identified approximately 100 potential mimicry relationships including well-characterized examples among the top-scoring hits (e.g., RalF, internalin, yopH, and others), with about 1/3 of predicted relationships supported by existing literature. Examination of homology to virulence factors, statistically enriched functions, and comparison with literature indicated that the detected mimics target key host structures (e.g., extracellular matrix, ECM) and pathways (e.g., cell adhesion, lipid metabolism, and immune signaling). The top-scoring and most widespread mimicry pattern detected among pathogens consisted of elevated sequence similarities to ECM proteins including collagens and leucine-rich repeat proteins. Unexpectedly, analysis of the pathogen counterparts of these proteins revealed that they have evolved independently in different species of bacterial pathogens from separate repeat amplifications. Thus, our analysis provides evidence for two classes of mimics: complex proteins such as enzymes that have been acquired by eukaryote-to-pathogen horizontal transfer, and simpler repeat proteins that have independently evolved to mimic the host ECM. Ultimately, computational detection of pathogen-specific and pathogen-enriched similarities to host proteins provides insights into potentially novel mimicry-mediated virulence mechanisms of pathogenic bacteria. PMID:23715053

Analysis of world terror networks from the reduced Google matrix of Wikipedia

NASA Astrophysics Data System (ADS)

El Zant, Samer; Frahm, Klaus M.; Jaffrès-Runser, Katia; Shepelyansky, Dima L.

2018-01-01

We apply the reduced Google matrix method to analyze interactions between 95 terrorist groups and determine their relationships and influence on 64 world countries. This is done on the basis of the Google matrix of the English Wikipedia (2017) composed of 5 416 537 articles which accumulate a great part of global human knowledge. The reduced Google matrix takes into account the direct and hidden links between a selection of 159 nodes (articles) appearing due to all paths of a random surfer moving over the whole network. As a result we obtain the network structure of terrorist groups and their relations with selected countries including hidden indirect links. Using the sensitivity of PageRank to a weight variation of specific links we determine the geopolitical sensitivity and influence of specific terrorist groups on world countries. The world maps of the sensitivity of various countries to influence of specific terrorist groups are obtained. We argue that this approach can find useful application for more extensive and detailed data bases analysis.

Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis.

PubMed

Cloete, Kevin Wesley; Ristow, Peter Gustav; Kasu, Mohaimin; D'Amato, Maria Eugenia

2017-03-01

CE equipment detects and deconvolutes mixtures containing up to six fluorescently labeled DNA fragments. This deconvolution is done by the collection software that requires a spectral calibration file. The calibration file is used to adjust for the overlap that occurs between the emission spectra of fluorescence dyes. All commercial genotyping and sequencing kits require the installation of a corresponding matrix standard to generate a calibration file. Due to the differences in emission spectrum overlap between fluorescent dyes, the application of existing commercial matrix standards to the electrophoretic separation of DNA labeled with other fluorescent dyes can yield undesirable results. Currently, the number of fluorescent dyes available for oligonucleotide labeling surpasses the availability of commercial matrix standards. Therefore, in this study we developed and evaluated a customized matrix standard using ATTO 633, ATTO 565, ATTO 550, ATTO Rho6G, and 6-FAM dyes for which no commercial matrix standard is available. We highlighted the potential genotyping errors of using an incorrect matrix standard by evaluating the relative performance of our custom dye set using six matrix standards. The specific performance of two genotyping kits (UniQTyper™ Y-10 version 1.0 and PowerPlex® Y23 System) was also evaluated using their specific matrix standards. The procedure we followed for the construction of our custom dye matrix standard can be extended to other fluorescent dyes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Procollagen III N-terminal Propeptide and Desmosine are Released by Matrix Destruction in Pulmonary Tuberculosis

PubMed Central

Seddon, Jo; Kasprowicz, Victoria; Walker, Naomi F.; Yuen, Ho Ming; Sunpath, Henry; Tezera, Liku; Meintjes, Graeme; Wilkinson, Robert J.; Bishai, William R.; Friedland, Jon S.; Elkington, Paul T.

2013-01-01

Background. Tuberculosis is transmitted by patients with pulmonary disease. Matrix metalloproteinases (MMPs) drive lung destruction in tuberculosis but the resulting matrix degradation products (MDPs) have not been studied. We investigate the hypothesis that MMP activity generates matrix turnover products as correlates of lung pathology. Methods. Induced sputum and plasma were collected prospectively from human immunodeficiency virus (HIV) positive and negative patients with pulmonary tuberculosis and controls. Concentrations of MDPs and MMPs were analyzed by ELISA and Luminex array in 2 patient cohorts. Results. Procollagen III N-terminal propeptide (PIIINP) was 3.8-fold higher in induced sputum of HIV-uninfected tuberculosis patients compared to controls and desmosine, released during elastin degradation, was 2.4-fold higher. PIIINP was elevated in plasma of tuberculosis patients. Plasma PIIINP correlated with induced sputum MMP-1 concentrations and radiological scores, demonstrating that circulating MDPs reflect lung destruction. In a second patient cohort of mixed HIV seroprevalence, plasma PIIINP concentration was increased 3.0-fold above controls (P < .001). Plasma matrix metalloproteinase-8 concentrations were also higher in tuberculosis patients (P = .001). Receiver operating characteristic analysis utilizing these 2 variables demonstrated an area under the curve of 0.832 (P < .001). Conclusions. In pulmonary tuberculosis, MMP-driven immunopathology generates matrix degradation products. PMID:23922364

Primary fascial closure with biologic mesh reinforcement results in lesser complication and recurrence rates than bridged biologic mesh repair for abdominal wall reconstruction: A propensity score analysis.

PubMed

Giordano, Salvatore; Garvey, Patrick B; Baumann, Donald P; Liu, Jun; Butler, Charles E

2017-02-01

Previous studies suggest that bridged mesh repair for abdominal wall reconstruction may result in worse outcomes than mesh-reinforced, primary fascial closure, particularly when acellular dermal matrix is used. We compared our outcomes of bridged versus reinforced repair using ADM in abdominal wall reconstruction procedures. This retrospective study included 535 consecutive patients at our cancer center who underwent abdominal wall reconstruction either for an incisional hernia or for abdominal wall defects left after excision of malignancies involving the abdominal wall with underlay mesh. A total of 484 (90%) patients underwent mesh-reinforced abdominal wall reconstruction and 51 (10%) underwent bridged repair abdominal wall reconstruction. Acellular dermal matrix was used, respectively, in 98% of bridged and 96% of reinforced repairs. We compared outcomes between these 2 groups using propensity score analysis for risk-adjustment in multivariate analysis and for 1-to-1 matching. Bridged repairs had a greater hernia recurrence rate (33.3% vs 6.2%, P < .001), a greater overall complication rate (59% vs 30%, P = .001), and worse freedom from hernia recurrence (log-rank P <.001) than reinforced repairs. Bridged repairs also had a greater rate of wound dehiscence (26% vs 14%, P = .034) and mesh exposure (10% vs 1%, P = .003) than mesh-reinforced abdominal wall reconstruction. When the treatment method was adjusted for propensity score in the propensity-score-matched pairs (n = 100), we found that the rates of hernia recurrence (32% vs 6%, P = .002), overall complications (32% vs 6%, P = .002), and freedom from hernia recurrence (68% vs 32%, P = .001) rates were worse after bridged repair. We did not observe differences in wound healing and mesh complications between the 2 groups. In our population of primarily cancer patients at MD Anderson Cancer Center bridged repair for abdominal wall reconstruction is associated with worse outcomes than mesh-reinforced abdominal wall reconstruction. Particularly when employing acellular dermal matrix, reinforced repairs should be used for abdominal wall reconstruction whenever possible. Copyright © 2016 Elsevier Inc. All rights reserved.

Identification of regional activation by factorization of high-density surface EMG signals: A comparison of Principal Component Analysis and Non-negative Matrix factorization.

PubMed

Gallina, Alessio; Garland, S Jayne; Wakeling, James M

2018-05-22

In this study, we investigated whether principal component analysis (PCA) and non-negative matrix factorization (NMF) perform similarly for the identification of regional activation within the human vastus medialis. EMG signals from 64 locations over the VM were collected from twelve participants while performing a low-force isometric knee extension. The envelope of the EMG signal of each channel was calculated by low-pass filtering (8 Hz) the monopolar EMG signal after rectification. The data matrix was factorized using PCA and NMF, and up to 5 factors were considered for each algorithm. Association between explained variance, spatial weights and temporal scores between the two algorithms were compared using Pearson correlation. For both PCA and NMF, a single factor explained approximately 70% of the variance of the signal, while two and three factors explained just over 85% or 90%. The variance explained by PCA and NMF was highly comparable (R > 0.99). Spatial weights and temporal scores extracted with non-negative reconstruction of PCA and NMF were highly associated (all p < 0.001, mean R > 0.97). Regional VM activation can be identified using high-density surface EMG and factorization algorithms. Regional activation explains up to 30% of the variance of the signal, as identified through both PCA and NMF. Copyright © 2018 Elsevier Ltd. All rights reserved.

Discovering mutated driver genes through a robust and sparse co-regularized matrix factorization framework with prior information from mRNA expression patterns and interaction network.

PubMed

Xi, Jianing; Wang, Minghui; Li, Ao

2018-06-05

Discovery of mutated driver genes is one of the primary objective for studying tumorigenesis. To discover some relatively low frequently mutated driver genes from somatic mutation data, many existing methods incorporate interaction network as prior information. However, the prior information of mRNA expression patterns are not exploited by these existing network-based methods, which is also proven to be highly informative of cancer progressions. To incorporate prior information from both interaction network and mRNA expressions, we propose a robust and sparse co-regularized nonnegative matrix factorization to discover driver genes from mutation data. Furthermore, our framework also conducts Frobenius norm regularization to overcome overfitting issue. Sparsity-inducing penalty is employed to obtain sparse scores in gene representations, of which the top scored genes are selected as driver candidates. Evaluation experiments by known benchmarking genes indicate that the performance of our method benefits from the two type of prior information. Our method also outperforms the existing network-based methods, and detect some driver genes that are not predicted by the competing methods. In summary, our proposed method can improve the performance of driver gene discovery by effectively incorporating prior information from interaction network and mRNA expression patterns into a robust and sparse co-regularized matrix factorization framework.

Comparison of Regenerative Tissue Quality following Matrix-Associated Cell Implantation Using Amplified Chondrocytes Compared to Synovium-Derived Stem Cells in a Rabbit Model for Cartilage Lesions.

PubMed

Schmal, Hagen; Kowal, Justyna M; Kassem, Moustapha; Seidenstuecker, Michael; Bernstein, Anke; Böttiger, Katharina; Xiong, Tanshiyue; Südkamp, Norbert P; Kubosch, Eva J

2018-01-01

Known problems of the autologous chondrocyte implantation motivate the search for cellular alternatives. The aim of the study was to test the potential of synovium-derived stem cells (SMSC) to regenerate cartilage using a matrix-associated implantation. In an osteochondral defect model of the medial femoral condyle in a rabbit, a collagen membrane was seeded with either culture-expanded allogenic chondrocytes or SMSC and then transplanted into the lesion. A tailored piece synovium served as a control. Rabbit SMSC formed typical cartilage in vitro. Macroscopic evaluation of defect healing and the thickness of the regenerated tissue did not reveal a significant difference between the intervention groups. However, instantaneous and shear modulus, reflecting the biomechanical strength of the repair tissue, was superior in the implantation group using allogenic chondrocytes ( p < 0.05). This correlated with a more chondrogenic structure and higher proteoglycan expression, resulting in a lower OARSI score ( p < 0.05). The repair tissue of all groups expressed comparable amounts of the collagen types I, II, and X. Cartilage regeneration following matrix-associated implantation using allogenic undifferentiated synovium-derived stem cells in a defect model in rabbits showed similar macroscopic results and collagen composition compared to amplified chondrocytes; however, biomechanical characteristics and histological scoring were inferior.

Comparison of Regenerative Tissue Quality following Matrix-Associated Cell Implantation Using Amplified Chondrocytes Compared to Synovium-Derived Stem Cells in a Rabbit Model for Cartilage Lesions

PubMed Central

Kowal, Justyna M.; Seidenstuecker, Michael; Bernstein, Anke; Böttiger, Katharina; Xiong, Tanshiyue; Südkamp, Norbert P.

2018-01-01

Known problems of the autologous chondrocyte implantation motivate the search for cellular alternatives. The aim of the study was to test the potential of synovium-derived stem cells (SMSC) to regenerate cartilage using a matrix-associated implantation. In an osteochondral defect model of the medial femoral condyle in a rabbit, a collagen membrane was seeded with either culture-expanded allogenic chondrocytes or SMSC and then transplanted into the lesion. A tailored piece synovium served as a control. Rabbit SMSC formed typical cartilage in vitro. Macroscopic evaluation of defect healing and the thickness of the regenerated tissue did not reveal a significant difference between the intervention groups. However, instantaneous and shear modulus, reflecting the biomechanical strength of the repair tissue, was superior in the implantation group using allogenic chondrocytes (p < 0.05). This correlated with a more chondrogenic structure and higher proteoglycan expression, resulting in a lower OARSI score (p < 0.05). The repair tissue of all groups expressed comparable amounts of the collagen types I, II, and X. Cartilage regeneration following matrix-associated implantation using allogenic undifferentiated synovium-derived stem cells in a defect model in rabbits showed similar macroscopic results and collagen composition compared to amplified chondrocytes; however, biomechanical characteristics and histological scoring were inferior. PMID:29765410

Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study.

PubMed

Zhao, Zhongming; Guo, An-Yuan; van den Oord, Edwin J C G; Aliev, Fazil; Jia, Peilin; Edenberg, Howard J; Riley, Brien P; Dick, Danielle M; Bettinger, Jill C; Davies, Andrew G; Grotewiel, Michael S; Schuckit, Marc A; Agrawal, Arpana; Kramer, John; Nurnberger, John I; Kendler, Kenneth S; Webb, Bradley T; Miles, Michael F

2012-01-01

A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation. In this study, we performed a unique multi-species evidence-based data integration using three microarray experiments in mice or humans that generated an initial alcohol dependence (AD) related genes list, human linkage and association results, and gene sets implicated in C. elegans and Drosophila. We then used permutation and false discovery rate (FDR) analyses on the genome-wide association studies (GWAS) dataset from the Collaborative Study on the Genetics of Alcoholism (COGA) to evaluate the ranking results and weighting matrices. We found one weighting score matrix could increase FDR based q-values for a list of 47 genes with a score greater than 2. Our follow up functional enrichment tests revealed these genes were primarily involved in brain responses to ethanol and neural adaptations occurring with alcoholism. These results, along with our experimental validation of specific genes in mice, C. elegans and Drosophila, suggest that a cross-species evidence-based approach is useful to identify candidate genes contributing to alcoholism.

Monocyte activation by smooth muscle cell-derived matrices.

PubMed

Kaufmann, J; Jorgensen, R W; Martin, B M; Franzblau, C

1990-12-01

Mononuclear phagocytes adhere to and penetrate the vessel wall endothelium and contact the subendothelial space prior to the development of the atherosclerotic plaque. In an attempt to model the early events of plaque development we used an elastin-rich, multicomponent, cell-derived matrix from neonatal rat aortic smooth muscle cells as a substratum for monocytes. Using this model, we show that human monocyte morphology and metabolism are markedly altered by the matrix substratum. When a mixed mononuclear cell population is seeded on matrix or plastic, only monocytes adhere to the matrix surface. In contrast, lymphocytes as well as monocytes adhere to the plastic surface. The matrix-adherent monocytes develop large intracellular granules and form extensive clusters of individual cells. Metabolically, these cells develop sodium fluoride resistant non-specific esterase activity and their media contain more growth factor activity and PGE2. Although total protein synthesis is equivalent in both cultures, the matrix contact induces an increase in specific proteins in the media. We also show that a purified alpha-elastin substratum induces some, but not all, of the monocyte changes seen when using the matrix substratum. Using the alpha-elastin substratum, there is selective adhesion of monocytes and increased growth factor activity, however, the cells are morphologically different from the matrix-adherent cells. Thus, the use of the smooth muscle cell-derived matrix, in conjunction with purified matrix components, serves as a model that can provide insight into the mechanisms of monocyte adhesion and stimulation by the matrix environment that exists in vivo. Such mechanisms may be particularly important in atherogenesis.

78 FR 20717 - Endangered and Threatened Wildlife and Plants; Proposed Endangered, Threatened, and Not Warranted...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-05

... prey item, followed by elasmobranchs, octopus and squid, and baitfish, with a positive correlation.... (2011) found a positive correlation between litter size and female shark length for scalloped... translate the risk matrix scores directly into a determination of overall extinction risk. Other descriptive...

The Predictive Value of Selection Criteria in an Urban Magnet School

ERIC Educational Resources Information Center

Lohmeier, Jill Hendrickson; Raad, Jennifer

2012-01-01

The predictive value of selection criteria on outcome data from two cohorts of students (Total N = 525) accepted to an urban magnet high school were evaluated. Regression analyses of typical screening variables (suspensions, absences, metropolitan achievement tests, middle school grade point averages [GPAs], Matrix Analogies test scores, and…

Is a matrix exponential specification suitable for the modeling of spatial correlation structures?

PubMed Central

Strauß, Magdalena E.; Mezzetti, Maura; Leorato, Samantha

2018-01-01

This paper investigates the adequacy of the matrix exponential spatial specifications (MESS) as an alternative to the widely used spatial autoregressive models (SAR). To provide as complete a picture as possible, we extend the analysis to all the main spatial models governed by matrix exponentials comparing them with their spatial autoregressive counterparts. We propose a new implementation of Bayesian parameter estimation for the MESS model with vague prior distributions, which is shown to be precise and computationally efficient. Our implementations also account for spatially lagged regressors. We further allow for location-specific heterogeneity, which we model by including spatial splines. We conclude by comparing the performances of the different model specifications in applications to a real data set and by running simulations. Both the applications and the simulations suggest that the spatial splines are a flexible and efficient way to account for spatial heterogeneities governed by unknown mechanisms. PMID:29492375

BiPPred: Combined sequence- and structure-based prediction of peptide binding to the Hsp70 chaperone BiP.

PubMed

Schneider, Markus; Rosam, Mathias; Glaser, Manuel; Patronov, Atanas; Shah, Harpreet; Back, Katrin Christiane; Daake, Marina Angelika; Buchner, Johannes; Antes, Iris

2016-10-01

Substrate binding to Hsp70 chaperones is involved in many biological processes, and the identification of potential substrates is important for a comprehensive understanding of these events. We present a multi-scale pipeline for an accurate, yet efficient prediction of peptides binding to the Hsp70 chaperone BiP by combining sequence-based prediction with molecular docking and MMPBSA calculations. First, we measured the binding of 15mer peptides from known substrate proteins of BiP by peptide array (PA) experiments and performed an accuracy assessment of the PA data by fluorescence anisotropy studies. Several sequence-based prediction models were fitted using this and other peptide binding data. A structure-based position-specific scoring matrix (SB-PSSM) derived solely from structural modeling data forms the core of all models. The matrix elements are based on a combination of binding energy estimations, molecular dynamics simulations, and analysis of the BiP binding site, which led to new insights into the peptide binding specificities of the chaperone. Using this SB-PSSM, peptide binders could be predicted with high selectivity even without training of the model on experimental data. Additional training further increased the prediction accuracies. Subsequent molecular docking (DynaDock) and MMGBSA/MMPBSA-based binding affinity estimations for predicted binders allowed the identification of the correct binding mode of the peptides as well as the calculation of nearly quantitative binding affinities. The general concept behind the developed multi-scale pipeline can readily be applied to other protein-peptide complexes with linearly bound peptides, for which sufficient experimental binding data for the training of classical sequence-based prediction models is not available. Proteins 2016; 84:1390-1407. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Relating actual with subfossil chironomid assemblages. Holocene habitat changes and paleoenvironmental reconstruction of Basa de la Mora Lake (Central Pyrenees)

NASA Astrophysics Data System (ADS)

Tarrats, Pol; Rieradevall, Maria; González-Sampériz, Penélope; Pérez-Sanz, Ana; Valero-Garcés, Blas; Moreno, Ana

2014-05-01

Analyses of subfossil and actual macroinvertebrate fauna and Chironomidae larvae (Insecta: Diptera) assemblages of Basa de la Mora Lake (Central Pyrenees, Spain, 1914 m a.s.l.) improves the environmental calibration for lake paleoreconstruction and allow to infer lake habitat changes throughout the Holocene. The results of the actual Chironomidae community are consistent with other mountain lake studies (either in the Pyrenees or other regions), with a few mismatching due to lake specific conditions. The actual and the subfossil Chironomidae taxa present in Basa de la Mora Lake are the same, which is an essential requirement to apply the analogue methods. Although we could not find habitat-specific taxa, significant differences between the different habitats present in the lake were found. This circumstance allowed applying the Modern Analogue Technique (MAT) to infer lake habitat changes. The MAT method relates the actual community, defined from the species abundance matrix and an environmental variable (which is the object of the inference), and the past community, defined from the species abundance matrix downcore. Because the first axis of DCA carried out for the study of the actual Chironomidae larvae explained the assemblage changes between the different habitats, the scores of this first axis were used as representative of the environmental variable (dominant habitat type) to be inferred. The application of the MAT has allowed identifying two periods of lake productivity increase through the Holocene: i) around 2800 cal. yrs BP, which coincides with the first documented human occupation of the area, and ii) the last four centuries, synchronous to the maximum population of mountain areas in the Pyrenees and development of stockbreeding activities.

Assessment of Matrix Multiplication Learning with a Rule-Based Analytical Model--"A Bayesian Network Representation"

ERIC Educational Resources Information Center

Zhang, Zhidong

2016-01-01

This study explored an alternative assessment procedure to examine learning trajectories of matrix multiplication. It took rule-based analytical and cognitive task analysis methods specifically to break down operation rules for a given matrix multiplication. Based on the analysis results, a hierarchical Bayesian network, an assessment model,…

Brief announcement: Hypergraph parititioning for parallel sparse matrix-matrix multiplication

DOE PAGES

Ballard, Grey; Druinsky, Alex; Knight, Nicholas; ...

2015-01-01

The performance of parallel algorithms for sparse matrix-matrix multiplication is typically determined by the amount of interprocessor communication performed, which in turn depends on the nonzero structure of the input matrices. In this paper, we characterize the communication cost of a sparse matrix-matrix multiplication algorithm in terms of the size of a cut of an associated hypergraph that encodes the computation for a given input nonzero structure. Obtaining an optimal algorithm corresponds to solving a hypergraph partitioning problem. Furthermore, our hypergraph model generalizes several existing models for sparse matrix-vector multiplication, and we can leverage hypergraph partitioners developed for that computationmore » to improve application-specific algorithms for multiplying sparse matrices.« less

Assessment of articular cartilage repair tissue after matrix-associated autologous chondrocyte transplantation or the microfracture technique in the ankle joint using diffusion-weighted imaging at 3 Tesla.

PubMed

Apprich, S; Trattnig, S; Welsch, G H; Noebauer-Huhmann, I M; Sokolowski, M; Sokolwski, M; Hirschfeld, C; Stelzeneder, D; Domayer, S

2012-07-01

The objective was to compare patients after matrix-associated autologous chondrocyte transplantation (MACT) and microfracture therapy (MFX) of the talus using diffusion-weighted imaging (DWI), with morphological and clinical scoring. Twenty patients treated with MACT or MFX (10 per group) were examined using 3 T magnetic resonance imaging (MRI) at 48 ± 21.5 and 59.6 ± 23 months after surgery, respectively. For comparability, patients from each group were matched by age, body mass index, and follow-up. American Orthopaedic Foot and Ankle Society (AOFAS) score served as clinical assessment tool pre- and postoperatively. DWI was obtained using a partially balanced, steady-state gradient echo pulse sequence, as well as the Magnetic Resonance Observation of Cartilage Repair Tissue (MOCART) score, based on a 2D proton density-weighted turbo spin-echo sequence and a 3D isotropic true fast imaging with steady-state precession sequence. Semi-quantitative diffusion quotients were calculated after region of interest analysis of repair tissue (RT) and healthy control cartilage, and compared among both groups. The mean AOFAS score improved significantly (P = 0.001) for both groups (MACT: 48.8 ± 20.4-83.6 ± 9.7; MFX: 44.3 ± 16.5-77.6 ± 13.2). No differences in the AOFAS (P = 0.327) and MOCART (P = 0.720) score were observed between MACT and MFX postoperatively. DWI distinguished between healthy cartilage and cartilage RT in the MFX group (P = 0.016), but not after MACT treatment (P = 0.105). Significant correlations were found between MOCART score and DWI index after MFX (Pearson: -0.648; P = 0.043), and between the diffusivity and longer follow-up interval in MACT group (Pearson: -0.647, P = 0.043). Whereas conventional scores reveal a similar outcome after MACT or MFX treatment in the ankle joint, DWI was able to distinguish between different RT qualities, as reported histologically for these diverse surgical procedures. Copyright © 2012 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Mapping cognitive structures of community college students engaged in basic electrostatics laboratories

NASA Astrophysics Data System (ADS)

Haggerty, Dennis Charles

Community college students need to be abstract thinkers in order to be successful in the introductory Physics curriculum. The purpose of this dissertation is to map the abstract thinking of community college Physics students. The laboratory environment was used as a vehicle for the mapping. Three laboratory experiments were encountered. One laboratory was based on the classic Piagetian task, the centripetal motion (CM) problem. The other two laboratories were introductory electrostatic Physics experiments, Resistance (RES) and Capacitance (CAP). The students performed all laboratories using the thinking-aloud technique. The researcher collected their verbal protocols using audiotapes. The audiotaped data was quantified by comparing it to a scoring matrix based on the Piagetian logical operators (Inhelder & Piaget, 1958) for abstract thinking. The students received scores for each laboratory experiment. These scores were compared to a reliable test of intellectual functioning, the Shipley Institute of Living Scale (SILS). Spearman rank correlation coefficients (SRCC) were obtained for SILS versus CM; SILS versus RES; and SILS versus CAP. Statistically significant results were obtained for SILS versus CM and SILS versus RES at the p < 0.05 level. When an outlier to the data was considered and suppressed, the SILS versus CAP was also statistically significant at the p < 0.05 level. The scoring matrix permits a bridge from the qualitative Piagetian level of cognitive development to a quantified, mapped level of cognitive development. The ability to quantify student abstract thinking in Physics education provides a means to adjust an instructional approach. This approach could lead to a proper state of Physics education.

Accuracy of Short Forms of the Dutch Wechsler Preschool and Primary Scale of Intelligence: Third Edition.

PubMed

Hurks, Petra; Hendriksen, Jos; Dek, Joelle; Kooij, Andress

2016-04-01

This article investigated the accuracy of six short forms of the Dutch Wechsler Preschool and Primary Scale of Intelligence-Third edition (WPPSI-III-NL) in estimating intelligent quotient (IQ) scores in healthy children aged 4 to 7 years (N = 1,037). Overall, accuracy for each short form was studied, comparing IQ equivalences based on the short forms with the original WPPSI-III-NL Full Scale IQ (FSIQ) scores. Next, our sample was divided into three groups: children performing below average, average, or above average, based on the WPPSI-III-NL FSIQ estimates of the original long form, to study the accuracy of WPPSI-III-NL short forms at the tails of the FSIQ distribution. While studying the entire sample, all IQ estimates of the WPPSI-III-NL short forms correlated highly with the FSIQ estimates of the original long form (all rs ≥ .83). Correlations decreased significantly while studying only the tails of the IQ distribution (rs varied between .55 and .83). Furthermore, IQ estimates of the short forms deviated significantly from the FSIQ score of the original long form, when the IQ estimates were based on short forms containing only two subtests. In contrast, unlike the short forms that contained two to four subtests, the Wechsler Abbreviated Scale of Intelligence short form (containing the subtests Vocabulary, Similarities, Block Design, and Matrix Reasoning) and the General Ability Index short form (containing the subtests Vocabulary, Similarities, Comprehension, Block Design, Matrix Reasoning, and Picture Concepts) produced less variations when compared with the original FSIQ score. © The Author(s) 2015.

PERFORMANCE OF TWO DIFFERENT CLINICAL SCORING SYSTEMS IN DIAGNOSING DISTAL SENSORY POLYNEUROPATHY IN PATIENTS WITH TYPE-2 DIABETES.

PubMed

Khan, Fehmeda Farrukh; Numan, Ahsan; Khawaja, Khadija Irfan; Atif, Ali; Fatima, Aziz; Masud, Faisal

2015-01-01

Early diagnosis of distal peripheral neuropathy (DSPN) the commonest diabetes complications, helps prevent significant morbidity. Clinical parameters are useful for detection, but subjectivity and lack of operator proficiency often results in inaccuracies. Comparative diagnostic accuracy of Diabetic Neuropathy Symptom (DNS) score and Diabetic Neuropathy Examination (DNE) score in detecting DSPN confirmed by nerve conduction studies (NCS) has not been evaluated. This study compares the performance of these scores in predicting the presence of electro physiologically proven DSPN. The objective of this, study was to compare the diagnostic accuracy of DNS and DNE scores in detecting NCS proven DSPN in type-2 diabetics, and to determine the frequency of sub-clinical DSPN among type-2 diabetics. In this cross-sectional study the DNS score and DNE score were determined in 110 diagnosed type-2 diabetic patients. NCS were carried out and amplitudes, velocities and latencies of sensory and motor nerves in lower limb were recorded. Comparison between the two clinical diagnostic modalities and NCS using Pearson's chi square test showed a significant association between NCS and DNE scores (p-value =.003, specificity 93%). The DNS score performed poorly in comparison (p-value = .068, specificity 77%). When the two scores were taken in combination the specificity in diagnosing DSPN was greater (p-value = .018, specificity 96%) than either alone. 33% of patients had subclinical neuropathy. DNE score alone and in combination with DNS score is reliable in predicting DSPN and is more specific than DNS score in evaluating DSPN. Both tests lack sensitivity. Patients without any evidence of clinical neuropathy manifest abnormalities on NCS.

Using Tradtional Ecological Knowledge to Protect Wetlands: the Swinomish Tribe's Wetland Cultural Assessment Project

NASA Astrophysics Data System (ADS)

Mitchell, T.

2017-12-01

"Traditional" wetland physical assessment modules do not adequately identify Tribal cultural values of wetlands and thus wetlands may not be adequately protected for cultural uses. This Swinomish Wetlands Cultural Assessment Project has developed a cultural resource scoring module that can be incorporated into wetland assessments to better inform wetland protections. Local native knowledge was gathered about the traditional uses of 99 native wetland plant species. A cultural scoring matrix was developed based on the presence of traditionally used plants in several use categories including: construction, ceremonial, subsistence, medicinal, common use, plant rarity, and place of value for each wetland. The combined score of the cultural and physcial modules provides an overall wetland score that relates to proscribed buffer protection widths. With this local native knowledge incorporated into wetland assessments, we are protecting and preserving Swinomish Reservation wetlands for both cultural uses and ecological functionality through the Tribe's wetland protection law.

Human cartilage repair with a photoreactive adhesive-hydrogel composite.

PubMed

Sharma, Blanka; Fermanian, Sara; Gibson, Matthew; Unterman, Shimon; Herzka, Daniel A; Cascio, Brett; Coburn, Jeannine; Hui, Alexander Y; Marcus, Norman; Gold, Garry E; Elisseeff, Jennifer H

2013-01-09

Surgical options for cartilage resurfacing may be significantly improved by advances and application of biomaterials that direct tissue repair. A poly(ethylene glycol) diacrylate (PEGDA) hydrogel was designed to support cartilage matrix production, with easy surgical application. A model in vitro system demonstrated deposition of cartilage-specific extracellular matrix in the hydrogel biomaterial and stimulation of adjacent cartilage tissue development by mesenchymal stem cells. For translation to the joint environment, a chondroitin sulfate adhesive was applied to covalently bond and adhere the hydrogel to cartilage and bone tissue in articular defects. After preclinical testing in a caprine model, a pilot clinical study was initiated where the biomaterials system was combined with standard microfracture surgery in 15 patients with focal cartilage defects on the medial femoral condyle. Control patients were treated with microfracture alone. Magnetic resonance imaging showed that treated patients achieved significantly higher levels of tissue fill compared to controls. Magnetic resonance spin-spin relaxation times (T(2)) showed decreasing water content and increased tissue organization over time. Treated patients had less pain compared with controls, whereas knee function [International Knee Documentation Committee (IKDC)] scores increased to similar levels between the groups over the 6 months evaluated. No major adverse events were observed over the study period. With further clinical testing, this practical biomaterials strategy has the potential to improve the treatment of articular cartilage defects.

A Coordinated Approach to Curricular Review and Development in Undergraduate Geoscience Programs: Using a Matrix to Identify and Track Skills and Skill Development

NASA Astrophysics Data System (ADS)

MacDonald, R.; Savina, M. E.

2003-12-01

One approach to curriculum review and development is to construct a matrix of the desired skills versus courses in the departmental curriculum. The matrix approach requires faculty to articulate their goals, identify specific skills, and assess where in the curriculum students will learn and practice these skills and where there are major skills gaps. Faculty members in the Geology Department at Carleton College developed a matrix of skills covered in geology courses with the following objectives: 1) Geology majors should begin their "senior integrative exercise" having practiced multiple times all of the formal steps in the research process (recognizing problems, writing proposals, carrying out a project, reporting a project in several ways); 2) Geology majors should learn and practice a variety of professional and life skills life (e.g. computer skills, field skills, lab skills, and interpretive skills).The matrix was used to identify where in the curriculum various research methods and skills were addressed and to map potential student experiences to the objectives. In Carleton's non-hierarchical curriculum, the matrix was used to verify that students have many opportunities to practice research and life skills regardless of the path they take to completion of the major. In William and Mary's more structured curriculum, the matrix was used to ensure that skills build upon each other from course to course. Faculty members in the Geology Department at the College of William and Mary first used this approach to focus on teaching quantitative skills across the geology curriculum, and later used it in terms of teaching research, communication, and information literacy skills. After articulating goals and skills, faculty members in both departments developed more specific skill lists within each category of skills, then described the current assignments and activities in each course relative to the specific components of the matrix and discussed whether to add assignment or activities. We have found that much conversation among faculty and change within courses happens simply as a result of compiling the matrix. One effect of the use of the matrix is that faculty in the department know fairly specifically what skills students are learning and practicing in their other geology courses. Moreover, some faculty members are better suited by background or inclination to teach certain sets of skills. This coordinated approach avoids unnecessary duplication and allows faculty to build on skills and topics developed in previous courses. The matrix can also be used as a planning tool to identify gaps in the curriculum. In our experience, the skills matrix is a powerful organizational and communication tool. The skills matrix is a representation of what the department believes actually happens in the curriculum. Thus, development of a skills matrix provides a basis for departmental discussions of student learning goals and objectives as well as for describing the existing curriculum. The matrix is also a graphic representation, to college administrators and outside evaluators, of the "intentionality" of an entire curriculum, going beyond single courses and their syllabi. It can be used effectively to engage administration in discussions of departmental planning and needs analysis.

Benchmark matrix and guide: Part II.

PubMed

1991-01-01

In the last issue of the Journal of Quality Assurance (September/October 1991, Volume 13, Number 5, pp. 14-19), the benchmark matrix developed by Headquarters Air Force Logistics Command was published. Five horizontal levels on the matrix delineate progress in TQM: business as usual, initiation, implementation, expansion, and integration. The six vertical categories that are critical to the success of TQM are leadership, structure, training, recognition, process improvement, and customer focus. In this issue, "Benchmark Matrix and Guide: Part II" will show specifically how to apply the categories of leadership, structure, and training to the benchmark matrix progress levels. At the intersection of each category and level, specific behavior objectives are listed with supporting behaviors and guidelines. Some categories will have objectives that are relatively easy to accomplish, allowing quick progress from one level to the next. Other categories will take considerable time and effort to complete. In the next issue, Part III of this series will focus on recognition, process improvement, and customer focus.

Dense fibrillar collagen is a potent inducer of invadopodia via a specific signaling network

PubMed Central

Swatkoski, Stephen; Matsumoto, Kazue; Campbell, Catherine B.; Petrie, Ryan J.; Dimitriadis, Emilios K.; Li, Xin; Mueller, Susette C.; Bugge, Thomas H.; Gucek, Marjan

2015-01-01

Cell interactions with the extracellular matrix (ECM) can regulate multiple cellular activities and the matrix itself in dynamic, bidirectional processes. One such process is local proteolytic modification of the ECM. Invadopodia of tumor cells are actin-rich proteolytic protrusions that locally degrade matrix molecules and mediate invasion. We report that a novel high-density fibrillar collagen (HDFC) matrix is a potent inducer of invadopodia, both in carcinoma cell lines and in primary human fibroblasts. In carcinoma cells, HDFC matrix induced formation of invadopodia via a specific integrin signaling pathway that did not require growth factors or even altered gene and protein expression. In contrast, phosphoproteomics identified major changes in a complex phosphosignaling network with kindlin2 serine phosphorylation as a key regulatory element. This kindlin2-dependent signal transduction network was required for efficient induction of invadopodia on dense fibrillar collagen and for local degradation of collagen. This novel phosphosignaling mechanism regulates cell surface invadopodia via kindlin2 for local proteolytic remodeling of the ECM. PMID:25646088

Near-optimal matrix recovery from random linear measurements.

PubMed

Romanov, Elad; Gavish, Matan

2018-06-25

In matrix recovery from random linear measurements, one is interested in recovering an unknown M-by-N matrix [Formula: see text] from [Formula: see text] measurements [Formula: see text], where each [Formula: see text] is an M-by-N measurement matrix with i.i.d. random entries, [Formula: see text] We present a matrix recovery algorithm, based on approximate message passing, which iteratively applies an optimal singular-value shrinker-a nonconvex nonlinearity tailored specifically for matrix estimation. Our algorithm typically converges exponentially fast, offering a significant speedup over previously suggested matrix recovery algorithms, such as iterative solvers for nuclear norm minimization (NNM). It is well known that there is a recovery tradeoff between the information content of the object [Formula: see text] to be recovered (specifically, its matrix rank r) and the number of linear measurements n from which recovery is to be attempted. The precise tradeoff between r and n, beyond which recovery by a given algorithm becomes possible, traces the so-called phase transition curve of that algorithm in the [Formula: see text] plane. The phase transition curve of our algorithm is noticeably better than that of NNM. Interestingly, it is close to the information-theoretic lower bound for the minimal number of measurements needed for matrix recovery, making it not only state of the art in terms of convergence rate, but also near optimal in terms of the matrices it successfully recovers. Copyright © 2018 the Author(s). Published by PNAS.

Matrix Training of Receptive Language Skills with a Toddler with Autism Spectrum Disorder: A Case Study

ERIC Educational Resources Information Center

Curiel, Emily S. L.; Sainato, Diane M.; Goldstein, Howard

2016-01-01

Matrix training is a systematic teaching approach that can facilitate generalized language. Specific responses are taught that result in the emergence of untrained responses. This type of training facilitates the use of generalized language in children with autism spectrum disorder (ASD). This study used a matrix training procedure with a toddler…

Non-localization and localization ROC analyses using clinically based scoring

NASA Astrophysics Data System (ADS)

Paquerault, Sophie; Samuelson, Frank W.; Myers, Kyle J.; Smith, Robert C.

2009-02-01

We are investigating the potential for differences in study conclusions when assessing the estimated impact of a computer-aided detection (CAD) system on readers' performance. The data utilized in this investigation were derived from a multi-reader multi-case observer study involving one hundred mammographic background images to which fixed-size and fixed-intensity Gaussian signals were added, generating a low- and high-intensity signal sets. The study setting allowed CAD assessment in two situations: when CAD sensitivity was 1) superior or 2) lower than the average reader. Seven readers were asked to review each set in the unaided and CAD-aided reading modes, mark and rate their findings. Using this data, we studied the effect on study conclusion of three clinically-based receiver operating characteristic (ROC) scoring definitions. These scoring definitions included both location-specific and non-location-specific rules. The results showed agreement in the estimated impact of CAD on the overall reader performance. In the study setting where CAD sensitivity is superior to the average reader, the mean difference in AUC between the CAD-aided read and unaided read was 0.049 (95%CIs: -0.027; 0.130) for the image scoring definition that is based on non-location-specific rules, and 0.104 (95%CIs: 0.036; 0.174) and 0.090 (95%CIs: 0.031; 0.155) for image scoring definitions that are based on location-specific rules. The increases in AUC were statistically significant for the location-specific scoring definitions. It was further observed that the variance on these estimates was reduced when using the location-specific scoring definitions compared to that using a non-location-specific scoring definition. In the study setting where CAD sensitivity is equivalent or lower than the average reader, the mean differences in AUC are slightly above 0.01 for all image scoring definitions. These increases in AUC were not statistical significant for any of the image scoring definitions. The results on the variance analysis differed from those observed in the other study setting. This investigation furthers our understanding of the relationships between non-localization-specific and localization-specific ROC assessment methodologies and their relevance to clinical practice.

Membranes having aligned 1-D nanoparticles in a matrix layer for improved fluid separation

DOEpatents

Revanur, Ravindra; Lulevich, Valentin; Roh, Il Juhn; Klare, Jennifer E.; Kim, Sangil; Noy, Aleksandr; Bakajin, Olgica

2015-12-22

Membranes for fluid separation are disclosed. These membranes have a matrix layer sandwiched between an active layer and a porous support layer. The matrix layer includes 1-D nanoparticles that are vertically aligned in a porous polymer matrix, and which substantially extend through the matrix layer. The active layer provides species-specific transport, while the support layer provides mechanical support. A matrix layer of this type has favorable surface morphology for forming the active layer. Furthermore, the pores that form in the matrix layer tend to be smaller and more evenly distributed as a result of the presence of aligned 1-D nanoparticles. Improved performance of separation membranes of this type is attributed to these effects.

Wound healing effects of collagen-laminin dermal matrix impregnated with resveratrol loaded hyaluronic acid-DPPC microparticles in diabetic rats.

PubMed

Gokce, Evren H; Tuncay Tanrıverdi, Sakine; Eroglu, Ipek; Tsapis, Nicolas; Gokce, Goksel; Tekmen, Isıl; Fattal, Elias; Ozer, Ozgen

2017-10-01

An alternative formulation for the treatment of diabetic foot wounds that heal slowly is a requirement in pharmaceutical field. The aim of this study was to develop a dermal matrix consisting of skin proteins and lipids with an antioxidant that will enhance healing and balance the oxidative stress in the diabetic wound area due to the high levels of glucose. Thus a novel three dimensional collagen-laminin porous dermal matrix was developed by lyophilization. Resveratrol-loaded hyaluronic acid and dipalmitoylphosphatidylcholine microparticles were combined with this dermal matrix. Characterization, in vitro release, microbiological and in vivo studies were performed. Spherical microparticles were obtained with a high RSV encapsulation efficacy. The microparticles were well dispersed in the dermal matrix from the surface to deeper layers. Collagenase degraded dermal matrix, however the addition of RSV loaded microparticles delayed the degradation time. The release of RSV was sustained and reached 70% after 6h. Histological changes and antioxidant parameters in different treatment groups were investigated in full-thickness excision diabetic rat model. Collagen fibers were intense and improved by the presence of formulation without any signs of inflammation. The highest healing score was obtained with the dermal matrix impregnated with RSV-microparticles with an increased antioxidant activity. Collagen-laminin dermal matrix with RSV microparticles was synergistically effective due to presence of skin components in the formulation and controlled release achieved. This combination is a safe and promising option for the treatment of diabetic wounds requiring long recovery. Copyright © 2017 Elsevier B.V. All rights reserved.

Prognostic value of biological markers in myocardial infarction patients.

PubMed

Berezin, Alexander E; Samura, Tatiana A

2013-04-01

The aim of this study was to compare the prognostic value of matrix metalloproteinase-3 and -9, and NT-pro-natriuretic peptide for fatal and nonfatal complications in Q-wave myocardial infarction patients in the acute and postinfarction periods. 85 men and women with documented Q-wave myocardial infarction were observed for 1 year after hospitalization. Clinical endpoints were identified through the hospital patient-tracking system, with a review of medical records for each recorded endpoint. Left ventricular ejection fraction and wall motion index were calculated. Measurements of matrix metalloproteinases and NT-pro-natriuretic peptide were performed by an enzyme-linked immunosorbent assay. A cutoff value of 9.7 ng·mL(-1) for matrix metalloproteinase-3 showed the best discriminatory power (sensitivity = 77.8%, specificity = 90.8%). The optimal cutoff value of matrix metalloproteinase-9 was 18.1 ng·mL(-1) (sensitivity, 70.5%; specificity, 75%), and the cutoff for NT-pro-natriuretic peptide was 885 pmol·L(-1) (sensitivity, 58%; specificity, 68.6%). Matrix metalloproteinase-3 and -9 were strongly related with a positive prognostic value of 70% (sensitivity and specificity, 84% and 82%, respectively). These data may be helpful for further stratification of patients into cardiovascular mortality risk groups.

The nuclear matrix protein NMP-1 is the transcription factor YY1.

PubMed Central

Guo, B; Odgren, P R; van Wijnen, A J; Last, T J; Nickerson, J; Penman, S; Lian, J B; Stein, J L; Stein, G S

1995-01-01

NMP-1 was initially identified as a nuclear matrix-associated DNA-binding factor that exhibits sequence-specific recognition for the site IV regulatory element of a histone H4 gene. This distal promoter domain is a nuclear matrix interaction site. In the present study, we show that NMP-1 is the multifunctional transcription factor YY1. Gel-shift and Western blot analyses demonstrate that NMP-1 is immunoreactive with YY1 antibody. Furthermore, purified YY1 protein specifically recognizes site IV and reconstitutes the NMP-1 complex. Western blot and gel-shift analyses indicate that YY1 is present within the nuclear matrix. In situ immunofluorescence studies show that a significant fraction of YY1 is localized in the nuclear matrix, principally but not exclusively associated with residual nucleoli. Our results confirm that NMP-1/YY1 is a ubiquitous protein that is present in both human cells and in rat osteosarcoma ROS 17/2.8 cells. The finding that NMP-1 is identical to YY1 suggests that this transcriptional regulator may mediate gene-matrix interactions. Our results are consistent with the concept that the nuclear matrix may functionally compartmentalize the eukaryotic nucleus to support regulation of gene expression. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:7479833

Chondroitin sulfates and their binding molecules in the central nervous system.

PubMed

Djerbal, L; Lortat-Jacob, H; Kwok, Jcf

2017-06-01

Chondroitin sulfate (CS) is the most abundant glycosaminoglycan (GAG) in the central nervous system (CNS) matrix. Its sulfation and epimerization patterns give rise to different forms of CS, which enables it to interact specifically and with a significant affinity with various signalling molecules in the matrix including growth factors, receptors and guidance molecules. These interactions control numerous biological and pathological processes, during development and in adulthood. In this review, we describe the specific interactions of different families of proteins involved in various physiological and cognitive mechanisms with CSs in CNS matrix. A better understanding of these interactions could promote a development of inhibitors to treat neurodegenerative diseases.

Meta-Analytic Structural Equation Modeling: A Two-Stage Approach

ERIC Educational Resources Information Center

Cheung, Mike W. L.; Chan, Wai

2005-01-01

To synthesize studies that use structural equation modeling (SEM), researchers usually use Pearson correlations (univariate r), Fisher z scores (univariate z), or generalized least squares (GLS) to combine the correlation matrices. The pooled correlation matrix is then analyzed by the use of SEM. Questionable inferences may occur for these ad hoc…

Data Stream Mining Based Dynamic Link Anomaly Analysis Using Paired Sliding Time Window Data

DTIC Science & Technology

2014-11-01

Conference on Knowledge Dis- covery and Data Mining, PAKDD’10, Hyderabad, India , (2010). [2] Almansoori, W., Gao, S., Jarada, T. N., Elsheikh, A. M...F., Greif, C., and Lakshmanan, L. V., “Fast Matrix Computations for Pairwise and Columnwise Commute Times and Katz Scores,” Internet Mathematics, Vol

VIC: A Computer Analysis of Verbal Interaction Category Systems.

ERIC Educational Resources Information Center

Kline, John A.; And Others

VIC is a computer program for the analysis of verbal interaction category systems, especially the Flanders interaction analysis system. The observer codes verbal behavior on coding sheets for later machine scoring. A matrix is produced by the program showing the number and percentages of times that a particular cell describes classroom behavior.…

MIXREG: a computer program for mixed-effects regression analysis with autocorrelated errors.

PubMed

Hedeker, D; Gibbons, R D

1996-05-01

MIXREG is a program that provides estimates for a mixed-effects regression model (MRM) for normally-distributed response data including autocorrelated errors. This model can be used for analysis of unbalanced longitudinal data, where individuals may be measured at a different number of timepoints, or even at different timepoints. Autocorrelated errors of a general form or following an AR(1), MA(1), or ARMA(1,1) form are allowable. This model can also be used for analysis of clustered data, where the mixed-effects model assumes data within clusters are dependent. The degree of dependency is estimated jointly with estimates of the usual model parameters, thus adjusting for clustering. MIXREG uses maximum marginal likelihood estimation, utilizing both the EM algorithm and a Fisher-scoring solution. For the scoring solution, the covariance matrix of the random effects is expressed in its Gaussian decomposition, and the diagonal matrix reparameterized using the exponential transformation. Estimation of the individual random effects is accomplished using an empirical Bayes approach. Examples illustrating usage and features of MIXREG are provided.

Rapid identification of pathogens directly from blood culture bottles by Bruker matrix-assisted laser desorption laser ionization-time of flight mass spectrometry versus routine methods.

PubMed

Jamal, Wafaa; Saleem, Rola; Rotimi, Vincent O

2013-08-01

The use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of microorganisms directly from blood culture is an exciting dimension to the microbiologists. We evaluated the performance of Bruker SepsiTyper kit™ (STK) for direct identification of bacteria from positive blood culture. This was done in parallel with conventional methods. Nonrepetitive positive blood cultures from 160 consecutive patients were prospectively evaluated by both methods. Of 160 positive blood cultures, the STK identified 114 (75.6%) isolates and routine conventional method 150 (93%). Thirty-six isolates were misidentified or not identified by the kit. Of these, 5 had score of >2.000 and 31 had an unreliable low score of <1.7. Four of 8 yeasts were identified correctly. The average turnaround time using the STK was 35 min, including extraction steps and 30:12 to 36:12 h with routine method. The STK holds promise for timely management of bacteremic patients. Copyright © 2013 Elsevier Inc. All rights reserved.

Matrix-directed differentiation of human adipose-derived mesenchymal stem cells to dermal-like fibroblasts that produce extracellular matrix.

PubMed

Sivan, Unnikrishnan; Jayakumar, K; Krishnan, Lissy K

2016-10-01

Commercially available skin substitutes lack essential non-immune cells for adequate tissue regeneration of non-healing wounds. A tissue-engineered, patient-specific, dermal substitute could be an attractive option for regenerating chronic wounds, for which adipose-derived mesenchymal stem cells (ADMSCs) could become an autologous source. However, ADMSCs are multipotent in nature and may differentiate into adipocytes, osteocytes and chondrocytes in vitro, and may develop into undesirable tissues upon transplantation. Therefore, ADMSCs committed to the fibroblast lineage could be a better option for in vitro or in vivo skin tissue engineering. The objective of this study was to standardize in vitro culture conditions for ADMSCs differentiation into dermal-like fibroblasts which can synthesize extracellular matrix (ECM) proteins. Biomimetic matrix composite, deposited on tissue culture polystyrene (TCPS), and differentiation medium (DM), supplemented with fibroblast-conditioned medium and growth factors, were used as a fibroblast-specific niche (FSN) for cell culture. For controls, ADMSCs were cultured on bare TCPS with either DM or basal medium (BM). Culture of ADMSCs on FSN upregulated the expression of differentiation markers such as fibroblast-specific protein-1 (FSP-1) and a panel of ECM molecules specific to the dermis, such as fibrillin-1, collagen I, collagen IV and elastin. Immunostaining showed the deposition of dermal-specific ECM, which was significantly higher in FSN compared to control. Fibroblasts derived from ADMSCs can synthesize elastin, which is an added advantage for successful skin tissue engineering as compared to fibroblasts from skin biopsy. To obtain rapid differentiation of ADMSCs to dermal-like fibroblasts for regenerative medicine, a matrix-directed differentiation strategy may be employed. Copyright © 2014 John Wiley & Sons, Ltd. Copyright © 2014 John Wiley & Sons, Ltd.

Child–Pugh Versus MELD Score for the Assessment of Prognosis in Liver Cirrhosis

PubMed Central

Peng, Ying; Qi, Xingshun; Guo, Xiaozhong

2016-01-01

Abstract Child–Pugh and MELD scores have been widely used for the assessment of prognosis in liver cirrhosis. A systematic review and meta-analysis aimed to compare the discriminative ability of Child–Pugh versus MELD score to assess the prognosis of cirrhotic patients. PubMed and EMBASE databases were searched. The statistical results were summarized from every individual study. The summary areas under receiver operating characteristic curves, sensitivities, specificities, positive and negative likelihood ratios, and diagnostic odds ratios were also calculated. Of the 1095 papers initially identified, 119 were eligible for the systematic review. Study population was heterogeneous among studies. They included 269 comparisons, of which 44 favored MELD score, 16 favored Child–Pugh score, 99 did not find any significant difference between them, and 110 did not report the statistical significance. Forty-two papers were further included in the meta-analysis. In patients with acute-on-chronic liver failure, Child–Pugh score had a higher sensitivity and a lower specificity than MELD score. In patients admitted to ICU, MELD score had a smaller negative likelihood ratio and a higher sensitivity than Child–Pugh score. In patients undergoing surgery, Child–Pugh score had a higher specificity than MELD score. In other subgroup analyses, Child–Pugh and MELD scores had statistically similar discriminative abilities or could not be compared due to the presence of significant diagnostic threshold effects. Although Child–Pugh and MELD scores had similar prognostic values in most of cases, their benefits might be heterogeneous in some specific conditions. The indications for Child–Pugh and MELD scores should be further identified. PMID:26937922

Transverse ductility of metal matrix composites

NASA Technical Reports Server (NTRS)

Gunawardena, S. R.; Jansson, S.; Leckie, F. A.

1991-01-01

The role of the fiber matrix interface bond on the transverse ductility of continuous fiber reinforced composites has been investigated. Two specific systems have been considered: an Aluminum alloy matrix reinforced by Alumina fibers, characterized by a strong interface and a Titanium alloy reinforced by coated Silicon Carbide fibers, characterized by a weak interface. A micro-mechanical study indicates that the bond condition has a significant effect on the state of stress in the matrix which in turn dictates the available matrix ductility. The micro-mechanical predictions are in good agreement with the experimental results for the two systems.

Emerging low-cost LED thermal management materials

NASA Astrophysics Data System (ADS)

Zweben, Carl H.

2004-10-01

As chip size and power levels continue to increase, thermal management, thermal stresses and cost have become key LED packaging issues. Until recently, low-coefficient-of-thermal-expansion (CTE) materials, which are needed to minimize thermal stresses, had thermal conductivities that are no better than those of aluminum alloys, about 200 W/m-K. Copper, which has a higher thermal conductivity (400 W/m-K), also has a high CTE, which can cause severe thermal stresses. We now have over a dozen low-CTE materials with thermal conductivities ranging between 400 and 1700 W/m-K, and almost a score with thermal conductivities at least 50% greater than that of aluminum. Some of these materials are low cost. Others have the potential to be low cost in high volume production. Emphasizing low cost, this paper reviews traditional packaging materials and the six categories of advanced materials: polymer matrix-, metal matrix-, ceramic matrix-, and carbon matrix composites; monolithic carbonaceous materials; and metal-metal composites/alloys. Topics include properties, status, applications, cost and likely future directions of new advanced materials, including carbon nanotubes and inexpensive graphite nanoplatelets.

Examining the validity of self-reports on scales measuring students' strategic processing.

PubMed

Samuelstuen, Marit S; Bråten, Ivar

2007-06-01

Self-report inventories trying to measure strategic processing at a global level have been much used in both basic and applied research. However, the validity of global strategy scores is open to question because such inventories assess strategy perceptions outside the context of specific task performance. The primary aim was to examine the criterion-related and construct validity of the global strategy data obtained with the Cross-Curricular Competencies (CCC) scale. Additionally, we wanted to compare the validity of these data with the validity of data obtained with a task-specific self-report inventory focusing on the same types of strategies. The sample included 269 10th-grade students from 12 different junior high schools. Global strategy use as assessed with the CCC was compared with task-specific strategy use reported in three different reading situations. Moreover, relationships between scores on the CCC and scores on measures of text comprehension were examined and compared with relationships between scores on the task-specific strategy measure and the same comprehension measures. The comparison between the CCC strategy scores and the task-specific strategy scores suggested only modest criterion-related validity for the data obtained with the global strategy inventory. The CCC strategy scores were also not related to the text comprehension measures, indicating poor construct validity. In contrast, the task-specific strategy scores were positively related to the comprehension measures, indicating good construct validity. Attempts to measure strategic processing at a global level seem to have limited validity and utility.

Shared dosimetry error in epidemiological dose-response analyses

DOE PAGES

Stram, Daniel O.; Preston, Dale L.; Sokolnikov, Mikhail; ...

2015-03-23

Radiation dose reconstruction systems for large-scale epidemiological studies are sophisticated both in providing estimates of dose and in representing dosimetry uncertainty. For example, a computer program was used by the Hanford Thyroid Disease Study to provide 100 realizations of possible dose to study participants. The variation in realizations reflected the range of possible dose for each cohort member consistent with the data on dose determinates in the cohort. Another example is the Mayak Worker Dosimetry System 2013 which estimates both external and internal exposures and provides multiple realizations of "possible" dose history to workers given dose determinants. This paper takesmore » up the problem of dealing with complex dosimetry systems that provide multiple realizations of dose in an epidemiologic analysis. In this paper we derive expected scores and the information matrix for a model used widely in radiation epidemiology, namely the linear excess relative risk (ERR) model that allows for a linear dose response (risk in relation to radiation) and distinguishes between modifiers of background rates and of the excess risk due to exposure. We show that treating the mean dose for each individual (calculated by averaging over the realizations) as if it was true dose (ignoring both shared and unshared dosimetry errors) gives asymptotically unbiased estimates (i.e. the score has expectation zero) and valid tests of the null hypothesis that the ERR slope β is zero. Although the score is unbiased the information matrix (and hence the standard errors of the estimate of β) is biased for β≠0 when ignoring errors in dose estimates, and we show how to adjust the information matrix to remove this bias, using the multiple realizations of dose. The use of these methods in the context of several studies including, the Mayak Worker Cohort, and the U.S. Atomic Veterans Study, is discussed.« less

Experimental Detection and Visualization of the Extracellular Matrix in Macrocolony Biofilms.

PubMed

Serra, Diego O; Hengge, Regine

2017-01-01

By adopting elaborate three-dimensional morphologies that vary according to their extracellular matrix composition, macrocolony biofilms offer a unique opportunity to interrogate about the roles of specific matrix components in shaping biofilm architecture. Here, we describe two methods optimized for Escherichia coli that profit from morphology and the high level of structural organization of macrocolonies to gain insight into the production and assembly of amyloid curli and cellulose-the two major biofilm matrix elements of E. coli-in biofilms. The first method, the macrocolony morphology assay, is based on the ability of curli and cellulose-either alone or in combination-to generate specific morphological and Congo Red-staining patterns in E. coli macrocolonies, which can then be used as a direct visual readout for the production of these matrix components. The second method involves thin sectioning of macrocolonies, which along with in situ staining of amyloid curli and cellulose and microscopic imaging allows gaining fine details of the spatial arrangement of both matrix elements inside macrocolonies. Beyond their current use with E. coli and related curli and cellulose-producing Enterobacteriaceae, both the methods offer the potential to be adapted to other bacterial species.

Magnostics: Image-Based Search of Interesting Matrix Views for Guided Network Exploration.

PubMed

Behrisch, Michael; Bach, Benjamin; Hund, Michael; Delz, Michael; Von Ruden, Laura; Fekete, Jean-Daniel; Schreck, Tobias

2017-01-01

In this work we address the problem of retrieving potentially interesting matrix views to support the exploration of networks. We introduce Matrix Diagnostics (or Magnostics), following in spirit related approaches for rating and ranking other visualization techniques, such as Scagnostics for scatter plots. Our approach ranks matrix views according to the appearance of specific visual patterns, such as blocks and lines, indicating the existence of topological motifs in the data, such as clusters, bi-graphs, or central nodes. Magnostics can be used to analyze, query, or search for visually similar matrices in large collections, or to assess the quality of matrix reordering algorithms. While many feature descriptors for image analyzes exist, there is no evidence how they perform for detecting patterns in matrices. In order to make an informed choice of feature descriptors for matrix diagnostics, we evaluate 30 feature descriptors-27 existing ones and three new descriptors that we designed specifically for MAGNOSTICS-with respect to four criteria: pattern response, pattern variability, pattern sensibility, and pattern discrimination. We conclude with an informed set of six descriptors as most appropriate for Magnostics and demonstrate their application in two scenarios; exploring a large collection of matrices and analyzing temporal networks.

How useful are Primary Trauma Care courses in sub-Saharan Africa?

PubMed

Nogaro, Marie-Caroline; Pandit, Hemant; Peter, Noel; Le, Grace; Oloruntoba, David; Muguti, Godfrey; Lavy, Christopher

2015-07-01

More than five million deaths occur each year from injury with the vast majority occurring in low and middle-income countries (LMICs). Africa bears the highest road traffic related mortality rates in the world. Despite this, formal training in trauma management is not widely adopted in these countries. We report our results of 10 consecutive Primary Trauma Care (PTC) courses delivered in seven East and Central African countries, as part of the COSECSA Oxford Orthopaedic Link (COOL) initiative. Candidate's knowledge and clinical confidence in trauma management were assessed using a multiple-choice questionnaire and a confidence matrix rating of eight clinical scenarios. We performed descriptive statistical analysis on knowledge and clinical confidence scores of candidates before and after the course. We sub-analysed these scores, examining specifically the difference that exist between gender, job-roles and instructors versus non-instructors. We have trained 345 new PTC providers and 99 new PTC instructors over the 10 courses. Data sets were complete for 322 candidates. Just under a third of candidates were women (n=94). Over two-thirds of candidates (n=240) were doctors, while the remainder comprised of nurses, medical students and clinical officers. Overall, the median pre-course MCQ score was 70% which increased to 87% post course (p<0.05). Men achieved a higher MCQ score both pre- and post-course compared to women (p<0.05); however there was no significant difference in the degree of improvement of MCQ scores between gender. Instructors outperform non-instructors (p<0.05), and similarly doctors outperform non-doctors on final MCQ scores (post-course). However, it was the non-doctors who showed a statistically significant improvement in scores before and after the course (20% non-doctors vs 16% doctors, p<0.05). Candidate's clinical confidence also demonstrated significant improvement following the course (p<0.05). Our work demonstrates that COOL-funded PTC courses in the COSECSA region delivered to front-line health staff have helped improve their knowledge and confidence in trauma management, irrespective of their job-roles and gender. Further follow-up is needed to establish the long-term impact of PTC courses in this region. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Randomised clinical trial: a phase 1, dose-ranging study of the anti-matrix metalloproteinase-9 monoclonal antibody GS-5745 versus placebo for ulcerative colitis.

PubMed

Sandborn, W J; Bhandari, B R; Fogel, R; Onken, J; Yen, E; Zhao, X; Jiang, Z; Ge, D; Xin, Y; Ye, Z; French, D; Silverman, J A; Kanwar, B; Subramanian, G M; McHutchison, J G; Lee, S D; Shackelton, L M; Pai, R K; Levesque, B G; Feagan, B G

2016-07-01

Matrix metalloproteinase-9 is a proteolytic enzyme whose expression is increased in ulcerative colitis. To evaluate the safety and efficacy of GS-5745, a fully humanised anti-matrix metalloproteinase-9 monoclonal antibody, in moderately-to-severely active ulcerative colitis. We randomised 74 patients with ulcerative colitis to treatment with single or multiple ascending intravenous or subcutaneous doses of GS-5745 or placebo. Multiple-dose cohorts received either IV infusions (0.3, 1.0, 2.5 or 5.0 mg/kg GS-5745 or placebo) every 2 weeks (three total IV infusions) or five weekly SC injections (150 mg GS-5745 or placebo). The primary outcomes were the safety, tolerability and pharmacokinetics of escalating single and multiple doses of GS-5745. Exploratory analyses in the multiple-dose cohorts included clinical response (≥3 points or 30% decrease from baseline in Mayo Clinic score and ≥1 point decrease in the rectal bleeding subscore or a rectal bleeding subscore ≤1) and clinical remission (a complete Mayo Clinic score ≤2 with no subscore >1) at Day 36. Biological effects associated with a clinical response to GS-5745 were explored using histological and molecular approaches. Twenty-three of the 42 patients (55%) receiving multiple doses of GS-5745 had adverse events, compared with 5/8 patients (63%) receiving placebo. GS-5745 showed target-mediated drug disposition, approximately dose-proportional increases in maximum plasma concentration and more than dose-proportional increases in the area under the plasma drug concentration-time curve. Clinical response occurred in 18/42 patients (43%) receiving GS-5745 compared with 1/8 patients (13%) receiving placebo. Clinical remission occurred in 6/42 patients (14%) receiving GS-5745 and 0/8 (0%) receiving placebo. Patients with a clinical response to GS-5745 had reductions in matrix metalloproteinase-9 tissue levels (mean 48.9% decrease from baseline compared with a mean 18.5% increase in nonresponders, P = 0.008) significant improvements in histopathology scores (confirmed with three separate histological disease activity indices), as well as changes in colonic gene expression that were consistent with reduced inflammation. This phase 1 trial provides preliminary evidence for the safety and therapeutic potential of GS-5745 in the treatment of ulcerative colitis. © 2016 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd.

Improving results for carotid artery stenting by validation of the anatomic scoring system for carotid artery stenting with patient-specific simulated rehearsal.

PubMed

Willaert, Willem I M; Cheshire, Nicholas J; Aggarwal, Rajesh; Van Herzeele, Isabelle; Stansby, Gerard; Macdonald, Sumaira; Vermassen, Frank E

2012-12-01

Carotid artery stenting (CAS) is a technically demanding procedure with a risk of periprocedural stroke. A scoring system based on anatomic criteria has been developed to facilitate patient selection for CAS. Advancements in simulation science also enable case evaluation through patient-specific virtual reality (VR) rehearsal on an endovascular simulator. This study aimed to validate the anatomic scoring system for CAS using the patient-specific VR technology. Three patients were selected and graded according to the CAS scoring system (maximum score, 9): one easy (score, <4.9), one intermediate (score, 5.0-5.9), and one difficult (score, >7.0). The three cases were performed on the simulator in random order by 20 novice interventionalists pretrained in CAS. Technical performances were assessed using simulator-based metrics and expert-based ratings. The interventionalists took significantly longer to perform the difficult CAS case (median, 31.6 vs 19.7 vs 14.6 minutes; P<.0001) compared with the intermediate and easy cases; similarly, more fluoroscopy time (20.7 vs 12.1 vs 8.2 minutes; P<.0001), contrast volume (56.5 vs 51.5 vs 50.0 mL; P=.0060), and roadmaps (10 vs 9 vs 9; P=.0040) were used. The quality of performance declined significantly as the cases became more challenging (score, 24 vs 22 vs 19; P<.0001). The anatomic scoring system for CAS can predict the difficulty of a CAS procedure as measured by patient-specific VR. This scoring system, with or without the additional use of patient-specific VR, can guide novice interventionalists in selecting appropriate patients for CAS. This may reduce the perioperative stroke risk and enhance patient safety. Copyright © 2012 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

[The diagnostic value of ultrasonic elastography and ultrasonography comprehensive score in cervical lesions].

PubMed

Lu, R; Xiao, Y

2017-07-18

Objective: To evaluate the clinical value of ultrasonic elastography and ultrasonography comprehensive scoring method in the diagnosis of cervical lesions. Methods: A total of 116 patients were selected from the Department of Gynecology of the first hospital affiliated with Central South University from March 2014 to September 2015.All of the lesions were preoperatively examined by Doppler Ultrasound and elastography.The elasticity score was determined by a 5-point scoring method. Calculation of the strain ratio was based on a comparison of the average strain measured in the lesion with the adjacent tissue of the same depth, size, and shape.All these ultrasonic parameters were quantified, added, and arrived at ultrasonography comprehensive scores.To use surgical pathology as the gold standard, the sensitivity, specificity, accuracy of Doppler Ultrasound, elasticity score and strain ratio methods and ultrasonography comprehensive scoring method were comparatively analyzed. Results: (1) The sensitivity, specificity, and accuracy of Doppler Ultrasound in diagnosing cervical lesions were 82.89% (63/76), 85.0% (34/40), and 83.62% (97/116), respectively.(2) The sensitivity, specificity, and accuracy of the elasticity score method were 77.63% (59/76), 82.5% (33/40), and 79.31% (92/116), respectively; the sensitivity, specificity, and accuracy of the strain ratio measure method were 84.21% (64/76), 87.5% (35/40), and 85.34% (99/116), respectively.(3) The sensitivity, specificity, and accuracy of ultrasonography comprehensive scoring method were 90.79% (69/76), 92.5% (37/40), and 91.38% (106/116), respectively. Conclusion: (1) It was obvious that ultrasonic elastography had certain diagnostic value in cervical lesions. Strain ratio measurement can be more objective than elasticity score method.(2) The combined application of ultrasonography comprehensive scoring method, ultrasonic elastography and conventional sonography was more accurate than single parameter.

Utility of the Spelling Sensitivity Score to Analyze Spellings of Children with Specific Language Impairment

ERIC Educational Resources Information Center

Werfel, Krystal L.; Krimm, Hannah

2015-01-01

The purpose of this study was to examine the utility of the Spelling Sensitivity Score (SSS) beyond percentage correct scoring in analyzing the spellings of children with specific language impairment (SLI). Participants were 31 children with SLI and 28 children with typical language in grades 2-4. Spellings of individual words were scored using…

Evaluation of the "e-rater"® Scoring Engine for the "GRE"® Issue and Argument Prompts. Research Report. ETS RR-12-02

ERIC Educational Resources Information Center

Ramineni, Chaitanya; Trapani, Catherine S.; Williamson, David M.; Davey, Tim; Bridgeman, Brent

2012-01-01

Automated scoring models for the "e-rater"® scoring engine were built and evaluated for the "GRE"® argument and issue-writing tasks. Prompt-specific, generic, and generic with prompt-specific intercept scoring models were built and evaluation statistics such as weighted kappas, Pearson correlations, standardized difference in…

Anti-Inflammatory Effects and Joint Protection in Collagen-Induced Arthritis after Treatment with IQ-1S, a Selective c-Jun N-Terminal Kinase Inhibitor

PubMed Central

Schepetkin, Igor A.; Kirpotina, Liliya N.; Hammaker, Deepa; Kochetkova, Irina; Khlebnikov, Andrei I.; Lyakhov, Sergey A.; Firestein, Gary S.

2015-01-01

c-Jun N-terminal kinases (JNKs) participate in many physiologic and pathologic processes, including inflammatory diseases. We recently synthesized the sodium salt of IQ-1S (11H-indeno[1,2-b]quinoxalin-11-one oxime) and demonstrated that it is a high-affinity JNK inhibitor and inhibits murine delayed-type hypersensitivity. Here we show that IQ-1S is highly specific for JNK and that its neutral form is the most abundant species at physiologic pH. Molecular docking of the IQ-1S syn isomer into the JNK1 binding site gave the best pose, which corresponded to the position of cocrystallized JNK inhibitor SP600125 (1,9-pyrazoloanthrone). Evaluation of the therapeutic potential of IQ-1S showed that it inhibited matrix metalloproteinase 1 and 3 gene expression induced by interleukin-1β in human fibroblast-like synoviocytes and significantly attenuated development of murine collagen-induced arthritis (CIA). Treatment with IQ-1S either before or after induction of CIA resulted in decreased clinical scores, and joint sections from IQ-1S–treated CIA mice exhibited only mild signs of inflammation and minimal cartilage loss compared with those from control mice. Collagen II–specific antibody responses were also reduced by IQ-1S treatment. By contrast, the inactive ketone derivative 11H-indeno[1,2-b]quinoxalin-11-one had no effect on CIA clinical scores or collagen II–specific antibody titers. IQ-1S treatment also suppressed proinflammatory cytokine and chemokine levels in joints and lymph node cells. Finally, treatment with IQ-1S increased the number of Foxp3+CD4+CD25+ regulatory T cells in lymph nodes. Thus, IQ-1S can reduce inflammation and cartilage loss associated with CIA and can serve as a small-molecule modulator for mechanistic studies of JNK function in rheumatoid arthritis. PMID:25784649

Anti-Inflammatory Effects and Joint Protection in Collagen-Induced Arthritis after Treatment with IQ-1S, a Selective c-Jun N-Terminal Kinase Inhibitor.

PubMed

Schepetkin, Igor A; Kirpotina, Liliya N; Hammaker, Deepa; Kochetkova, Irina; Khlebnikov, Andrei I; Lyakhov, Sergey A; Firestein, Gary S; Quinn, Mark T

2015-06-01

c-Jun N-terminal kinases (JNKs) participate in many physiologic and pathologic processes, including inflammatory diseases. We recently synthesized the sodium salt of IQ-1S (11H-indeno[1,2-b]quinoxalin-11-one oxime) and demonstrated that it is a high-affinity JNK inhibitor and inhibits murine delayed-type hypersensitivity. Here we show that IQ-1S is highly specific for JNK and that its neutral form is the most abundant species at physiologic pH. Molecular docking of the IQ-1S syn isomer into the JNK1 binding site gave the best pose, which corresponded to the position of cocrystallized JNK inhibitor SP600125 (1,9-pyrazoloanthrone). Evaluation of the therapeutic potential of IQ-1S showed that it inhibited matrix metalloproteinase 1 and 3 gene expression induced by interleukin-1β in human fibroblast-like synoviocytes and significantly attenuated development of murine collagen-induced arthritis (CIA). Treatment with IQ-1S either before or after induction of CIA resulted in decreased clinical scores, and joint sections from IQ-1S-treated CIA mice exhibited only mild signs of inflammation and minimal cartilage loss compared with those from control mice. Collagen II-specific antibody responses were also reduced by IQ-1S treatment. By contrast, the inactive ketone derivative 11H-indeno[1,2-b]quinoxalin-11-one had no effect on CIA clinical scores or collagen II-specific antibody titers. IQ-1S treatment also suppressed proinflammatory cytokine and chemokine levels in joints and lymph node cells. Finally, treatment with IQ-1S increased the number of Foxp3(+)CD4(+)CD25(+) regulatory T cells in lymph nodes. Thus, IQ-1S can reduce inflammation and cartilage loss associated with CIA and can serve as a small-molecule modulator for mechanistic studies of JNK function in rheumatoid arthritis. Copyright © 2015 by The American Society for Pharmacology and Experimental Therapeutics.

Ubiquitination of specific mitochondrial matrix proteins

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

Lehmann, Gilad; Ziv, Tamar; Braten, Ori

2016-06-17

Several protein quality control systems in bacteria and/or mitochondrial matrix from lower eukaryotes are absent in higher eukaryotes. These are transfer-messenger RNA (tmRNA), The N-end rule ATP-dependent protease ClpAP, and two more ATP-dependent proteases, HslUV and ClpXP (in yeast). The lost proteases resemble the 26S proteasome and the role of tmRNA and the N-end rule in eukaryotic cytosol is performed by the ubiquitin proteasome system (UPS). Therefore, we hypothesized that the UPS might have substituted these systems – at least partially – in the mitochondrial matrix of higher eukaryotes. Using three independent experimental approaches, we demonstrated the presence of ubiquitinatedmore » proteins in the matrix of isolated yeast mitochondria. First, we show that isolated mitochondria contain ubiquitin (Ub) conjugates, which remained intact after trypsin digestion. Second, we demonstrate that the mitochondrial soluble fraction contains Ub-conjugates, several of which were identified by mass spectrometry and are localized to the matrix. Third, using immunoaffinity enrichment by specific antibodies recognizing digested ubiquitinated peptides, we identified a group of Ub-modified matrix proteins. The modification was further substantiated by separation on SDS-PAGE and immunoblots. Last, we attempted to identify the ubiquitin ligase(s) involved, and identified Dma1p as a trypsin-resistant protein in our mitochondrial preparations. Taken together, these data suggest a yet undefined role for the UPS in regulation of the mitochondrial matrix proteins. -- Highlights: •Mitochondrial matrix contains ubiquitinated proteins. •Ubiquitination occurs most probably in the matrix. •Dma1p is a ubiquitin ligase present in mitochondrial preparations.« less

Q-mode versus R-mode principal component analysis for linear discriminant analysis (LDA)

NASA Astrophysics Data System (ADS)

Lee, Loong Chuen; Liong, Choong-Yeun; Jemain, Abdul Aziz

2017-05-01

Many literature apply Principal Component Analysis (PCA) as either preliminary visualization or variable con-struction methods or both. Focus of PCA can be on the samples (R-mode PCA) or variables (Q-mode PCA). Traditionally, R-mode PCA has been the usual approach to reduce high-dimensionality data before the application of Linear Discriminant Analysis (LDA), to solve classification problems. Output from PCA composed of two new matrices known as loadings and scores matrices. Each matrix can then be used to produce a plot, i.e. loadings plot aids identification of important variables whereas scores plot presents spatial distribution of samples on new axes that are also known as Principal Components (PCs). Fundamentally, the scores matrix always be the input variables for building classification model. A recent paper uses Q-mode PCA but the focus of analysis was not on the variables but instead on the samples. As a result, the authors have exchanged the use of both loadings and scores plots in which clustering of samples was studied using loadings plot whereas scores plot has been used to identify important manifest variables. Therefore, the aim of this study is to statistically validate the proposed practice. Evaluation is based on performance of external error obtained from LDA models according to number of PCs. On top of that, bootstrapping was also conducted to evaluate the external error of each of the LDA models. Results show that LDA models produced by PCs from R-mode PCA give logical performance and the matched external error are also unbiased whereas the ones produced with Q-mode PCA show the opposites. With that, we concluded that PCs produced from Q-mode is not statistically stable and thus should not be applied to problems of classifying samples, but variables. We hope this paper will provide some insights on the disputable issues.

The Functional Arm Scale for Throwers (FAST)-Part II: Reliability and Validity of an Upper Extremity Region-Specific and Population-Specific Patient-Reported Outcome Scale for Throwing Athletes.

PubMed

Huxel Bliven, Kellie C; Snyder Valier, Alison R; Bay, R Curtis; Sauers, Eric L

2017-04-01

The Functional Arm Scale for Throwers (FAST) is an upper extremity (UE) region-specific and population-specific patient-reported outcome (PRO) scale developed to measure health-related quality of life in throwers with UE injuries. Stages I and II, described in a companion paper, of FAST development produced a 22-item scale and a 9-item pitcher module. Stage III of scale development, establishing reliability and validity of the FAST, is reported herein. To describe stage III of scale development: reliability and validity of the FAST. Cohort study (diagnosis); Level of evidence, 2. Data from throwing athletes collected over 5 studies were pooled to assess reliability and validity of the FAST. Reliability was estimated using FAST scores from 162 throwing athletes who were injured (n = 23) and uninjured (n = 139). Concurrent validity was estimated using FAST scores and Disabilities of the Arm, Shoulder, and Hand (DASH) and Kerlan-Jobe Orthopaedic Clinic (KJOC) scores from 106 healthy, uninjured throwing athletes. Known-groups validity was estimated using FAST scores from 557 throwing athletes who were injured (n = 142) and uninjured (n = 415). Reliability and validity were assessed using intraclass correlation coefficients (ICCs), and measurement error was assessed using standard error of measurement (SEM) and minimum detectable change (MDC). Receiver operating characteristic curves and sensitivity/specificity values were estimated for known-groups validity. Data from a separate group (n = 18) of postsurgical and nonoperative/conservative rehabilitation patients were analyzed to report responsiveness of the FAST. The FAST total, subscales, and pitcher module scores demonstrated excellent test-retest reliability (ICC, 0.91-0.98). The SEM 95 and MDC 95 for the FAST total score were 3.8 and 10.5 points, respectively. The SEM 95 and MDC 95 for the pitcher module score were 5.7 and 15.7 points, respectively. The FAST scores showed acceptable correlation with DASH (ICC, 0.49-0.82) and KJOC (ICC, 0.62-0.81) scores. The FAST total score classified 85.1% of players into the correct injury group. For predicting UE injury status, a FAST total cutoff score of 10.0 out of 100.0 was 91% sensitive and 75% specific, and a pitcher module score of 10.0 out of 100.0 was 87% sensitive and 78% specific. The FAST total score demonstrated responsiveness on several indices between intake and discharge time points. The FAST is a reliable, valid, and responsive UE region-specific and population-specific PRO scale for measuring patient-reported health care outcomes in throwing athletes with injury.

The Functional Arm Scale for Throwers (FAST)—Part II: Reliability and Validity of an Upper Extremity Region-Specific and Population-Specific Patient-Reported Outcome Scale for Throwing Athletes

PubMed Central

Huxel Bliven, Kellie C.; Snyder Valier, Alison R.; Bay, R. Curtis; Sauers, Eric L.

2017-01-01

Background: The Functional Arm Scale for Throwers (FAST) is an upper extremity (UE) region-specific and population-specific patient-reported outcome (PRO) scale developed to measure health-related quality of life in throwers with UE injuries. Stages I and II, described in a companion paper, of FAST development produced a 22-item scale and a 9-item pitcher module. Stage III of scale development, establishing reliability and validity of the FAST, is reported herein. Purpose: To describe stage III of scale development: reliability and validity of the FAST. Study Design: Cohort study (diagnosis); Level of evidence, 2. Methods: Data from throwing athletes collected over 5 studies were pooled to assess reliability and validity of the FAST. Reliability was estimated using FAST scores from 162 throwing athletes who were injured (n = 23) and uninjured (n = 139). Concurrent validity was estimated using FAST scores and Disabilities of the Arm, Shoulder, and Hand (DASH) and Kerlan-Jobe Orthopaedic Clinic (KJOC) scores from 106 healthy, uninjured throwing athletes. Known-groups validity was estimated using FAST scores from 557 throwing athletes who were injured (n = 142) and uninjured (n = 415). Reliability and validity were assessed using intraclass correlation coefficients (ICCs), and measurement error was assessed using standard error of measurement (SEM) and minimum detectable change (MDC). Receiver operating characteristic curves and sensitivity/specificity values were estimated for known-groups validity. Data from a separate group (n = 18) of postsurgical and nonoperative/conservative rehabilitation patients were analyzed to report responsiveness of the FAST. Results: The FAST total, subscales, and pitcher module scores demonstrated excellent test-retest reliability (ICC, 0.91-0.98). The SEM95 and MDC95 for the FAST total score were 3.8 and 10.5 points, respectively. The SEM95 and MDC95 for the pitcher module score were 5.7 and 15.7 points, respectively. The FAST scores showed acceptable correlation with DASH (ICC, 0.49-0.82) and KJOC (ICC, 0.62-0.81) scores. The FAST total score classified 85.1% of players into the correct injury group. For predicting UE injury status, a FAST total cutoff score of 10.0 out of 100.0 was 91% sensitive and 75% specific, and a pitcher module score of 10.0 out of 100.0 was 87% sensitive and 78% specific. The FAST total score demonstrated responsiveness on several indices between intake and discharge time points. Conclusion: The FAST is a reliable, valid, and responsive UE region-specific and population-specific PRO scale for measuring patient-reported health care outcomes in throwing athletes with injury. PMID:28451614

Development of a rapid and simplified protocol for direct bacterial identification from positive blood cultures by using matrix assisted laser desorption ionization time-of- flight mass spectrometry.

PubMed

Jakovljev, Aleksandra; Bergh, Kåre

2015-11-06

Bloodstream infections represent serious conditions carrying a high mortality and morbidity rate. Rapid identification of microorganisms and prompt institution of adequate antimicrobial therapy is of utmost importance for a successful outcome. Aiming at the development of a rapid, simplified and efficient protocol, we developed and compared two in-house preparatory methods for the direct identification of bacteria from positive blood culture flasks (BD BACTEC FX system) by using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF MS). Both methods employed saponin and distilled water for erythrocyte lysis. In method A the cellular pellet was overlaid with formic acid on the MALDI TOF target plate for protein extraction, whereas in method B the pellet was exposed to formic acid followed by acetonitrile prior to placing on the target plate. Best results were obtained by method A. Direct identification was achieved for 81.9 % and 65.8 % (50.3 % and 26.2 % with scores >2.0) of organisms by method A and method B, respectively. Overall concordance with final identification was 100 % to genus and 97.9 % to species level. By applying a lower cut-off score value, the levels of identification obtained by method A and method B increased to 89.3 % and 77.8 % of organisms (81.9 % and 65.8 % identified with scores >1.7), respectively. Using the lowered score criteria, concordance with final results was obtained for 99.3 % of genus and 96.6 % of species identifications. The reliability of results, rapid performance (approximately 25 min) and applicability of in-house method A have contributed to implementation of this robust and cost-effective method in our laboratory.

Presynaptic neurones may contribute a unique glycoprotein to the extracellular matrix at the synapse

NASA Astrophysics Data System (ADS)

Caroni, Pico; Carlson, Steven S.; Schweitzer, Erik; Kelly, Regis B.

1985-04-01

As the extracellular matrix at the original site of a neuromuscular junction seems to play a major part in the specificity of synaptic regeneration1-5, considerable attention has been paid to unique molecules localized to this region6-11. Here we describe an extracellular matrix glycoprotein of the elasmobranch electric organ that is localized near the nerve endings. By immunological criteria, it is synthesized in the cell bodies, transported down the axons and is related to a glycoprotein in the synaptic vesicles of the neurones that innervate the electric organ. It is apparently specific for these neurones, as it cannot be detected elsewhere in the nervous system of the fish. Therefore, neurones seem to contribute unique extracellular matrix glycoproteins to the synaptic region. Synaptic vesicles could be involved in transporting these glycoproteins to or from the nerve terminal surface.

RAId_aPS: MS/MS Analysis with Multiple Scoring Functions and Spectrum-Specific Statistics

PubMed Central

Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

2010-01-01

Statistically meaningful comparison/combination of peptide identification results from various search methods is impeded by the lack of a universal statistical standard. Providing an -value calibration protocol, we demonstrated earlier the feasibility of translating either the score or heuristic -value reported by any method into the textbook-defined -value, which may serve as the universal statistical standard. This protocol, although robust, may lose spectrum-specific statistics and might require a new calibration when changes in experimental setup occur. To mitigate these issues, we developed a new MS/MS search tool, RAId_aPS, that is able to provide spectrum-specific -values for additive scoring functions. Given a selection of scoring functions out of RAId score, K-score, Hyperscore and XCorr, RAId_aPS generates the corresponding score histograms of all possible peptides using dynamic programming. Using these score histograms to assign -values enables a calibration-free protocol for accurate significance assignment for each scoring function. RAId_aPS features four different modes: (i) compute the total number of possible peptides for a given molecular mass range, (ii) generate the score histogram given a MS/MS spectrum and a scoring function, (iii) reassign -values for a list of candidate peptides given a MS/MS spectrum and the scoring functions chosen, and (iv) perform database searches using selected scoring functions. In modes (iii) and (iv), RAId_aPS is also capable of combining results from different scoring functions using spectrum-specific statistics. The web link is http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html. Relevant binaries for Linux, Windows, and Mac OS X are available from the same page. PMID:21103371

Holistic rubric vs. analytic rubric for measuring clinical performance levels in medical students.

PubMed

Yune, So Jung; Lee, Sang Yeoup; Im, Sun Ju; Kam, Bee Sung; Baek, Sun Yong

2018-06-05

Task-specific checklists, holistic rubrics, and analytic rubrics are often used for performance assessments. We examined what factors evaluators consider important in holistic scoring of clinical performance assessment, and compared the usefulness of applying holistic and analytic rubrics respectively, and analytic rubrics in addition to task-specific checklists based on traditional standards. We compared the usefulness of a holistic rubric versus an analytic rubric in effectively measuring the clinical skill performances of 126 third-year medical students who participated in a clinical performance assessment conducted by Pusan National University School of Medicine. We conducted a questionnaire survey of 37 evaluators who used all three evaluation methods-holistic rubric, analytic rubric, and task-specific checklist-for each student. The relationship between the scores on the three evaluation methods was analyzed using Pearson's correlation. Inter-rater agreement was analyzed by Kappa index. The effect of holistic and analytic rubric scores on the task-specific checklist score was analyzed using multiple regression analysis. Evaluators perceived accuracy and proficiency to be major factors in objective structured clinical examinations evaluation, and history taking and physical examination to be major factors in clinical performance examinations evaluation. Holistic rubric scores were highly related to the scores of the task-specific checklist and analytic rubric. Relatively low agreement was found in clinical performance examinations compared to objective structured clinical examinations. Meanwhile, the holistic and analytic rubric scores explained 59.1% of the task-specific checklist score in objective structured clinical examinations and 51.6% in clinical performance examinations. The results show the usefulness of holistic and analytic rubrics in clinical performance assessment, which can be used in conjunction with task-specific checklists for more efficient evaluation.

Development of a Valid and Reliable Knee Articular Cartilage Condition-Specific Study Methodological Quality Score.

PubMed

Harris, Joshua D; Erickson, Brandon J; Cvetanovich, Gregory L; Abrams, Geoffrey D; McCormick, Frank M; Gupta, Anil K; Verma, Nikhil N; Bach, Bernard R; Cole, Brian J

2014-02-01

Condition-specific questionnaires are important components in evaluation of outcomes of surgical interventions. No condition-specific study methodological quality questionnaire exists for evaluation of outcomes of articular cartilage surgery in the knee. To develop a reliable and valid knee articular cartilage-specific study methodological quality questionnaire. Cross-sectional study. A stepwise, a priori-designed framework was created for development of a novel questionnaire. Relevant items to the topic were identified and extracted from a recent systematic review of 194 investigations of knee articular cartilage surgery. In addition, relevant items from existing generic study methodological quality questionnaires were identified. Items for a preliminary questionnaire were generated. Redundant and irrelevant items were eliminated, and acceptable items modified. The instrument was pretested and items weighed. The instrument, the MARK score (Methodological quality of ARticular cartilage studies of the Knee), was tested for validity (criterion validity) and reliability (inter- and intraobserver). A 19-item, 3-domain MARK score was developed. The 100-point scale score demonstrated face validity (focus group of 8 orthopaedic surgeons) and criterion validity (strong correlation to Cochrane Quality Assessment score and Modified Coleman Methodology Score). Interobserver reliability for the overall score was good (intraclass correlation coefficient [ICC], 0.842), and for all individual items of the MARK score, acceptable to perfect (ICC, 0.70-1.000). Intraobserver reliability ICC assessed over a 3-week interval was strong for 2 reviewers (≥0.90). The MARK score is a valid and reliable knee articular cartilage condition-specific study methodological quality instrument. This condition-specific questionnaire may be used to evaluate the quality of studies reporting outcomes of articular cartilage surgery in the knee.

Magnetic resonance index of activity (MaRIA) and Clermont score are highly and equally effective MRI indices in detecting mucosal healing in Crohn's disease.

PubMed

Buisson, Anthony; Pereira, Bruno; Goutte, Marion; Reymond, Maud; Allimant, Christophe; Obritin-Guilhen, Hélène; Bommelaer, Gilles; Hordonneau, Constance

2017-11-01

Magnetic resonance index of activity (MaRIA) and Clermont score are currently the two main MRI indices that have been validated compared to endoscopy in Crohn's disease (CD). To compare the accuracy of MaRIA and Clermont score in assessing CD mucosal healing. Fourty-four CD patients underwent prospectively and consecutively MRI and colonoscopy. Considering 207 segments, MaRIA>7 and Clermont score>8.4 demonstrated substantial accuracy to detect endoscopic ulcerations (73.9% and 74.0%, respectively) and presented with high specificity (82.1% and 81.3%) and high negative predictive value (NPV) (82.1% and 82.4%) for MaRIA and Clermont score, respectively. The sensitivity for detecting deep ulcerations was 90.9% for both MaRIA>11 and Clermont score>12.5, with a specificity of 82.0% and 80.0%, respectively. Among 44 patients, deep MRI remission predicted mucosal healing with specificity=85.3% and NPV=85.3% according to Barcelona criteria (no segmental MaRIA>7), and specificity=88.2% and NPV=85.7% according to Clermont criteria (no segmental Clermont score>8.4). In addition, MRI remission predicted mucosal healing with specificity=76.5% and NPV=86.7% according to Barcelona criteria (no segmental MaRIA>11), and specificity=79.4% and NPV=84.4% according to Clermont criteria (no segmental Clermont score>12.5). MaRIA and Clermont score are equally effective in detecting CD endoscopic ulcerations supporting their use as therapeutic endpoints. Copyright © 2017 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

Defining the "proven technology" technical criterion in the reactor technology assessment for Malaysia's nuclear power program

NASA Astrophysics Data System (ADS)

Anuar, Nuraslinda; Kahar, Wan Shakirah Wan Abdul; Manan, Jamal Abdul Nasir Abd

2015-04-01

Developing countries that are considering the deployment of nuclear power plants (NPPs) in the near future need to perform reactor technology assessment (RTA) in order to select the most suitable reactor design. The International Atomic Energy Agency (IAEA) reported in the Common User Considerations (CUC) document that "proven technology" is one of the most important technical criteria for newcomer countries in performing the RTA. The qualitative description of five desired features for "proven technology" is relatively broad and only provides a general guideline to its characterization. This paper proposes a methodology to define the "proven technology" term according to a specific country's requirements using a three-stage evaluation process. The first evaluation stage screens the available technologies in the market against a predefined minimum Technology Readiness Level (TRL) derived as a condition based on national needs and policy objectives. The result is a list of technology options, which are then assessed in the second evaluation stage against quantitative definitions of CUC desired features for proven technology. The potential technology candidates produced from this evaluation is further narrowed down to obtain a list of proven technology candidates by assessing them against selected risk criteria and the established maximum allowable total score using a scoring matrix. The outcome of this methodology is the proven technology candidates selected using an accurate definition of "proven technology" that fulfills the policy objectives, national needs and risk, and country-specific CUC desired features of the country that performs this assessment. A simplified assessment for Malaysia is carried out to demonstrate and suggest the use of the proposed methodology. In this exercise, ABWR, AP1000, APR1400 and EPR designs assumed the top-ranks of proven technology candidates according to Malaysia's definition of "proven technology".

Peroxisome proliferator-activated receptor δ promotes the progression of posttraumatic osteoarthritis in a mouse model.

PubMed

Ratneswaran, A; LeBlanc, E A; Walser, E; Welch, I; Mort, J S; Borradaile, N; Beier, F

2015-02-01

Osteoarthritis (OA) is a serious disease of the entire joint, characterized by articular cartilage degeneration, subchondral bone changes, osteophyte formation, and synovial hyperplasia. Currently, there are no pharmaceutical treatments that can slow the disease progression, resulting in greatly reduced quality of life for patients and the need for joint replacement surgeries in many cases. The lack of available treatments for OA is partly due to our incomplete understanding of the molecular mechanisms that promote disease initiation and progression. The purpose of the present study was to examine the role of the nuclear receptor peroxisome proliferator-activated receptor δ (PPARδ) as a promoter of cartilage degeneration in a mouse model of posttraumatic OA. Mouse chondrocytes and knee explants were treated with a pharmacologic agonist of PPARδ (GW501516) to evaluate changes in gene expression, histologic features, and matrix glycosaminoglycan breakdown. In vivo, PPARδ was specifically deleted from the cartilage of mice. Histopathologic scoring according to the Osteoarthritis Research Society International (OARSI) system and immunohistochemical analysis were used to compare mutant and control mice subjected to surgical destabilization of the medial meniscus (DMM). In vitro, PPARδ activation by GW501516 resulted in increased expression of several proteases in chondrocytes, as well as aggrecan degradation and glycosaminoglycan release in knee joint explants. In vivo, cartilage-specific PPARδ-knockout mice did not display any abnormalities of skeletal development but showed marked protection in the DMM model of posttraumatic OA (as compared to control littermates). OARSI scoring and immunohistochemical analyses confirmed strong protection of mutant mice from DMM-induced cartilage degeneration. These data demonstrate a catabolic role of endogenous PPARδ in posttraumatic OA and suggest that pharmacologic inhibition of PPARδ is a promising therapeutic strategy. Copyright © 2015 by the American College of Rheumatology.

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

Anuar, Nuraslinda, E-mail: nuraslinda@uniten.edu.my; Kahar, Wan Shakirah Wan Abdul, E-mail: shakirah@tnb.com.my; Manan, Jamal Abdul Nasir Abd

Developing countries that are considering the deployment of nuclear power plants (NPPs) in the near future need to perform reactor technology assessment (RTA) in order to select the most suitable reactor design. The International Atomic Energy Agency (IAEA) reported in the Common User Considerations (CUC) document that “proven technology” is one of the most important technical criteria for newcomer countries in performing the RTA. The qualitative description of five desired features for “proven technology” is relatively broad and only provides a general guideline to its characterization. This paper proposes a methodology to define the “proven technology” term according to amore » specific country’s requirements using a three-stage evaluation process. The first evaluation stage screens the available technologies in the market against a predefined minimum Technology Readiness Level (TRL) derived as a condition based on national needs and policy objectives. The result is a list of technology options, which are then assessed in the second evaluation stage against quantitative definitions of CUC desired features for proven technology. The potential technology candidates produced from this evaluation is further narrowed down to obtain a list of proven technology candidates by assessing them against selected risk criteria and the established maximum allowable total score using a scoring matrix. The outcome of this methodology is the proven technology candidates selected using an accurate definition of “proven technology” that fulfills the policy objectives, national needs and risk, and country-specific CUC desired features of the country that performs this assessment. A simplified assessment for Malaysia is carried out to demonstrate and suggest the use of the proposed methodology. In this exercise, ABWR, AP1000, APR1400 and EPR designs assumed the top-ranks of proven technology candidates according to Malaysia’s definition of “proven technology”.« less

Mapping of polycrystalline films of biological fluids utilizing the Jones-matrix formalism

NASA Astrophysics Data System (ADS)

Ushenko, Vladimir A.; Dubolazov, Alexander V.; Pidkamin, Leonid Y.; Sakchnovsky, Michael Yu; Bodnar, Anna B.; Ushenko, Yuriy A.; Ushenko, Alexander G.; Bykov, Alexander; Meglinski, Igor

2018-02-01

Utilizing a polarized light approach, we reconstruct the spatial distribution of birefringence and optical activity in polycrystalline films of biological fluids. The Jones-matrix formalism is used for an accessible quantitative description of these types of optical anisotropy. We demonstrate that differentiation of polycrystalline films of biological fluids can be performed based on a statistical analysis of the distribution of rotation angles and phase shifts associated with the optical activity and birefringence, respectively. Finally, practical operational characteristics, such as sensitivity, specificity and accuracy of the Jones-matrix reconstruction of optical anisotropy, were identified with special emphasis on biomedical application, specifically for differentiation of bile films taken from healthy donors and from patients with cholelithiasis.

Detection of Protein Complexes Based on Penalized Matrix Decomposition in a Sparse Protein⁻Protein Interaction Network.

PubMed

Cao, Buwen; Deng, Shuguang; Qin, Hua; Ding, Pingjian; Chen, Shaopeng; Li, Guanghui

2018-06-15

High-throughput technology has generated large-scale protein interaction data, which is crucial in our understanding of biological organisms. Many complex identification algorithms have been developed to determine protein complexes. However, these methods are only suitable for dense protein interaction networks, because their capabilities decrease rapidly when applied to sparse protein⁻protein interaction (PPI) networks. In this study, based on penalized matrix decomposition ( PMD ), a novel method of penalized matrix decomposition for the identification of protein complexes (i.e., PMD pc ) was developed to detect protein complexes in the human protein interaction network. This method mainly consists of three steps. First, the adjacent matrix of the protein interaction network is normalized. Second, the normalized matrix is decomposed into three factor matrices. The PMD pc method can detect protein complexes in sparse PPI networks by imposing appropriate constraints on factor matrices. Finally, the results of our method are compared with those of other methods in human PPI network. Experimental results show that our method can not only outperform classical algorithms, such as CFinder, ClusterONE, RRW, HC-PIN, and PCE-FR, but can also achieve an ideal overall performance in terms of a composite score consisting of F-measure, accuracy (ACC), and the maximum matching ratio (MMR).

Cryogenic regenerator including sarancarbon heat conduction matrix

NASA Technical Reports Server (NTRS)

Jones, Jack A. (Inventor); Petrick, S. Walter (Inventor); Britcliffe, Michael J. (Inventor)

1989-01-01

A saran carbon matrix is employed to conduct heat through the heat storing volume of a cryogenic regenerator. When helium is adsorbed into the saran carbon matrix, the combination exhibits a volumetric specific heat much higher than previously used lead balls. A helium adsorbed saran regenerator should allow much lower refrigerator temperatures than those practically obtainable with lead based regenerators for regenerator type refrigeration systems.

Bioengineered anterior cruciate ligament

NASA Technical Reports Server (NTRS)

Martin, Ivan (Inventor); Altman, Gregory (Inventor); Kaplan, David (Inventor); Vunjak-Novakovic, Gordana (Inventor)

2001-01-01

The present invention provides a method for producing an anterior cruciate ligament ex vivo. The method comprises seeding pluripotent stem cells in a three dimensional matrix, anchoring the seeded matrix by attachment to two anchors, and culturing the cells within the matrix under conditions appropriate for cell growth and regeneration, while subjecting the matrix to one or more mechanical forces via movement of one or both of the attached anchors. Bone marrow stromal cells are preferably used as the pluripotent cells in the method. Suitable matrix materials are materials to which cells can adhere, such as a gel made from collagen type I. Suitable anchor materials are materials to which the matrix can attach, such as Goinopra coral and also demineralized bone. Optimally, the mechanical forces to which the matrix is subjected mimic mechanical stimuli experienced by an anterior cruciate ligament in vivo. This is accomplished by delivering the appropriate combination of tension, compression, torsion, and shear, to the matrix. The bioengineered ligament which is produced by this method is characterized by a cellular orientation and/or matrix crimp pattern in the direction of the applied mechanical forces, and also by the production of collagen type I, collagen type III, and fibronectin proteins along the axis of mechanical load produced by the mechanical forces. Optimally, the ligament produced has fiber bundles which are arranged into a helical organization. The method for producing an anterior cruciate ligament can be adapted to produce a wide range of tissue types ex vivo by adapting the anchor size and attachment sites to reflect the size of the specific type of tissue to be produced, and also adapting the specific combination of forces applied, to mimic the mechanical stimuli experienced in vivo by the specific type of tissue to be produced. The methods of the present invention can be further modified to incorporate other stimuli experienced in vivo by the particular developing tissue, some examples of the stimuli being chemical stimuli, and electro-magnetic stimuli. Some examples of tissue which can be produced include other ligaments in the body (hand, wrist, elbow, knee), tendon, cartilage, bone, muscle, and blood vessels.

Data Collection Design for Equivalent Groups Equating: Using a Matrix Stratification Framework for Mixed-Format Assessment

ERIC Educational Resources Information Center

Mbella, Kinge Keka

2012-01-01

Mixed-format assessments are increasingly being used in large scale standardized assessments to measure a continuum of skills ranging from basic recall to higher order thinking skills. These assessments are usually comprised of a combination of (a) multiple-choice items which can be efficiently scored, have stable psychometric properties, and…

A Multitrait-Multimethod Examination of the Reynolds Intellectual Assessment Scales in a College Sample

ERIC Educational Resources Information Center

Beaujean, A. Alexander; Firmin, Michael W.; Michonski, Jared D.; Berry, Theodore; Johnson, Courtney

2010-01-01

This study assessed trait validity of the Reynolds Intellectual Assessment Scales' (RIAS) Verbal Index (VIX) and Nonverbal Index (NIX) scores in a group of college students. Using both observation of patterns and latent variable modeling of a multitrait-multimethod correlation/covariance matrix, the results indicate that the RIAS VIX scores…

Family Reintegration Experiences of Soldiers with Mild Traumatic Brain Injury

DTIC Science & Technology

2014-02-26

depression scores in the spouse. Weak within-couple correlation were indicated on the other measures. Table 3 presents the Spearman correlation matrix...separately. Table 2: Spearman Correlation Coefficients for Couples Spouse MAT Spouse Depression Spouse...Anxiety Soldier MAT -0.06 Soldier Depression -0.61 Soldier Anxiety -0.12 Table 3: Spearman Correlation Coefficients for Soldiers and

Matrix-specific protein kinase A signaling regulates p21 activated kinase activation by flow in endothelial cells

PubMed Central

Funk, Steven Daniel; Yurdagul, Arif; Green, Jonette M.; Jhaveri, Krishna A.; Schwartz, Martin Alexander; Orr, A. Wayne

2010-01-01

Rationale Atherosclerosis is initiated by blood flow patterns that activate inflammatory pathways in endothelial cells. Activation of inflammatory signaling by fluid shear stress is highly dependent on the composition of the subendothelial extracellular matrix. The basement membrane proteins laminin and collagen found in normal vessels suppress flow-induced p21 activated kinase (PAK) and NF-κB activation. By contrast, the provisional matrix proteins fibronectin and fibrinogen found in wounded or inflamed vessels support flow-induced PAK and NF-κB activation. PAK mediates both flow-induced permeability and matrix-specific activation of NF-κB. Objective To elucidate the mechanisms regulating matrix-specific PAK activation. Methods and Results We now show that matrix composition does not affect the upstream pathway by which flow activates PAK (integrin activation, Rac). Instead basement membrane proteins enhance flow-induced protein kinase A (PKA) activation, which suppresses PAK. Inhibiting PKA restored flow-induced PAK and NF-κB activation in cells on basement membrane proteins, whereas stimulating PKA inhibited flow-induced activation of inflammatory signaling in cells on fibronectin. PKA suppressed inflammatory signaling through PAK inhibition. Activating PKA by injection of the PGI2 analog iloprost reduced PAK activation and inflammatory gene expression at sites of disturbed flow in vivo, whereas inhibiting PKA by PKI injection enhanced PAK activation and inflammatory gene expression. Inhibiting PAK prevented the enhancement of inflammatory gene expression by PKI. Conclusions Basement membrane proteins inhibit inflammatory signaling in endothelial cells via PKA-dependent inhibition of PAK. PMID:20224042

Simultaneous Detection of Metalloprotease Activities in Complex Biological Samples Using the PrAMA (Proteolytic Activity Matrix Assay) Method.

PubMed

Conrad, Catharina; Miller, Miles A; Bartsch, Jörg W; Schlomann, Uwe; Lauffenburger, Douglas A

2017-01-01

Proteolytic Activity Matrix Analysis (PrAMA) is a method for simultaneously determining the activities of specific Matrix Metalloproteinases (MMPs) and A Disintegrin and Metalloproteinases (ADAMs) in complex biological samples. In mixtures of unknown proteases, PrAMA infers selective metalloproteinase activities by using a panel of moderately specific FRET-based polypeptide protease substrates in parallel, typically monitored by a plate-reader in a 96-well format. Fluorescence measurements are then quantitatively compared to a standard table of catalytic efficiencies measured from purified mixtures of individual metalloproteinases and FRET substrates. Computational inference of specific activities is performed with an easily used Matlab program, which is provided herein. Thus, we describe PrAMA as a combined experimental and mathematical approach to determine real-time metalloproteinase activities, which has previously been applied to live-cell cultures, cellular lysates, cell culture supernatants, and body fluids from patients.

Sensitivity and Specificity of the Coma Recovery Scale--Revised Total Score in Detection of Conscious Awareness.

PubMed

Bodien, Yelena G; Carlowicz, Cecilia A; Chatelle, Camille; Giacino, Joseph T

2016-03-01

To describe the sensitivity and specificity of Coma Recovery Scale-Revised (CRS-R) total scores in detecting conscious awareness. Data were retrospectively extracted from the medical records of patients enrolled in a specialized disorders of consciousness (DOC) program. Sensitivity and specificity analyses were completed using CRS-R-derived diagnoses of minimally conscious state (MCS) or emerged from minimally conscious state (EMCS) as the reference standard for conscious awareness and the total CRS-R score as the test criterion. A receiver operating characteristic curve was constructed to demonstrate the optimal CRS-R total cutoff score for maximizing sensitivity and specificity. Specialized DOC program. Patients enrolled in the DOC program (N=252, 157 men; mean age, 49y; mean time from injury, 48d; traumatic etiology, n=127; nontraumatic etiology, n=125; diagnosis of coma or vegetative state, n=70; diagnosis of MCS or EMCS, n=182). Not applicable. Sensitivity and specificity of CRS-R total scores in detecting conscious awareness. A CRS-R total score of 10 or higher yielded a sensitivity of .78 for correct identification of patients in MCS or EMCS, and a specificity of 1.00 for correct identification of patients who did not meet criteria for either of these diagnoses (ie, were diagnosed with vegetative state or coma). The area under the curve in the receiver operating characteristic curve analysis is .98. A total CRS-R score of 10 or higher provides strong evidence of conscious awareness but resulted in a false-negative diagnostic error in 22% of patients who demonstrated conscious awareness based on CRS-R diagnostic criteria. A cutoff score of 8 provides the best balance between sensitivity and specificity, accurately classifying 93% of cases. The optimal total score cutoff will vary depending on the user's objective. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens.

PubMed

Panni, Simona; Montecchi-Palazzi, Luisa; Kiemer, Lars; Cabibbo, Andrea; Paoluzi, Serena; Santonico, Elena; Landgraf, Christiane; Volkmer-Engert, Rudolf; Bachi, Angela; Castagnoli, Luisa; Cesareni, Gianni

2011-01-01

Large-scale interaction studies contribute the largest fraction of protein interactions information in databases. However, co-purification of non-specific or indirect ligands, often results in data sets that are affected by a considerable number of false positives. For the fraction of interactions mediated by short linear peptides, we present here a combined experimental and computational strategy for ranking the reliability of the inferred partners. We apply this strategy to the family of 14-3-3 domains. We have first characterized the recognition specificity of this domain family, largely confirming the results of previous analyses, while revealing new features of the preferred sequence context of 14-3-3 phospho-peptide partners. Notably, a proline next to the carboxy side of the phospho-amino acid functions as a potent inhibitor of 14-3-3 binding. The position-specific information about residue preference was encoded in a scoring matrix and two regular expressions. The integration of these three features in a single predictive model outperforms publicly available prediction tools. Next we have combined, by a naïve Bayesian approach, these "peptide features" with "protein features", such as protein co-expression and co-localization. Our approach provides an orthogonal reliability assessment and maps with high confidence the 14-3-3 peptide target on the partner proteins. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Screening for cognitive dysfunction in ALS: validation of the Edinburgh Cognitive and Behavioural ALS Screen (ECAS) using age and education adjusted normative data.

PubMed

Pinto-Grau, Marta; Burke, Tom; Lonergan, Katie; McHugh, Caroline; Mays, Iain; Madden, Caoifa; Vajda, Alice; Heverin, Mark; Elamin, Marwa; Hardiman, Orla; Pender, Niall

2017-02-01

Cognitive and behavioural changes are an important aspect in Amyotrophic Lateral Sclerosis (ALS). The Edinburgh Cognitive and Behavioural ALS Screen (ECAS) briefly assesses these changes in ALS. To validate the ECAS against a standardised neuropsychological battery and assess its sensitivity and specificity using age and education adjusted cut-off scores. 30 incident ALS cases were assessed on both, ECAS and neuropsychological battery. Age and education adjusted cut-off scores were created from a sample of 82 healthy controls. ECAS composite scores (Total, ALS Specific and Non-Specific) were highly correlated with battery composite scores. High correlations were also observed between ECAS and full battery cognitive domains and subtests. The ECAS Total, ALS Specific and Non-Specific scores were highly sensitive to cognitive impairment. ECAS ALS-Specific cognitive domains also evidenced high sensitivity. Individual subtest sensitivity was medium to low, suggesting that caution should be used when interpreting these scores. Low positive predictive values indicated the presence of false positives. Psychometric properties of the ECAS using age and education adjusted norms indicate that the ECAS, when used as an overall measure of cognitive decline, is highly sensitive. Further comprehensive assessment is required for patients that present as impaired on the ECAS.

Score Matrix for HWBI Forecast Model

EPA Pesticide Factsheets

2000-2010 Annual State-Scale Service and Domain scores used to support the approach for forecasting EPA's Human Well-Being Index. A modeling approach was developed based relationship function equations derived from select economic, social and ecosystem final goods and service scores and calculated human well-being index and related domain scores. These data are being used in a secondary capacity. The foundational data and scoring techniques were originally described in: a) U.S. EPA. 2012. Indicators and Methods for Constructing a U.S. Human Well-being Index (HWBI) for Ecosystem Services Research. Report. EPA/600/R-12/023. pp. 121; and b) U.S. EPA. 2014. Indicators and Methods for Evaluating Economic, Ecosystem and Social Services Provisioning. Report. EPA/600/R-14/184. pp. 174. Mode Smith, L. M., Harwell, L. C., Summers, J. K., Smith, H. M., Wade, C. M., Straub, K. R. and J.L. Case (2014).This dataset is associated with the following publication:Summers , K., L. Harwell , and L. Smith. A Model For Change: An Approach for Forecasting Well-Being From Service-Based Decisions. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 69: 295-309, (2016).

Association between the epidermal growth factor gene and intelligence in major depression patients.

PubMed

Tian, Wen-min; Zhang, Ke-ran; Zhang, Juan; Shen, Yan; Xu, Qi

2010-06-01

To study the association between the epidermal growth factor (EGF) gene and intelligence in patients with major depression. Intelligence measurement using Wechsler Adult Intelligence Scale (WAIS) was performed on 120 unrelated patients with major depression and 46 control subjects. Blood was collected from all subjects for extraction of genomic DNA. Four single nucleotide polymorphisms (SNPs) in the EGF gene were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI- TOF-MS). Mean scores of both score lang and score task, two subtests in WAIS, differed significantly between major depression patients and controls (P<0.0001). Quantitative trait analysis showed that the genotype of rs2250724 was closely associated with score lang and score task in major depression patients. The associations were still significant after 10 000 permutations. Although preliminary, our results provide evidence for association between the EGF gene and intelligence in patients with major depression. Genetic variation in the EGF gene may increase the susceptibility of major depression.

Associations between cortical thickness and general intelligence in children, adolescents and young adults

PubMed Central

Menary, Kyle; Collins, Paul F.; Porter, James N.; Muetzel, Ryan; Olson, Elizabeth A.; Kumar, Vipin; Steinbach, Michael; Lim, Kelvin O.; Luciana, Monica

2013-01-01

Neuroimaging research indicates that human intellectual ability is related to brain structure including the thickness of the cerebral cortex. Most studies indicate that general intelligence is positively associated with cortical thickness in areas of association cortex distributed throughout both brain hemispheres. In this study, we performed a cortical thickness mapping analysis on data from 182 healthy typically developing males and females ages 9 to 24 years to identify correlates of general intelligence (g) scores. To determine if these correlates also mediate associations of specific cognitive abilities with cortical thickness, we regressed specific cognitive test scores on g scores and analyzed the residuals with respect to cortical thickness. The effect of age on the association between cortical thickness and intelligence was examined. We found a widely distributed pattern of positive associations between cortical thickness and g scores, as derived from the first unrotated principal factor of a factor analysis of Wechsler Abbreviated Scale of Intelligence (WASI) subtest scores. After WASI specific cognitive subtest scores were regressed on g factor scores, the residual score variances did not correlate significantly with cortical thickness in the full sample with age covaried. When participants were grouped at the age median, significant positive associations of cortical thickness were obtained in the older group for g-residualized scores on Block Design (a measure of visual-motor integrative processing) while significant negative associations of cortical thickness were observed in the younger group for g-residualized Vocabulary scores. These results regarding correlates of general intelligence are concordant with the existing literature, while the findings from younger versus older subgroups have implications for future research on brain structural correlates of specific cognitive abilities, as well as the cognitive domain specificity of behavioral performance correlates of normative gray matter thinning during adolescence. PMID:24744452

Predicting the risk of patients with biopsy Gleason score 6 to harbor a higher grade cancer.

PubMed

Gofrit, Ofer N; Zorn, Kevin C; Taxy, Jerome B; Lin, Shang; Zagaja, Gregory P; Steinberg, Gary D; Shalhav, Arieh L

2007-11-01

Prostate cancer Gleason score 3 + 3 = 6 is currently the most common score assigned on prostatic biopsies. We analyzed the clinical variables that predict the likelihood of a patient with biopsy Gleason score 6 to harbor a higher grade tumor. The study population consisted of 448 patients with a mean age of 59.1 years who underwent radical prostatectomy between February 2003 to October 2006 for Gleason score 6 adenocarcinoma. The effect of preoperative variables on the probability of a Gleason score upgrade on final pathological evaluation was evaluated using logistic regression, and classification and regression tree analysis. Gleason score upgrade was found in 91 of 448 patients (20.3%). Logistic regression showed that only serum prostate specific antigen and the greatest percent of cancer in a core were significantly associated with a score upgrade (p = 0.0014 and 0.023, respectively). Classification and regression tree analysis showed that the risk of a Gleason score upgrade was 62% when serum prostate specific antigen was higher than 12 ng/ml and 18% when serum prostate specific antigen was 12 ng/ml or less. In patients with serum prostate specific antigen lower than 12 ng/ml the risk of a score upgrade could be dichotomized at a greatest percent of cancer in a core of 5%. The risk was 22.6% and 10.5% when the greatest percent of cancer in a core was higher than 5% and 5% or lower, respectively. The probability of patients with a prostate biopsy Gleason score of 6 to conceal a Gleason score of 7 or higher can be predicted using serum prostate specific antigen and the greatest percent of cancer in a core. With these parameters it is possible to predict upgrade rates as high as 62% and as low as 10.5%.

Assessing the role of feed water constituents in irreversible membrane fouling of pilot-scale ultrafiltration drinking water treatment systems.

PubMed

Peiris, R H; Jaklewicz, M; Budman, H; Legge, R L; Moresoli, C

2013-06-15

Fluorescence excitation-emission matrix (EEM) approach together with principal component analysis (PCA) was used for assessing hydraulically irreversible fouling of three pilot-scale ultrafiltration (UF) systems containing full-scale and bench-scale hollow fiber membrane modules in drinking water treatment. These systems were operated for at least three months with extensive cycles of permeation, combination of back-pulsing and scouring and chemical cleaning. The principal component (PC) scores generated from the PCA of the fluorescence EEMs were found to be related to humic substances (HS), protein-like and colloidal/particulate matter content. PC scores of HS- and protein-like matter of the UF feed water, when considered separately, showed reasonably good correlations with the rate of hydraulically irreversible fouling for long-term UF operations. In contrast, comparatively weaker correlations for PC scores of colloidal/particulate matter and the rate of hydraulically irreversible fouling were obtained for all UF systems. Since, individual correlations could not fully explain the evolution of the rate of irreversible fouling, multi-linear regression models were developed to relate the combined effect of HS-like, protein-like and colloidal/particulate matter PC scores to the rate of hydraulically irreversible fouling for each specific UF system. These multi-linear regression models revealed significant individual and combined contribution of HS- and protein-like matter to the rate of hydraulically irreversible fouling, with protein-like matter generally showing the greatest contribution. The contribution of colloidal/particulate matter to the rate of hydraulically irreversible fouling was not as significant. The addition of polyaluminum chloride, as coagulant, to UF feed appeared to have a positive impact in reducing hydraulically irreversible fouling by these constituents. The proposed approach has applications in quantifying the individual and synergistic contribution of major natural water constituents to the rate of hydraulically irreversible membrane fouling and shows potential for controlling UF irreversible fouling in the production of drinking water. Copyright © 2013 Elsevier Ltd. All rights reserved.

Applying transpose matrix on advanced encryption standard (AES) for database content

NASA Astrophysics Data System (ADS)

Manurung, E. B. P.; Sitompul, O. S.; Suherman

2018-03-01

Advanced Encryption Standard (AES) is a specification for the encryption of electronic data established by the U.S. National Institute of Standards and Technology (NIST) and has been adopted by the U.S. government and is now used worldwide. This paper reports the impact of transpose matrix integration to AES. Transpose matrix implementation on AES is aimed at first stage of chypertext modifications for text based database security so that the confidentiality improves. The matrix is also able to increase the avalanche effect of the cryptography algorithm 4% in average.

Diagnostic value of fibronectin discriminant score for predicting liver fibrosis stages in chronic hepatitis C virus patients.

PubMed

Attallah, Abdelfattah M; Abdallah, Sanaa O; Attallah, Ahmed A; Omran, Mohamed M; Farid, Khaled; Nasif, Wesam A; Shiha, Gamal E; Abdel-Aziz, Abdel-Aziz F; Rasafy, Nancy; Shaker, Yehia M

2013-01-01

Several noninvasive predictive models were developed to substitute liver biopsy for fibrosis assessment. To evaluate the diagnostic value of fibronectin which reflect extracellular matrix metabolism and standard liver functions tests which reflect alterations in hepatic functions. Chronic hepatitis C (CHC) patients (n = 145) were evaluated using ROC curves and stepwise multivariate discriminant analysis (MDA) and was validated in 180 additional patients. Liver biochemical profile including transaminases, bilirubin, alkaline phosphatase, albumin, complete blood count were estimated. Fibronectin concentration was determined using monoclonal antibody and ELISA. A novel index named fibronectin discriminant score (FDS) based on fibronectin, APRI and albumin was developed. FDS produced areas under ROC curves (AUC) of 0.91 for significant fibrosis and 0.81 for advanced fibrosis. The FDS correctly classified 79% of the significant liver fibrosis patients (F2-F4) with 87% sensitivity and 75% specificity. The relative risk [odds ratio (OR)] of having significant liver fibrosis using the cut-off values determined by ROC curve analyses were 6.1 for fibronectin, 4.9 for APRI, and 4.2 for albumin. FDS predicted liver fibrosis with an OR of 16.8 for significant fibrosis and 8.6 for advanced fibrosis. The FDS had similar AUC and OR in the validation group to the estimation group without statistically significant difference. FDS predicted liver fibrosis with high degree of accuracy, potentially decreasing the number of liver biopsy required.

Early postoperative healing following buccal single flap approach to access intraosseous periodontal defects.

PubMed

Farina, Roberto; Simonelli, Anna; Rizzi, Alessandro; Pramstraller, Mattia; Cucchi, Alessandro; Trombelli, Leonardo

2013-07-01

This study aims to evaluate the early postoperative healing of papillary incision wounds and its association with (1) patient/site-related factors and technical (surgical) aspects as well as with (2) 6-month clinical outcomes following buccal single flap approach (SFA) in the treatment of intraosseous periodontal defects. Forty-three intraosseous defects in 35 patients were accessed with a buccal SFA alone or in combination with a reconstructive technology (graft, enamel matrix derivative (EMD), graft + EMD, or graft + membrane). Postoperative healing was evaluated at 2 weeks using the Early Wound-Healing Index (EHI). EHI ranged from score 1 (i.e., complete flap closure and optimal healing) to score 4 (i.e., loss of primary closure and partial tissue necrosis). SFA resulted in a complete wound closure at 2 weeks in the great majority of sites. A significantly more frequent presence of interdental contact point and interdental soft tissue crater, and narrower base of the interdental papilla were observed at sites with either EHI > 1 or EHI = 4 compared to sites with EHI = 1. No association between EHI and the 6-month clinical outcomes was observed. At 2 weeks, buccal SFA may result in highly predictable complete flap closure. Site-specific characteristics may influence the early postoperative healing of the papillary incision following SFA procedure. Two-week soft tissue healing, however, was not associated with the 6-month clinical outcomes.

Protein Solvent-Accessibility Prediction by a Stacked Deep Bidirectional Recurrent Neural Network.

PubMed

Zhang, Buzhong; Li, Linqing; Lü, Qiang

2018-05-25

Residue solvent accessibility is closely related to the spatial arrangement and packing of residues. Predicting the solvent accessibility of a protein is an important step to understand its structure and function. In this work, we present a deep learning method to predict residue solvent accessibility, which is based on a stacked deep bidirectional recurrent neural network applied to sequence profiles. To capture more long-range sequence information, a merging operator was proposed when bidirectional information from hidden nodes was merged for outputs. Three types of merging operators were used in our improved model, with a long short-term memory network performing as a hidden computing node. The trained database was constructed from 7361 proteins extracted from the PISCES server using a cut-off of 25% sequence identity. Sequence-derived features including position-specific scoring matrix, physical properties, physicochemical characteristics, conservation score and protein coding were used to represent a residue. Using this method, predictive values of continuous relative solvent-accessible area were obtained, and then, these values were transformed into binary states with predefined thresholds. Our experimental results showed that our deep learning method improved prediction quality relative to current methods, with mean absolute error and Pearson's correlation coefficient values of 8.8% and 74.8%, respectively, on the CB502 dataset and 8.2% and 78%, respectively, on the Manesh215 dataset.

Metal matrix composite micromechanics: In-situ behavior influence on composite properties

NASA Technical Reports Server (NTRS)

Murthy, P. L. N.; Hopkins, D. A.; Chamis, C. C.

1989-01-01

Recent efforts in computational mechanics methods for simulating the nonlinear behavior of metal matrix composites have culminated in the implementation of the Metal Matrix Composite Analyzer (METCAN) computer code. In METCAN material nonlinearity is treated at the constituent (fiber, matrix, and interphase) level where the current material model describes a time-temperature-stress dependency of the constituent properties in a material behavior space. The composite properties are synthesized from the constituent instantaneous properties by virtue of composite micromechanics and macromechanics models. The behavior of metal matrix composites depends on fabrication process variables, in situ fiber and matrix properties, bonding between the fiber and matrix, and/or the properties of an interphase between the fiber and matrix. Specifically, the influence of in situ matrix strength and the interphase degradation on the unidirectional composite stress-strain behavior is examined. These types of studies provide insight into micromechanical behavior that may be helpful in resolving discrepancies between experimentally observed composite behavior and predicted response.

Computational Prediction of Protein Epsilon Lysine Acetylation Sites Based on a Feature Selection Method.

PubMed

Gao, JianZhao; Tao, Xue-Wen; Zhao, Jia; Feng, Yuan-Ming; Cai, Yu-Dong; Zhang, Ning

2017-01-01

Lysine acetylation, as one type of post-translational modifications (PTM), plays key roles in cellular regulations and can be involved in a variety of human diseases. However, it is often high-cost and time-consuming to use traditional experimental approaches to identify the lysine acetylation sites. Therefore, effective computational methods should be developed to predict the acetylation sites. In this study, we developed a position-specific method for epsilon lysine acetylation site prediction. Sequences of acetylated proteins were retrieved from the UniProt database. Various kinds of features such as position specific scoring matrix (PSSM), amino acid factors (AAF), and disorders were incorporated. A feature selection method based on mRMR (Maximum Relevance Minimum Redundancy) and IFS (Incremental Feature Selection) was employed. Finally, 319 optimal features were selected from total 541 features. Using the 319 optimal features to encode peptides, a predictor was constructed based on dagging. As a result, an accuracy of 69.56% with MCC of 0.2792 was achieved. We analyzed the optimal features, which suggested some important factors determining the lysine acetylation sites. We developed a position-specific method for epsilon lysine acetylation site prediction. A set of optimal features was selected. Analysis of the optimal features provided insights into the mechanism of lysine acetylation sites, providing guidance of experimental validation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The RIPASA score is sensitive and specific for the diagnosis of acute appendicitis in a western population.

PubMed

Malik, Muhammad Usman; Connelly, Tara M; Awan, Faisal; Pretorius, Frederik; Fiuza-Castineira, Constantino; El Faedy, Osama; Balfe, Paul

2017-04-01

The definitive diagnosis of acute appendicitis (AA) requires histopathological examination. Various clinical diagnostic scoring systems attempt to reduce negative appendectomy rates. The most commonly used in Western Europe and the USA is the Alvarado score. The Raja Isteri Pengiran Anak Saleha appendicitis (RIPASA) score achieves better sensitivity and specificity in Asian and Middle Eastern populations. We aimed to determine the diagnostic accuracy of the RIPASA score in Irish patients with AA. All patients who presented to our institution with right iliac fossa pain and clinically suspected AA between January 1 and December 31, 2015, were indentified from our hospital inpatient enquiry database and retrospectively studied. Operating theatre records and histology reports confirmed those who underwent a non-elective operative procedure and the presence or absence of AA. SPSS version 22 was used for statistical analysis. Standard deviation is provided where appropriate. Two hundred eight patients were included in the study (106/51% male, mean age 22.7 ± 9.2 years). One hundred thirty-five (64.9%) had histologically confirmed AA (mean symptom duration = 36.19 ± 15.90 h). At a score ≥7.5, the previously determined score most likely associated with AA in Eastern populations, the RIPASA scoring system demonstrated a sensitivity of 85.39%, specificity of 69.86%, positive predictive value of 84.06%, negative predictive value of 72.86% and diagnostic accuracy of 80% in our cohort. The RIPASA score is a useful tool to aid in the diagnosis of acute appendicitis in the Irish population. A score of ≥7.5 provides sensitivity and specificity exceeding that previously documented for the Alvarado score in Western populations. WHAT DOES THIS PAPER ADD TO THE LITERATURE?: This is the first study evaluating the utility of the RIPASA score in predicting acute appendicitis in a Western population. At a value of 7.5, a cut-off score suggestive of appendicitis in the Eastern population, RIPASA demonstrated a high-sensitivity, specificity, positive predictive value and diagnostic accuracy in our cohort and was more accurate than the commonly used Alvarado score.

Monocyte-specific Accessibility of a Matrix Attachment Region in the Tumor Necrosis Factor Locus*

PubMed Central

Biglione, Sebastian; Tsytsykova, Alla V.; Goldfeld, Anne E.

2011-01-01

Regulation of TNF gene expression is cell type- and stimulus-specific. We have previously identified highly conserved noncoding regulatory elements within DNase I-hypersensitive sites (HSS) located 9 kb upstream (HSS−9) and 3 kb downstream (HSS+3) of the TNF gene, which play an important role in the transcriptional regulation of TNF in T cells. They act as enhancers and interact with the TNF promoter and with each other, generating a higher order chromatin structure. Here, we report a novel monocyte-specific AT-rich DNase I-hypersensitive element located 7 kb upstream of the TNF gene (HSS−7), which serves as a matrix attachment region in monocytes. We show that HSS−7 associates with topoisomerase IIα (Top2) in vivo and that induction of endogenous TNF mRNA expression is suppressed by etoposide, a Top2 inhibitor. Moreover, Top2 binds to and cleaves HSS−7 in in vitro analysis. Thus, HSS−7, which is selectively accessible in monocytes, can tether the TNF locus to the nuclear matrix via matrix attachment region formation, potentially promoting TNF gene expression by acting as a Top2 substrate. PMID:22027829

Optimizing protection efforts for amphibian conservation in Mediterranean landscapes

NASA Astrophysics Data System (ADS)

García-Muñoz, Enrique; Ceacero, Francisco; Carretero, Miguel A.; Pedrajas-Pulido, Luis; Parra, Gema; Guerrero, Francisco

2013-05-01

Amphibians epitomize the modern biodiversity crisis, and attract great attention from the scientific community since a complex puzzle of factors has influence on their disappearance. However, these factors are multiple and spatially variable, and declining in each locality is due to a particular combination of causes. This study shows a suitable statistical procedure to determine threats to amphibian species in medium size administrative areas. For our study case, ten biological and ecological variables feasible to affect the survival of 15 amphibian species were categorized and reduced through Principal Component Analysis. The principal components extracted were related to ecological plasticity, reproductive potential, and specificity of breeding habitats. Finally, the factor scores of species were joined in a presence-absence matrix that gives us information to identify where and why conservation management are requires. In summary, this methodology provides the necessary information to maximize benefits of conservation measures in small areas by identifying which ecological factors need management efforts and where should we focus them on.

Allometric considerations when assessing aortic aneurysms in Turner syndrome: Implications for activity recommendations and medical decision-making.

PubMed

Corbitt, Holly; Maslen, Cheryl; Prakash, Siddharth; Morris, Shaine A; Silberbach, Michael

2018-02-01

In Turner syndrome, the potential to form thoracic aortic aneurysms requires routine patient monitoring. However, the short stature that typically occurs complicates the assessment of severity and risk because the relationship of body size to aortic dimensions is different in Turner syndrome compared to the general population. Three allometric formula have been proposed to adjust aortic dimensions, all employing body surface area: aortic size index, Turner syndrome-specific Z-scores, and Z-scores based on a general pediatric and young adult population. In order to understand the differences between these formula we evaluated the relationship between age and aortic size index and compared Turner syndrome-specific Z-scores and pediatric/young adult based Z-scores in a group of girls and women with Turner syndrome. Our results suggest that the aortic size index is highly age-dependent for those under 15 years; and that Turner-specific Z-scores are significantly lower than Z-scores referenced to the general population. Higher Z-scores derived from the general reference population could result in stigmatization, inappropriate restriction from sports, and increasing the risk of unneeded medical or operative treatments. We propose that when estimating aortic dissection risk clinicians use Turner syndrome-specific Z-score for those under fifteen years of age. © 2017 Wiley Periodicals, Inc.

Ability to return to sports 5 years after matrix-associated autologous chondrocyte transplantation in an average population of active patients.

PubMed

Zak, Lukas; Aldrian, Silke; Wondrasch, Barbara; Albrecht, Christian; Marlovits, Stefan

2012-12-01

Cartilage injuries often occur during sports activities, and return to sports after cartilage surgery is an important outcome parameter for different treatment methods in the competitive as well as the recreationally active population. At the time of midterm follow-up after matrix-associated autologous chondrocyte transplantation (MACT), return to recreational sports at the preinjury level will be possible. Case series; Level of evidence, 4. Seventy patients (51 men, 19 women; age [mean ± standard deviation], 34.9 ± 8.6 y; range, 18-55 y) were clinically evaluated 5 years after MACT through subjective clinical scores such as the Knee Injury and Osteoarthritis Outcome Score (KOOS) sport and recreation subscales, the Tegner activity scale, and the Noyes sports activity rating scale. The level of sports participation was included in the investigation. The results 5 years after MACT showed mean values of 60.1 for the KOOS-sport, 67.4 for the Noyes, and 3.8 for the Tegner scores, meaning that regular sports activity such as cycling or running on flat ground, as well as medium-level manual labor, is possible. We noted that 74.3% of our patients returned to at least their preinjury sports level. Midterm postoperative results after MACT show that in a moderately active population, participation in regular sports is possible for most patients, at least at their preinjury recreational level and intensity, and there is a good rate of return to sports.

Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Aspergillus Species Directly from Growth on Solid Agar Media

PubMed Central

Li, Ying; Wang, He; Zhao, Yu-Pei; Xu, Ying-Chun; Hsueh, Po-Ren

2017-01-01

We evaluated the accuracy of the Bruker Biotyper matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) system at identifying clinical isolates of Aspergillus species that were grown on agar media. A total of 381 non-duplicate Aspergillus isolates representing 21 different Aspergillus species identified by molecular analysis were included in this study. The Bruker Biotyper MALDI-TOF MS system was able to identify 30.2% (115/381) of the isolates to the species level (score values of ≥2.000) and 49.3% to the genus level (score values of 1.700–1.999). When the identification cutoff value was lowered from ≥2.000 to ≥1.700, the species-level identification rate increased to 79.5% with a slight rise of false identification from 2.6 to 5.0%. From another aspect, a correct species-level identification rate of 89% could be reached by the Bruker Biotyper MALDI-TOF MS system regardless of the score values obtained. The Bruker Biotyper MALDI-TOF MS system had a moderate performance in identification of Aspergillus directly inoculated on solid agar media. Continued expansion of the Bruker Biotyper MALDI-TOF MS database and adoption of alternative cutoff values for interpretation are required to improve the performance of the system for identifying highly diverse species of clinically encountered Aspergillus isolates. PMID:28706514

Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Aspergillus Species Directly from Growth on Solid Agar Media.

PubMed

Li, Ying; Wang, He; Zhao, Yu-Pei; Xu, Ying-Chun; Hsueh, Po-Ren

2017-01-01

We evaluated the accuracy of the Bruker Biotyper matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) system at identifying clinical isolates of Aspergillus species that were grown on agar media. A total of 381 non-duplicate Aspergillus isolates representing 21 different Aspergillus species identified by molecular analysis were included in this study. The Bruker Biotyper MALDI-TOF MS system was able to identify 30.2% (115/381) of the isolates to the species level (score values of ≥2.000) and 49.3% to the genus level (score values of 1.700-1.999). When the identification cutoff value was lowered from ≥2.000 to ≥1.700, the species-level identification rate increased to 79.5% with a slight rise of false identification from 2.6 to 5.0%. From another aspect, a correct species-level identification rate of 89% could be reached by the Bruker Biotyper MALDI-TOF MS system regardless of the score values obtained. The Bruker Biotyper MALDI-TOF MS system had a moderate performance in identification of Aspergillus directly inoculated on solid agar media. Continued expansion of the Bruker Biotyper MALDI-TOF MS database and adoption of alternative cutoff values for interpretation are required to improve the performance of the system for identifying highly diverse species of clinically encountered Aspergillus isolates.

Clinical risk analysis with failure mode and effect analysis (FMEA) model in a dialysis unit.

PubMed

Bonfant, Giovanna; Belfanti, Pietro; Paternoster, Giuseppe; Gabrielli, Danila; Gaiter, Alberto M; Manes, Massimo; Molino, Andrea; Pellu, Valentina; Ponzetti, Clemente; Farina, Massimo; Nebiolo, Pier E

2010-01-01

The aim of clinical risk management is to improve the quality of care provided by health care organizations and to assure patients' safety. Failure mode and effect analysis (FMEA) is a tool employed for clinical risk reduction. We applied FMEA to chronic hemodialysis outpatients. FMEA steps: (i) process study: we recorded phases and activities. (ii) Hazard analysis: we listed activity-related failure modes and their effects; described control measures; assigned severity, occurrence and detection scores for each failure mode and calculated the risk priority numbers (RPNs) by multiplying the 3 scores. Total RPN is calculated by adding single failure mode RPN. (iii) Planning: we performed a RPNs prioritization on a priority matrix taking into account the 3 scores, and we analyzed failure modes causes, made recommendations and planned new control measures. (iv) Monitoring: after failure mode elimination or reduction, we compared the resulting RPN with the previous one. Our failure modes with the highest RPN came from communication and organization problems. Two tools have been created to ameliorate information flow: "dialysis agenda" software and nursing datasheets. We scheduled nephrological examinations, and we changed both medical and nursing organization. Total RPN value decreased from 892 to 815 (8.6%) after reorganization. Employing FMEA, we worked on a few critical activities, and we reduced patients' clinical risk. A priority matrix also takes into account the weight of the control measures: we believe this evaluation is quick, because of simple priority selection, and that it decreases action times.

WISC-IV and WIAT-II profiles in children with high-functioning autism.

PubMed

Mayes, Susan Dickerson; Calhoun, Susan L

2008-03-01

Children with high-functioning autism earned above normal scores on the Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) Perceptual Reasoning and Verbal Comprehension Indexes and below normal scores on the Working Memory and Processing Speed Indexes and Wechsler Individual Achievement Test-Second Edition (WIAT-II) Written Expression. Full Scale IQ (FSIQ) and reading and math scores were similar to the norm. Profiles were consistent with previous WISC-III research, except that the new WISC-IV motor-free visual reasoning subtests (Matrix Reasoning and Picture Concepts) were the highest of the nonverbal subtests. The WISC-IV may be an improvement over the WISC-III for children with high-functioning autism because it captures their visual reasoning strength, while identifying their attention, graphomotor, and processing speed weaknesses. FSIQ was the best single predictor of academic achievement.

Spatially and temporally controlled biomineralization is facilitated by interaction between self-assembled dentin matrix protein 1 and calcium phosphate nuclei in solution.

PubMed

He, Gen; Gajjeraman, Sivakumar; Schultz, David; Cookson, David; Qin, Chunlin; Butler, William T; Hao, Jianjun; George, Anne

2005-12-13

Bone and dentin biomineralization are well-regulated processes mediated by extracellular matrix proteins. It is widely believed that specific matrix proteins in these tissues modulate nucleation of apatite nanoparticles and their growth into micrometer-sized crystals via molecular recognition at the protein-mineral interface. However, this assumption has been supported only circumstantially, and the exact mechanism remains unknown. Dentin matrix protein 1 (DMP1) is an acidic matrix protein, present in the mineralized matrix of bone and dentin. In this study, we have demonstrated using synchrotron small-angle X-ray scattering that DMP1 in solution can undergo oligomerization and temporarily stabilize the newly formed calcium phosphate nanoparticle precursors by sequestering them and preventing their further aggregation and precipitation. The solution structure represents the first low-resolution structural information for DMP1. Atomic force microscopy and transmission electron microscopy studies further confirmed that the nascent calcium phosphate nuclei formed in solution were assembled into ordered protein-mineral complexes with the aid of oligomerized DMP1, recombinant and native. This study reveals a novel mechanism by which DMP1 might facilitate initiation of mineral nucleation at specific sites during bone and dentin mineralization and prevent spontaneous calcium phosphate precipitation in areas in which mineralization is not desirable.

Score tests for independence in semiparametric competing risks models.

PubMed

Saïd, Mériem; Ghazzali, Nadia; Rivest, Louis-Paul

2009-12-01

A popular model for competing risks postulates the existence of a latent unobserved failure time for each risk. Assuming that these underlying failure times are independent is attractive since it allows standard statistical tools for right-censored lifetime data to be used in the analysis. This paper proposes simple independence score tests for the validity of this assumption when the individual risks are modeled using semiparametric proportional hazards regressions. It assumes that covariates are available, making the model identifiable. The score tests are derived for alternatives that specify that copulas are responsible for a possible dependency between the competing risks. The test statistics are constructed by adding to the partial likelihoods for the individual risks an explanatory variable for the dependency between the risks. A variance estimator is derived by writing the score function and the Fisher information matrix for the marginal models as stochastic integrals. Pitman efficiencies are used to compare test statistics. A simulation study and a numerical example illustrate the methodology proposed in this paper.

Proteomic Analysis of Tendon Extracellular Matrix Reveals Disease Stage-specific Fragmentation and Differential Cleavage of COMP (Cartilage Oligomeric Matrix Protein)*

PubMed Central

Dakin, Stephanie Georgina; Smith, Roger Kenneth Whealands; Heinegård, Dick; Önnerfjord, Patrik; Khabut, Areej; Dudhia, Jayesh

2014-01-01

During inflammatory processes the extracellular matrix (ECM) is extensively remodeled, and many of the constituent components are released as proteolytically cleaved fragments. These degradative processes are better documented for inflammatory joint diseases than tendinopathy even though the pathogenesis has many similarities. The aims of this study were to investigate the proteomic composition of injured tendons during early and late disease stages to identify disease-specific cleavage patterns of the ECM protein cartilage oligomeric matrix protein (COMP). In addition to characterizing fragments released in naturally occurring disease, we hypothesized that stimulation of tendon explants with proinflammatory mediators in vitro would induce fragments of COMP analogous to natural disease. Therefore, normal tendon explants were stimulated with IL-1β and prostaglandin E2, and their effects on the release of COMP and its cleavage patterns were characterized. Analyses of injured tendons identified an altered proteomic composition of the ECM at all stages post injury, showing protein fragments that were specific to disease stage. IL-1β enhanced the proteolytic cleavage and release of COMP from tendon explants, whereas PGE2 had no catabolic effect. Of the cleavage fragments identified in early stage tendon disease, two fragments were generated by an IL-1-mediated mechanism. These fragments provide a platform for the development of neo-epitope assays specific to injury stage for tendon disease. PMID:24398684

An electroglottographical analysis-based discriminant function model differentiating multiple sclerosis patients from healthy controls.

PubMed

Vavougios, George D; Doskas, Triantafyllos; Konstantopoulos, Kostas

2018-05-01

Dysarthrophonia is a predominant symptom in many neurological diseases, affecting the quality of life of the patients. In this study, we produced a discriminant function equation that can differentiate MS patients from healthy controls, using electroglottographic variables not analyzed in a previous study. We applied stepwise linear discriminant function analysis in order to produce a function and score derived from electroglottographic variables extracted from a previous study. The derived discriminant function's statistical significance was determined via Wilk's λ test (and the associated p value). Finally, a 2 × 2 confusion matrix was used to determine the function's predictive accuracy, whereas the cross-validated predictive accuracy is estimated via the "leave-one-out" classification process. Discriminant function analysis (DFA) was used to create a linear function of continuous predictors. DFA produced the following model (Wilk's λ = 0.043, χ2 = 388.588, p < 0.0001, Tables 3 and 4): D (MS vs controls) = 0.728*DQx1 mean monologue + 0.325*CQx monologue + 0.298*DFx1 90% range monologue + 0.443*DQx1 90% range reading - 1.490*DQx1 90% range monologue. The derived discriminant score (S1) was used subsequently in order to form the coordinates of a ROC curve. Thus, a cutoff score of - 0.788 for S1 corresponded to a perfect classification (100% sensitivity and 100% specificity, p = 1.67e -22 ). Consistent with previous findings, electroglottographic evaluation represents an easy to implement and potentially important assessment in MS patients, achieving adequate classification accuracy. Further evaluation is needed to determine its use as a biomarker.

Selection and Investigation of a Primate Model of Spontaneous Degenerative Knee Osteoarthritis, the Cynomolgus Monkey (Macaca Fascicularis).

PubMed

Liu, Gang; Zhang, Lei; Zhou, Xin; Zhang, Bao L; Guo, Guang X; Xu, Ping; Wang, Guo Y; Fu, Shi J

2018-07-01

BACKGROUND The aim of this study was to identify a primate model of degenerative knee osteoarthritis (KOA) that may be more relevant for research studies on degenerative KOA in humans. MATERIAL AND METHODS Sixteen specific-pathogen-free (SPF) male cynomolgus monkeys (Macaca fascicularis) were divided into group A (n=8), an old group (22.0-25.3 years of age), and group B (n=8), a young group (3.0-5.2 years of age). For each primate, the behavior was observed, knee circumference was measured, knee joint X-rays were performed, and peripheral blood white blood cell (WBC) counts were measured, and the Kellgren and Lawrence (K-L) system was used for the classification of osteoarthritis. An enzyme-linked immunoassay (ELISA) was performed on knee joint fluid to measure levels of interleukin (IL)-1β, transforming growth factor (TGF)-β1, and matrix metalloproteinase (MMP)13. Changes in articular cartilage were evaluated using the Brittberg score and the Mankin histopathology grading score, respectively. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blot were used to measure the expression of the NOTCH3, JAG1, and ACAN genes in knee cartilage specimens, and the findings in the two groups of primates were compared. RESULTS Seven old aged primates in group A were compared with group B, and showed significant differences in WBC count, synovial fluid IL-1β, TGF-β1, and MMP13 levels, expression levels of the NOTCH3, JAG1, and ACAN genes in knee cartilage specimens, and in the Brittberg and Mankin scores (all, P<0.05). CONCLUSIONS Cynomolgus monkeys (Macaca fascicularis) might be a model for age-related degenerative KOA.

Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements

PubMed Central

Tharakaraman, Kannan; Mariño-Ramírez, Leonardo; Sheetlin, Sergey L; Landsman, David; Spouge, John L

2006-01-01

Background Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such an element in a sequence set. Results We describe an improvement to the A-GLAM computer program, which predicts regulatory elements within DNA sequences with Gibbs sampling. The improvement adds an optional "scanning step" after Gibbs sampling. Gibbs sampling produces a position specific scoring matrix (PSSM). The new scanning step resembles an iterative PSI-BLAST search based on the PSSM. First, it assigns an "individual score" to each subsequence of appropriate length within the input sequences using the initial PSSM. Second, it computes an E-value from each individual score, to assess the agreement between the corresponding subsequence and the PSSM. Third, it permits subsequences with E-values falling below a threshold to contribute to the underlying PSSM, which is then updated using the Bayesian calculus. A-GLAM iterates its scanning step to convergence, at which point no new subsequences contribute to the PSSM. After convergence, A-GLAM reports predicted regulatory elements within each sequence in order of increasing E-values, so users have a statistical evaluation of the predicted elements in a convenient presentation. Thus, although the Gibbs sampling step in A-GLAM finds at most one regulatory element per input sequence, the scanning step can now rapidly locate further instances of the element in each sequence. Conclusion Datasets from experiments determining the binding sites of transcription factors were used to evaluate the improvement to A-GLAM. Typically, the datasets included several sequences containing multiple instances of a regulatory motif. The improvements to A-GLAM permitted it to predict the multiple instances. PMID:16961919

Computer-based coding of free-text job descriptions to efficiently identify occupations in epidemiological studies

PubMed Central

Russ, Daniel E.; Ho, Kwan-Yuet; Colt, Joanne S.; Armenti, Karla R.; Baris, Dalsu; Chow, Wong-Ho; Davis, Faith; Johnson, Alison; Purdue, Mark P.; Karagas, Margaret R.; Schwartz, Kendra; Schwenn, Molly; Silverman, Debra T.; Johnson, Calvin A.; Friesen, Melissa C.

2016-01-01

Background Mapping job titles to standardized occupation classification (SOC) codes is an important step in identifying occupational risk factors in epidemiologic studies. Because manual coding is time-consuming and has moderate reliability, we developed an algorithm called SOCcer (Standardized Occupation Coding for Computer-assisted Epidemiologic Research) to assign SOC-2010 codes based on free-text job description components. Methods Job title and task-based classifiers were developed by comparing job descriptions to multiple sources linking job and task descriptions to SOC codes. An industry-based classifier was developed based on the SOC prevalence within an industry. These classifiers were used in a logistic model trained using 14,983 jobs with expert-assigned SOC codes to obtain empirical weights for an algorithm that scored each SOC/job description. We assigned the highest scoring SOC code to each job. SOCcer was validated in two occupational data sources by comparing SOC codes obtained from SOCcer to expert assigned SOC codes and lead exposure estimates obtained by linking SOC codes to a job-exposure matrix. Results For 11,991 case-control study jobs, SOCcer-assigned codes agreed with 44.5% and 76.3% of manually assigned codes at the 6- and 2-digit level, respectively. Agreement increased with the score, providing a mechanism to identify assignments needing review. Good agreement was observed between lead estimates based on SOCcer and manual SOC assignments (kappa: 0.6–0.8). Poorer performance was observed for inspection job descriptions, which included abbreviations and worksite-specific terminology. Conclusions Although some manual coding will remain necessary, using SOCcer may improve the efficiency of incorporating occupation into large-scale epidemiologic studies. PMID:27102331

Cardiovascular risk scores for coronary atherosclerosis.

PubMed

Yalcin, Murat; Kardesoglu, Ejder; Aparci, Mustafa; Isilak, Zafer; Uz, Omer; Yiginer, Omer; Ozmen, Namik; Cingozbay, Bekir Yilmaz; Uzun, Mehmet; Cebeci, Bekir Sitki

2012-10-01

The objective of this study was to compare frequently used cardiovascular risk scores in predicting the presence of coronary artery disease (CAD) and 3-vessel disease. In 350 consecutive patients (218 men and 132 women) who underwent coronary angiography, the cardiovascular risk level was determined using the Framingham Risk Score (FRS), the Modified Framingham Risk Score (MFRS), the Prospective Cardiovascular Münster (PROCAM) score, and the Systematic Coronary Risk Evaluation (SCORE). The area under the curve for receiver operating characteristic curves showed that FRS had more predictive value than the other scores for CAD (area under curve, 0.76, P < or = 0.001), but all scores had good specificity and positive predictive value. For 3-vessel disease, the FRS had better predictive value than the other scores (area under curve, 0.74, P < or = 0.001), but all scores had good specificity and negative predictive value. The risk scores (FRS, MFRS, PROCAM, and SCORE) may predict the presence and severity of coronary atherosclerosis.The FRS had better predictive value than the other scores.

Respiratory Inductance Plethysmography Improved Diagnostic Sensitivity and Specificity of Obstructive Sleep Apnea.

PubMed

Kogan, Dmitriy; Jain, Arad; Kimbro, Shawn; Gutierrez, Guillermo; Jain, Vivek

2016-08-01

Respiratory inductance plethysmography (RIP) is a tool used during a polysomnogram (PSG), which serves as a surrogate of respiratory effort and can help detect inspiratory air-flow limitation. We hypothesize that RIP can improve the sensitivity and specificity of scoring hypopneas when compared with both the recommended and acceptable criteria of the American Academy of Sleep Medicine. We retrospectively analyzed a cohort of 12 subjects who had no obstructive sleep apnea (OSA) or mild OSA on PSG when scored by the American Academy of Sleep Medicine acceptable criteria for hypopneas but had high clinical suspicion for a diagnosis of OSA. These subjects were rescored using the American Academy of Sleep Medicine recommended criteria as well as RIP. Hypopnea was scored when there was a 50% decrease in the amplitude of the RIP sum channel (which combined input from chest and abdominal belts). OSA was diagnosed if the subjects had >5 respiratory events/h of sleep. The subject's response to CPAP was assessed by using a short questionnaire called the post-PSG sleep assessment. which evaluated subjective sleep quality. A positive response was considered an improvement in the post-PSG sleep assessment score after CPAP use. When scored using the American Academy of Sleep Medicine acceptable criteria, 10 subjects had a negative study, and 2 subjects had mild OSA for a sensitivity of 11% and specificity of 50%. When scored using the recommended criteria, 10 subjects had OSA, and 2 were negative, for a sensitivity of 78% and specificity of 70%. By RIP scoring, all 12 subjects had >5 respiratory events/h for a sensitivity of 100% and specificity of 75%. This small retrospective pilot study showed improved sensitivity and specificity when scoring hypopneas by RIP sum channel. Copyright © 2016 by Daedalus Enterprises.

Olfactory-specific quality of life outcomes after endoscopic sinus surgery

PubMed Central

Soler, Zachary M.; Smith, Timothy L.; Alt, Jeremiah A.; Ramakrishnan, Vijay R; Mace, Jess C.; Schlosser, Rodney J.

2015-01-01

Introduction Olfactory loss is a cardinal symptom of chronic rhinosinusitis (CRS) and affects 40–80% of patients. However, common sinus-specific quality-of-life (QOL) instruments include only single questions related to olfaction. Few studies have explored olfactory outcomes after surgery utilizing validated, olfaction-specific QOL questionnaires. Methods Patients with CRS were enrolled from 3 centers across North America into a prospective cohort study. Patients completed the short modified version of the Questionnaire of Olfactory Disorders (QOD-NS) and the 40-item Smell Identification Test (SIT-40) before and at least 6 months after endoscopic sinus surgery (ESS). Multivariate linear regression was used to determine whether specific demographic, comorbidity, or disease severity measures were independently associated with QOD scores at baseline or predicted change after surgery. Results A total of 121 patients, equally split between genders, were enrolled with an average age of 47.9 years (range: 18–80). Baseline total QOD-NS scores were significantly associated with SIT-40 scores, with a moderate strength of correlation (Rs=0.400; p<0.001). The average QOD-NS score improved after ESS (35.7±13.0 vs. 39.7±12.2; p=0.006). Allergy, polyps, and steroid dependent conditions were found to be independently associated with worse preoprerative QOD-NS scores, while septal deviation was associated with better QOD-NS scores. Baseline computed tomography (CT) scores were the only variable which significantly predicted change in QOD-NS after surgery. Conclusion Olfaction-specific QOL is worse in patients with polyps and comorbid allergy. Significant improvements in olfaction-specific QOL are seen after ESS, with the greatest gains seen in those with worse CT scores at baseline. PMID:26678351

Matrix metalloproteinase-3 gene polymorphism in renal transplant patients with gingival overgrowth.

PubMed

Drozdzik, A; Kurzawski, M; Lener, A; Kozak, M; Banach, J; Drozdzik, M

2010-02-01

Gingival enlargement frequently occurs in transplant patients receiving immunosuppressive drugs. It was hypothesized that gingival enlargement associated with cyclosporine use results from reduced degradation of extracellular matrix in the gingiva. Matrix metalloproteinase-3 (MMP-3) is involved in biodegradation of the extracellular matrix, and its inhibition may contribute to an abnormal accumulation of fibronectin and proteoglycans, which are MMP-3 substrates. The aim of this study was to investigate whether an association exists between MMP-3 genotypes and gingival enlargement in kidney transplant patients medicated with cyclosporine A. Sixty-four unrelated kidney transplant patients suffering from gingival overgrowth, as well as 111 control transplant patients without gingival overgrowth, were enrolled in the study. Gingival overgrowth was assessed 6 mo after transplantation. During the post-transplant period all patients were given cyclosporine A as a principal immunosuppressive agent. MMP-3 polymorphism was determined using a PCR restriction fragment length polymorphism assay. In kidney transplant patients suffering from gingival overgrowth the mean gingival overgrowth score was 1.35 +/- 0.57, whereas in control subjects the mean gingival overgrowth score was 0.0. The distribution of MMP-3-1178A/dupA alleles among all kidney transplant patients, as well as in the two study subgroups, did not differ significantly from Hardy-Weinberg equilibrium. The frequency of the MMP-3-1171A/A genotype (28.1% for gingival overgrowth vs. 26.1% for controls) and of the MMP-3-1171dupA/dupA genotype (32.8% for gingival overgrowth vs. 22.5% for controls) was similar for both study groups. The risk of gingival overgrowth was lowest among patients carrying the MMP-3-1171A/dupA genotype (odds ratio 0.52), but this did not differ markedly from the other genotypes. No association between MMP-3 gene polymorphism and gingival overgrowth was revealed in kidney transplant patients administered cyclosporine A.

A colinear backscattering Mueller matrix microscope for reflection Muller matrix imaging

NASA Astrophysics Data System (ADS)

Chen, Zhenhua; Yao, Yue; Zhu, Yuanhuan; Ma, Hui

2018-02-01

In a recent attempt, we developed a colinear backscattering Mueller matrix microscope by adding polarization state generator (PSG) and polarization state analyzer (PSA) into the illumination and detection optical paths of a commercial metallurgical microscope. It is found that specific efforts have to be made to reduce the artifacts due to the intrinsic residual polarizations of the optical system, particularly the dichroism due to the 45 degrees beam splitter. In this paper, we present a new calibration method based on numerical reconstruction of the instrument matrix to remove the artifacts introduced by beam splitter. Preliminary tests using a mirror as a standard sample show that the maximum Muller matrix element error of the colinear backscattering Muller matrix microscope can be reduced to a few percent.

General formalism for partial spatial coherence in reflection Mueller matrix polarimetry.

PubMed

Ossikovski, Razvigor; Hingerl, Kurt

2016-09-01

Starting from the first principles, we derive the expressions governing partially coherent Mueller matrix reflection polarimetry on spatially inhomogeneous samples. These are reported both in their general form and in the practically important specific form for two juxtaposed media.

Viscoplastic Matrix Materials for Embedded 3D Printing.

PubMed

Grosskopf, Abigail K; Truby, Ryan L; Kim, Hyoungsoo; Perazzo, Antonio; Lewis, Jennifer A; Stone, Howard A

2018-03-16

Embedded three-dimensional (EMB3D) printing is an emerging technique that enables free-form fabrication of complex architectures. In this approach, a nozzle is translated omnidirectionally within a soft matrix that surrounds and supports the patterned material. To optimize print fidelity, we have investigated the effects of matrix viscoplasticity on the EMB3D printing process. Specifically, we determine how matrix composition, print path and speed, and nozzle diameter affect the yielded region within the matrix. By characterizing the velocity and strain fields and analyzing the dimensions of the yielded regions, we determine that scaling relationships based on the Oldroyd number, Od, exist between these dimensions and the rheological properties of the matrix materials and printing parameters. Finally, we use EMB3D printing to create complex architectures within an elastomeric silicone matrix. Our methods and findings will both facilitate future characterization of viscoplastic matrices and motivate the development of new materials for EMB3D printing.

Might "Unique" Factors Be "Common"? On the Possibility of Indeterminate Common-Unique Covariances

ERIC Educational Resources Information Center

Grayson, Dave

2006-01-01

The present paper shows that the usual factor analytic structured data dispersion matrix lambda psi lambda' + delta can readily arise from a set of scores y = lambda eta + epsilon, shere the "common" (eta) and "unique" (epsilon) factors have nonzero covariance: gamma = Cov epsilon,eta) is not equal to 0. Implications of this finding are discussed…

A Parametric Analysis of Structured and Unstructured Q-Sort Data.

DTIC Science & Technology

1981-06-09

this consideration, a hypothesis intermediate between H0 and the general alternative of the form H’: Odk m 0, d = DI p....,D 2 and k=i, (where wjl -, the...judging-perceiving (J-P). The scores E-I and J-P, with the intercept, made up the subject design matrix. 56 (7) Sherlock collected Q-sorts from 80

Test Design Project: Studies in Test Bias. Annual Report.

ERIC Educational Resources Information Center

McArthur, David

Item bias in a multiple-choice test can be detected by appropriate analyses of the persons x items scoring matrix. This permits comparison of groups of examinees tested with the same instrument. The test may be biased if it is not measuring the same thing in comparable groups, if groups are responding to different aspects of the test items, or if…

On the Use, the Misuse, and the Very Limited Usefulness of Cronbach's Alpha

ERIC Educational Resources Information Center

Sijtsma, Klaas

2009-01-01

This discussion paper argues that both the use of Cronbach's alpha as a reliability estimate and as a measure of internal consistency suffer from major problems. First, alpha always has a value, which cannot be equal to the test score's reliability given the inter-item covariance matrix and the usual assumptions about measurement error. Second, in…

Rapid Identification of Bacteria in Positive Blood Culture Broths by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry▿

PubMed Central

Stevenson, Lindsay G.; Drake, Steven K.; Murray, Patrick R.

2010-01-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid, accurate method for identifying bacteria and fungi recovered on agar culture media. We report herein a method for the direct identification of bacteria in positive blood culture broths by MALDI-TOF mass spectrometry. A total of 212 positive cultures were examined, representing 32 genera and 60 species or groups. The identification of bacterial isolates by MALDI-TOF mass spectrometry was compared with biochemical testing, and discrepancies were resolved by gene sequencing. No identification (spectral score of <1.7) was obtained for 42 (19.8%) of the isolates, due most commonly to insufficient numbers of bacteria in the blood culture broth. Of the bacteria with a spectral score of ≥1.7, 162 (95.3%) of 170 isolates were correctly identified. All 8 isolates of Streptococcus mitis were misidentified as being Streptococcus pneumoniae isolates. This method provides a rapid, accurate, definitive identification of bacteria within 1 h of detection in positive blood cultures with the caveat that the identification of S. pneumoniae would have to be confirmed by an alternative test. PMID:19955282

Basic list of veterinary medical serials, third edition: using a decision matrix to update the core list of veterinary journals.

PubMed

Ugaz, Ana G; Boyd, C Trenton; Croft, Vicki F; Carrigan, Esther E; Anderson, Katherine M

2010-10-01

This paper presents the methods and results of a study designed to produce the third edition of the "Basic List of Veterinary Medical Serials," which was established by the Veterinary Medical Libraries Section in 1976 and last updated in 1986. A set of 238 titles were evaluated using a decision matrix in order to systematically assign points for both objective and subjective criteria and determine an overall score for each journal. Criteria included: coverage in four major indexes, scholarly impact rank as tracked in two sources, identification as a recommended journal in preparing for specialty board examinations, and a veterinary librarian survey rating. Of the 238 titles considered, a minimum scoring threshold determined the 123 (52%) journals that constituted the final list. The 36 subject categories represented on the list include general and specialty disciplines in veterinary medicine. A ranked list of journals and a list by subject category were produced. Serials appearing on the third edition of the "Basic List of Veterinary Medical Serials" met expanded objective measures of quality and impact as well as subjective perceptions of value by both librarians and veterinary practitioners.

Basic list of veterinary medical serials, third edition: using a decision matrix to update the core list of veterinary journals

PubMed Central

Ugaz, Ana G; Boyd, C. Trenton; Croft, Vicki F; Carrigan, Esther E; Anderson, Katherine M

2010-01-01

Objective: This paper presents the methods and results of a study designed to produce the third edition of the “Basic List of Veterinary Medical Serials,” which was established by the Veterinary Medical Libraries Section in 1976 and last updated in 1986. Methods: A set of 238 titles were evaluated using a decision matrix in order to systematically assign points for both objective and subjective criteria and determine an overall score for each journal. Criteria included: coverage in four major indexes, scholarly impact rank as tracked in two sources, identification as a recommended journal in preparing for specialty board examinations, and a veterinary librarian survey rating. Results: Of the 238 titles considered, a minimum scoring threshold determined the 123 (52%) journals that constituted the final list. The 36 subject categories represented on the list include general and specialty disciplines in veterinary medicine. A ranked list of journals and a list by subject category were produced. Conclusion: Serials appearing on the third edition of the “Basic List of Veterinary Medical Serials” met expanded objective measures of quality and impact as well as subjective perceptions of value by both librarians and veterinary practitioners. PMID:20936066

Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Stevenson, Lindsay G; Drake, Steven K; Murray, Patrick R

2010-02-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid, accurate method for identifying bacteria and fungi recovered on agar culture media. We report herein a method for the direct identification of bacteria in positive blood culture broths by MALDI-TOF mass spectrometry. A total of 212 positive cultures were examined, representing 32 genera and 60 species or groups. The identification of bacterial isolates by MALDI-TOF mass spectrometry was compared with biochemical testing, and discrepancies were resolved by gene sequencing. No identification (spectral score of < 1.7) was obtained for 42 (19.8%) of the isolates, due most commonly to insufficient numbers of bacteria in the blood culture broth. Of the bacteria with a spectral score of > or = 1.7, 162 (95.3%) of 170 isolates were correctly identified. All 8 isolates of Streptococcus mitis were misidentified as being Streptococcus pneumoniae isolates. This method provides a rapid, accurate, definitive identification of bacteria within 1 h of detection in positive blood cultures with the caveat that the identification of S. pneumoniae would have to be confirmed by an alternative test.

EMMPRIN Is an Independent Negative Prognostic Factor for Patients with Astrocytic Glioma

PubMed Central

Chen, Yu; Cai, Min; Dong, Hailong; Xiong, Lize

2013-01-01

Extracellular matrix metalloproteinase inducer (EMMPRIN), also known as CD147, is a member of the immunoglobulin superfamily that is present on the surface of tumor cells and stimulates adjacent fibroblasts to produce matrix metalloproteinases (MMPs). It has been proved to be associated with tumor invasion and metastasis in various human malignancies. In our study, the protein expression level of EMMPRIN in 306 cases of astrocytic glioma is investigated by immunohistochemistry assay. Statistical analysis was utilized to evaluate the association of EMMPRIN with clinicopathological characteristics and prognosis of patients. It was proved that EMMPRIN protein expression was increased in glioma compared with that in normal brain tissue. Moreover, EMMPRIN immunohistochemical staining was correlated with WHO grade and Karnofsky performance score for strong positive EMMPRIN staining is more frequently detected in glioma of advanced grade or low KPS score. It is also demonstrated that EMMPRIN could be an independent negative prognostic factor in glioma for patients with glioma of strong EMMPRIN staining tend to have high risk of death. These results proved that EMMPRIN is associated with prognosis of glioma, which may also suggest the potential role of EMMPRIN in glioma management. PMID:23516431

EMMPRIN is an independent negative prognostic factor for patients with astrocytic glioma.

PubMed

Tian, Li; Zhang, Yang; Chen, Yu; Cai, Min; Dong, Hailong; Xiong, Lize

2013-01-01

Extracellular matrix metalloproteinase inducer (EMMPRIN), also known as CD147, is a member of the immunoglobulin superfamily that is present on the surface of tumor cells and stimulates adjacent fibroblasts to produce matrix metalloproteinases (MMPs). It has been proved to be associated with tumor invasion and metastasis in various human malignancies. In our study, the protein expression level of EMMPRIN in 306 cases of astrocytic glioma is investigated by immunohistochemistry assay. Statistical analysis was utilized to evaluate the association of EMMPRIN with clinicopathological characteristics and prognosis of patients. It was proved that EMMPRIN protein expression was increased in glioma compared with that in normal brain tissue. Moreover, EMMPRIN immunohistochemical staining was correlated with WHO grade and Karnofsky performance score for strong positive EMMPRIN staining is more frequently detected in glioma of advanced grade or low KPS score. It is also demonstrated that EMMPRIN could be an independent negative prognostic factor in glioma for patients with glioma of strong EMMPRIN staining tend to have high risk of death. These results proved that EMMPRIN is associated with prognosis of glioma, which may also suggest the potential role of EMMPRIN in glioma management.

Multi-dimensional scores to predict mortality in patients with idiopathic pulmonary fibrosis undergoing lung transplantation assessment.

PubMed

Fisher, Jolene H; Al-Hejaili, Faris; Kandel, Sonja; Hirji, Alim; Shapera, Shane; Mura, Marco

2017-04-01

The heterogeneous progression of idiopathic pulmonary fibrosis (IPF) makes prognostication difficult and contributes to high mortality on the waitlist for lung transplantation (LTx). Multi-dimensional scores (Composite Physiologic index [CPI], [Gender-Age-Physiology [GAP]; RIsk Stratification scorE [RISE]) demonstrated enhanced predictive power towards outcome in IPF. The lung allocation score (LAS) is a multi-dimensional tool commonly used to stratify patients assessed for LTx. We sought to investigate whether IPF-specific multi-dimensional scores predict mortality in patients with IPF assessed for LTx. The study included 302 patients with IPF who underwent a LTx assessment (2003-2014). Multi-dimensional scores were calculated. The primary outcome was 12-month mortality after assessment. LTx was considered as competing event in all analyses. At the end of the observation period, there were 134 transplants, 63 deaths, and 105 patients were alive without LTx. Multi-dimensional scores predicted mortality with accuracy similar to LAS, and superior to that of individual variables: area under the curve (AUC) for LAS was 0.78 (sensitivity 71%, specificity 86%); CPI 0.75 (sensitivity 67%, specificity 82%); GAP 0.67 (sensitivity 59%, specificity 74%); RISE 0.78 (sensitivity 71%, specificity 84%). A separate analysis conducted only in patients actively listed for LTx (n = 247; 50 deaths) yielded similar results. In patients with IPF assessed for LTx as well as in those actually listed, multi-dimensional scores predict mortality better than individual variables, and with accuracy similar to the LAS. If validated, multi-dimensional scores may serve as inexpensive tools to guide decisions on the timing of referral and listing for LTx. Copyright © 2017 Elsevier Ltd. All rights reserved.

Prediction of Post-operative Mortality in Patients with HCV-related Cirrhosis Undergoing Non-Hepatic Surgeries

PubMed Central

Hemida, Khalid; Shabana, Sherif Sadek; Said, Hani; Ali-Eldin, Fatma

2016-01-01

Introduction Patients with chronic liver diseases are at great risk for both morbidity and mortality during the post-operative period due to the stress of surgery and the effects of general anaesthesia. Aim The main aim of this study was to evaluate the value of Model for End-stage Liver Disease (MELD) score, as compared to Child-Turcotte-Pugh (CTP) score, for prediction of 30- day post-operative mortality in Egyptian patients with liver cirrhosis undergoing non-hepatic surgery under general anaesthesia. Materials and Methods A total of 60 patients with Hepatitis C Virus (HCV) - related liver cirrhosis were included in this study. Sensitivity and specificity of MELD and CTP scores were evaluated for the prediction of post-operative mortality. A total of 20 patients who had no clinical, biochemical or radiological evidence of liver disease were included to serve as a control group. Results The highest sensitivity and specificity for detection of post-operative mortality was detected at a MELD score of 13.5. CTP score had a sensitivity of 75%, a specificity of 96.4%, and an overall accuracy of 95% for prediction of post-operative mortality. On the other side and at a cut-off value of 13.5, MELD score had a sensitivity of 100%, a specificity of 64.0%, and an overall accuracy of 66.6% for prediction of post-operative mortality in patients with HCV- related liver cirrhosis. Conclusion MELD score proved to be more sensitive but less specific than CTP score for prediction of post-operative mortality. CTP and MELD scores may be complementary rather than competitive in predicting post-operative mortality in patients with HCV- related liver cirrhosis. PMID:27891371

Assessment of Quality and Content of Online Information About Hip Arthroscopy.

PubMed

Ellsworth, Bridget; Patel, Hiren; Kamath, Atul F

2016-10-01

The purpose of this study was to assess the quality of information available to patients on the Internet when using popular search engines to search the term "hip arthroscopy." We analyzed the quality and content of information about hip arthroscopy (HA) on the first 50 websites returned by the search engines Google and Bing for the search term "hip arthroscopy." The sites were categorized by type, and quality and content were measured using the DISCERN score, along with an HA-specific content score. The HA-specific content score was used to assess each website for the presence or absence of 19 topics about HA determined to be important for a patient seeking information about the procedure. The Health on the Net Code (HONcode) status of each website was also noted. The mean DISCERN score for all websites analyzed was 39.5, considered "poor," while only 44.6% of sites were considered "fair" or "good." Governmental and nonprofit organization (NPO) websites had the highest average DISCERN score. The mean HA-specific content score was 8.6 (range, 2 to 16). The commercial website category had the highest average HA-specific content score, followed by the governmental and NPO category. Sites that bore the HONcode certification obtained significantly higher DISCERN scores than those without the certification (P = .0032) but did not obtain significantly higher HA-specific content scores. "Hip arthroscopy" is a fairly general term, and there is significant variability in the quality of HA information available online. The HONcode is useful to identify quality patient information websites; however, it is not commonly used in HA-specific websites and does not encompass all quality websites about HA. This study increases awareness of the quality of information on HA available online. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

The Association Between Dietary Quality and Overall and Cancer-Specific Mortality Among Cancer Survivors, NHANES III.

PubMed

Deshmukh, Ashish A; Shirvani, Shervin M; Likhacheva, Anna; Chhatwal, Jagpreet; Chiao, Elizabeth Y; Sonawane, Kalyani

2018-04-01

Given the recent emphasis on the totality of the diet by national guidelines, we examined the relationship between the quality of diet and overall and cancer-specific mortality among cancer survivors. From the Third National Health and Nutrition Examination Survey (NHANES III), 1191 participants diagnosed with cancer were identified. Healthy Eating Index (HEI) scores were utilized; higher HEI score indicated better adherence to dietary recommendations. During a median follow-up of 17.2 years, a total of 607 cancer-specific deaths occurred. A high-quality diet (highest-quartile HEI score) was associated with decreased risk of overall (hazard ratio [HR] = 0.59, 95% confidence interval [CI] = 0.45 to 0.77) and cancer-specific (HR = 0.35, 95% CI = 0.19 to 0.63) mortality when compared with a poor-quality diet (lowest-quartile HEI score). Among individual dietary components, the highest-quartile score for saturated fat intake was associated decreased cancer-specific mortality (HR = 0.55, 95% CI = 0.36 to 0.86). Our results highlight the importance of a "total diet" approach to improving survival among cancer patients.

Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis.

PubMed

Lindén, Rolf O; Eronen, Ville-Pekka; Aittokallio, Tero

2011-03-24

High-throughput genetic screening approaches have enabled systematic means to study how interactions among gene mutations contribute to quantitative fitness phenotypes, with the aim of providing insights into the functional wiring diagrams of genetic interaction networks on a global scale. However, it is poorly known how well these quantitative interaction measurements agree across the screening approaches, which hinders their integrated use toward improving the coverage and quality of the genetic interaction maps in yeast and other organisms. Using large-scale data matrices from epistatic miniarray profiling (E-MAP), genetic interaction mapping (GIM), and synthetic genetic array (SGA) approaches, we carried out here a systematic comparative evaluation among these quantitative maps of genetic interactions in yeast. The relatively low association between the original interaction measurements or their customized scores could be improved using a matrix-based modelling framework, which enables the use of single- and double-mutant fitness estimates and measurements, respectively, when scoring genetic interactions. Toward an integrative analysis, we show how the detections from the different screening approaches can be combined to suggest novel positive and negative interactions which are complementary to those obtained using any single screening approach alone. The matrix approximation procedure has been made available to support the design and analysis of the future screening studies. We have shown here that even if the correlation between the currently available quantitative genetic interaction maps in yeast is relatively low, their comparability can be improved by means of our computational matrix approximation procedure, which will enable integrative analysis and detection of a wider spectrum of genetic interactions using data from the complementary screening approaches.

Pro-angiogenic capacities of microvesicles produced by skin wound myofibroblasts.

PubMed

Merjaneh, Mays; Langlois, Amélie; Larochelle, Sébastien; Cloutier, Chanel Beaudoin; Ricard-Blum, Sylvie; Moulin, Véronique J

2017-08-01

Wound healing is a very highly organized process where numerous cell types are tightly regulated to restore injured tissue. Myofibroblasts are cells that produce new extracellular matrix and contract wound edges. We previously reported that the human myofibroblasts isolated from normal wound (WMyos) produced microvesicles (MVs) in the presence of the serum. In this study, MVs were further characterized using a proteomic strategy and potential functions of the MVs were determined. MV proteins isolated from six WMyo populations were separated using two-dimensional differential gel electrophoresis. Highly conserved spots were selected and analyzed using mass spectrometry resulting in the identification of 381 different human proteins. Using the DAVID database, clusters of proteins involved in cell motion, apoptosis and adhesion, but also in extracellular matrix production (21 proteins, enrichment score: 3.32) and in blood vessel development/angiogenesis (19 proteins, enrichment score: 2.66) were identified. Another analysis using the functional enrichment analysis tool FunRich was consistent with these results. While the action of the myofibroblasts on extracellular matrix formation is well known, their angiogenic potential is less studied. To further characterize the angiogenic activity of the MVs, they were added to cultured microvascular endothelial cells to evaluate their influence on cell growth and migration using scratch test and capillary-like structure formation in Matrigel ® . The addition of a MV-enriched preparation significantly increased endothelial cell growth, migration and capillary formation compared with controls. The release of microvesicles by the wound myofibroblasts brings new perspectives to the field of communication between cells during the normal healing process.

Students' proficiency scores within multitrait item response theory

NASA Astrophysics Data System (ADS)

Scott, Terry F.; Schumayer, Daniel

2015-12-01

In this paper we present a series of item response models of data collected using the Force Concept Inventory. The Force Concept Inventory (FCI) was designed to poll the Newtonian conception of force viewed as a multidimensional concept, that is, as a complex of distinguishable conceptual dimensions. Several previous studies have developed single-trait item response models of FCI data; however, we feel that multidimensional models are also appropriate given the explicitly multidimensional design of the inventory. The models employed in the research reported here vary in both the number of fitting parameters and the number of underlying latent traits assumed. We calculate several model information statistics to ensure adequate model fit and to determine which of the models provides the optimal balance of information and parsimony. Our analysis indicates that all item response models tested, from the single-trait Rasch model through to a model with ten latent traits, satisfy the standard requirements of fit. However, analysis of model information criteria indicates that the five-trait model is optimal. We note that an earlier factor analysis of the same FCI data also led to a five-factor model. Furthermore the factors in our previous study and the traits identified in the current work match each other well. The optimal five-trait model assigns proficiency scores to all respondents for each of the five traits. We construct a correlation matrix between the proficiencies in each of these traits. This correlation matrix shows strong correlations between some proficiencies, and strong anticorrelations between others. We present an interpretation of this correlation matrix.

Real-world surgical outcomes of a gelatin-hemostatic matrix in women requiring a hysterectomy: a matched case-control study.

PubMed

Obermair, Helena; Janda, Monika; Obermair, Andreas

2016-09-01

The aim of this study was to compare adverse events and surgical outcomes of hysterectomy with or without use of a gelatin-hemostatic matrix (SURGIFLO(®) ). Prospective case-control study (Canadian Task Force classification II2) of total hysterectomy (Piver Type 1) provided by surgeons in Australia between November 2005 and May 2015. Data were collected via SurgicalPerformance, a web-based data project which aims to provide confidential feedback to surgeons about their surgical outcomes. Of 2440 records of women who received a hysterectomy, 1351 were eligible for these analyses; 107 received SURGIFLO(®) hemostatic matrix to prevent postoperative blood loss and 1244 did not. Patients with or without SURGIFLO(®) differed in age, Charlson comorbidity index, and American Society of Anesthesiologists physical status classification system score (ASA), and also differed in clinical outcomes. After matching for patient's age and ASA at surgery, patients with and without SURGIFLO(®) had comparable baseline characteristics. Matched patients with and without SURGIFLO(®) had comparable clinical outcomes including risk of developing vault hematoma, return to the operating room, transfusion of red cells, surgical site infection (pelvis), readmission within 30 days and unplanned ICU admission. In a sample matched by age and ASA, SURGIFLO(®) neither prevented nor caused additional adverse events in women undergoing hysterectomy. Surgeons used SURGIFLO(®) more commonly among women who were older, had more comorbidities and a higher ASA score. This indicates that it may be most useful in complicated surgery or cases. © 2016 Nordic Federation of Societies of Obstetrics and Gynecology.

Mapping Cultural Ecosystem Services in Vilnius using Hot-Spot Analysis.

NASA Astrophysics Data System (ADS)

Pereira, Paulo; Depellegrin, Daniel; Egarter-Vigl, Lukas; Oliva, Marc; Misiune, Ieva; Keesstra, Saskia; Estebaranz, Ferran; Cerda, Artemi

2017-04-01

Cultural services in urban areas are very important to promote tourism activities and develop the economy. These activities are fundamental for the sustainability of the urban areas since can represent an important monetary source. However, one of the major threats to the sustainability of cultural services is the high amount of visitants that can lead to a degradation of the services provided (Depellegrin et al., 2016). Mapping the potential of cultural ecosystems services is fundamental to assess the capacity that the territory have to provide it. Previous works used land use classification to identify the ecosystem services potential, and revealed to be a good methodology to attribute to each type of land use a specific capacity (Burkhard et al., 2008). The objective of this work is to map the cultural services in Vilnius area using a hot-spot analysis. Ecosystem services potential was assessed using the matrix developed by Burkhard et al. (2009), which ranks ES capacity from 0= no capacity to 5=very high relevant capacity to a different land use type. The results showed that with the exception of Cultural Heritage ecosystem services that had a random pattern (Z-score=0.62, p<0.530), all the others had clustered pattern: Recreation and Tourism (Z-score=4.02, p<0.001), Landscape Aesthetics (Z-score=4.44, p<0.001), Knowledge Systems (Z-score=4.15, p<0.001), Religious and Spiritual (Z-score=3.80, p<0.001) and Natural Heritage (Z-score=5.64, p<0.001). The incremental Moran's I result showed that Recreation and Tourism ecosystem services had the maximum spatial correlation at the distance of 5125.12 m, Landscape Aesthetics at 3495.70 m, Knowledge Systems at 5218.66 m, Religious and Spiritual at 3495.70 m, Cultural Heritage at 6746.17 m and Natural Heritage at 6205.82 m. This showed that the cultural services studied have a different spatial correlation. References Burkhard B, Kroll F, Müller F, Windhorst W. 2009. Landscapes' capacities to provide ecosystem services- a concept for land-cover based assessments. Landscape Online. 15, 1-22. Depellegrin, D.A., Pereira, P., Misiune, I., Egarter-Vigl, L. Mapping Ecosystem Services potential in Lithuania. International Journal of Sustainable Development and World Ecology, 23, 441-455.

Black box multigrid

NASA Technical Reports Server (NTRS)

Dendy, J. E., Jr.

1981-01-01

The black box multigrid (BOXMG) code, which only needs specification of the matrix problem for application in the multigrid method was investigated. It is contended that a major problem with the multigrid method is that each new grid configuration requires a major programming effort to develop a code that specifically handles that grid configuration. The SOR and ICCG methods only specify the matrix problem, no matter what the grid configuration. It is concluded that the BOXMG does everything else necessary to set up the auxiliary coarser problems to achieve a multigrid solution.

A Comparison of Methods for Estimating the Determinant of High-Dimensional Covariance Matrix.

PubMed

Hu, Zongliang; Dong, Kai; Dai, Wenlin; Tong, Tiejun

2017-09-21

The determinant of the covariance matrix for high-dimensional data plays an important role in statistical inference and decision. It has many real applications including statistical tests and information theory. Due to the statistical and computational challenges with high dimensionality, little work has been proposed in the literature for estimating the determinant of high-dimensional covariance matrix. In this paper, we estimate the determinant of the covariance matrix using some recent proposals for estimating high-dimensional covariance matrix. Specifically, we consider a total of eight covariance matrix estimation methods for comparison. Through extensive simulation studies, we explore and summarize some interesting comparison results among all compared methods. We also provide practical guidelines based on the sample size, the dimension, and the correlation of the data set for estimating the determinant of high-dimensional covariance matrix. Finally, from a perspective of the loss function, the comparison study in this paper may also serve as a proxy to assess the performance of the covariance matrix estimation.

Development of Risk Assessment Matrix for NASA Engineering and Safety Center

NASA Technical Reports Server (NTRS)

Malone, Roy W., Jr.; Moses, Kelly

2004-01-01

This paper describes a study, which had as its principal goal the development of a sufficiently detailed 5 x 5 Risk Matrix Scorecard. The purpose of this scorecard is to outline the criteria by which technical issues can be qualitatively and initially prioritized. The tool using this score card has been proposed to be one of the information resources the NASA Engineering and Safety Center (NESC) takes into consideration when making decisions with respect to incoming information on safety concerns across the entire NASA agency. The contents of this paper discuss in detail each element of the risk matrix scorecard, definitions for those elements and the rationale behind the development of those definitions. This scorecard development was performed in parallel with the tailoring of the existing Futron Corporation Integrated Risk Management Application (IRMA) software tool. IRMA was tailored to fit NESC needs for evaluating incoming safety concerns and was renamed NESC Assessment Risk Management Application (NAFMA) which is still in developmental phase.

Method for the removal and recovery of mercury

DOEpatents

Easterly, Clay E.; Vass, Arpad A.; Tyndall, Richard L.

1997-01-01

The present invention is an enhanced method for the removal and recovery of mercury from mercury-contaminated matrices. The method involves contacting a mercury-contaminated matrix with an aqueous dispersant solution derived from specific intra-amoebic isolates to release the mercury from the mercury-contaminated matrix and emulsify the mercury; then, contacting the matrix with an amalgamating metal from a metal source to amalgamate the mercury to the amalgamating metal; removing the metallic source from the mercury-contaminated matrix; and heating the metallic source to vaporize the mercury in a closed system to capture the mercury vapors.

Method for the removal and recovery of mercury

DOEpatents

Easterly, C.E.; Vass, A.A.; Tyndall, R.L.

1997-01-28

The present invention is an enhanced method for the removal and recovery of mercury from mercury-contaminated matrices. The method involves contacting a mercury-contaminated matrix with an aqueous dispersant solution derived from specific intra-amoebic isolates to release the mercury from the mercury-contaminated matrix and emulsify the mercury; then, contacting the matrix with an amalgamating metal from a metal source to amalgamate the mercury to the amalgamating metal; removing the metallic source from the mercury-contaminated matrix; and heating the metallic source to vaporize the mercury in a closed system to capture the mercury vapors.

Lameness scoring system for dairy cows using force plates and artificial intelligence.

PubMed

Ghotoorlar, S Mokaram; Ghamsari, S Mehdi; Nowrouzian, I; Ghotoorlar, S Mokaram; Ghidary, S Shiry

2012-02-04

Lameness scoring is a routine procedure in dairy industry to screen the herds for new cases of lameness. Subjective lameness scoring, which is the most popular lameness detection and screening method in dairy herds, has several limitations. They include low intra-observer and inter-observer agreement and the discrete nature of the scores which limits its usage in monitoring the lameness. The aim of this study is to develop an automated lameness scoring system comparable with conventional subjective lameness scoring by means of artificial neural networks. The system is composed of four balanced force plates installed in a hoof-trimming box. A group of 105 dairy cows was used for the study. Twenty-three features extracted from ground reaction force (GRF) data were used in a computer training process which was performed on 60 per cent of the data. The remaining 40 per cent of the data were used to test the trained system. Repeatability of the lameness scoring system was determined by GRF samples from 25 cows, captured at two different times from the same animals. The mean sd was 0.31 and the mean coefficient of variation was 14.55 per cent, which represents a high repeatability in comparison with subjective vision-based scoring methods. Although the highest sensitivity and specificity values were seen in locomotion score groups 1 and 4, the automatic lameness system was both sensitive and specific in all groups. The sensitivity and specificity were higher than 72 per cent in locomotion score groups 1 to 4, and it was 100 per cent specific and 50 per cent sensitive for group 5.

Tissue matrix arrays for high throughput screening and systems analysis of cell function

PubMed Central

Beachley, Vince Z.; Wolf, Matthew T.; Sadtler, Kaitlyn; Manda, Srikanth S.; Jacobs, Heather; Blatchley, Michael; Bader, Joel S.; Pandey, Akhilesh; Pardoll, Drew; Elisseeff, Jennifer H.

2015-01-01

Cell and protein arrays have demonstrated remarkable utility in the high-throughput evaluation of biological responses; however, they lack the complexity of native tissue and organs. Here, we describe tissue extracellular matrix (ECM) arrays for screening biological outputs and systems analysis. We spotted processed tissue ECM particles as two-dimensional arrays or incorporated them with cells to generate three-dimensional cell-matrix microtissue arrays. We then investigated the response of human stem, cancer, and immune cells to tissue ECM arrays originating from 11 different tissues, and validated the 2D and 3D arrays as representative of the in vivo microenvironment through quantitative analysis of tissue-specific cellular responses, including matrix production, adhesion and proliferation, and morphological changes following culture. The biological outputs correlated with tissue proteomics, and network analysis identified several proteins linked to cell function. Our methodology enables broad screening of ECMs to connect tissue-specific composition with biological activity, providing a new resource for biomaterials research and translation. PMID:26480475

Correlates of disease-specific knowledge in Chinese patients with COPD.

PubMed

Wong, Carlos Kh; Yu, W C

2016-01-01

This study aimed to determine the associations of various sociodemographic factors with the level of disease-specific knowledge among Hong Kong Chinese patients with COPD. A cross-sectional survey of 100 Chinese adults with COPD recruited from outpatient clinics was conducted from September 2009 to September 2010. Data on the knowledge specific to COPD and patients' sociodemographics were collected from face-to-face interviews. Primary outcome of disease-specific knowledge was measured using 65-item Bristol COPD Knowledge Questionnaire (BCKQ), summing up the 65 items as the BCKQ overall score. Associations of sociodemographic factors with the BCKQ overall score were evaluated using the linear regression model. The mean BCKQ overall score of our patients was 41.01 (SD: 10.64). The knowledge in topics of "Smoking" and "Phlegm" achieved the first (3.97, SD: 0.82) and second (3.91, SD: 1.17) highest mean scores, respectively, while the topic of "Oral steroids" returned the lowest mean score of 1.89 (SD: 1.64). The BCKQ overall score progressively declined ( P <0.001) with increase in education level, with the highest BCKQ overall score of 46.71 at no formal education among all subgroups. Compared to nondrinkers, current drinkers were associated with lower total BCKQ score. We found that among COPD patients in outpatient clinics, impairments in the level of COPD knowledge were evident in patients who were current drinkers or had higher level of education.

Constructing the matrix

NASA Astrophysics Data System (ADS)

Elliott, John

2012-09-01

As part of our 'toolkit' for analysing an extraterrestrial signal, the facility for calculating structural affinity to known phenomena must be part of our core capabilities. Without such a resource, we risk compromising our potential for detection and decipherment or at least causing significant delay in the process. To create such a repository for assessing structural affinity, all known systems (language parameters) need to be structurally analysed to 'place' their 'system' within a relational communication matrix. This will need to include all known variants of language structure, whether 'living' (in current use) or ancient; this must also include endeavours to incorporate yet undeciphered scripts and non-human communication, to provide as complete a picture as possible. In creating such a relational matrix, post-detection decipherment will be assisted by a structural 'map' that will have the potential for 'placing' an alien communication with its nearest known 'neighbour', to assist subsequent categorisation of basic parameters as a precursor to decipherment. 'Universal' attributes and behavioural characteristics of known communication structure will form a range of templates (Elliott, 2001 [1] and Elliott et al., 2002 [2]), to support and optimise our attempt at categorising and deciphering the content of an extraterrestrial signal. Detection of the hierarchical layers, which comprise intelligent, complex communication, will then form a matrix of calculations that will ultimately score affinity through a relational matrix of structural comparison. In this paper we develop the rationales and demonstrate functionality with initial test results.

A Bayesian Method for Evaluating Passing Scores: The PPoP Curve

ERIC Educational Resources Information Center

Wainer, Howard; Wang, X. A.; Skorupski, William P.; Bradlow, Eric T.

2005-01-01

In this note, we demonstrate an interesting use of the posterior distributions (and corresponding posterior samples of proficiency) that are yielded by fitting a fully Bayesian test scoring model to a complex assessment. Specifically, we examine the efficacy of the test in combination with the specific passing score that was chosen through expert…

Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.

PubMed

Sasse, Alexander; de Vries, Sjoerd J; Schindler, Christina E M; de Beauchêne, Isaure Chauvot; Zacharias, Martin

2017-01-01

Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scoring step is one of the bottlenecks in the performance of many state-of-the-art protocols. The performance of scoring functions depends on the quality of the generated structures and its coupling to the sampling algorithm. A tool kit, GRADSCOPT (GRid Accelerated Directly SCoring OPTimizing), was designed to allow rapid development and optimization of different knowledge-based scoring potentials for specific objectives in protein-protein docking. Different atomistic and coarse-grained potentials can be created by a grid-accelerated directly scoring dependent Monte-Carlo annealing or by a linear regression optimization. We demonstrate that the scoring functions generated by our approach are similar to or even outperform state-of-the-art scoring functions for predicting near-native solutions. Of additional importance, we find that potentials specifically trained to identify the native bound complex perform rather poorly on identifying acceptable or medium quality (near-native) solutions. In contrast, atomistic long-range contact potentials can increase the average fraction of near-native poses by up to a factor 2.5 in the best scored 1% decoys (compared to existing scoring), emphasizing the need of specific docking potentials for different steps in the docking protocol.

Dynamic Compression Promotes the Matrix Synthesis of Nucleus Pulposus Cells Through Up-Regulating N-CDH Expression in a Perfusion Bioreactor Culture.

PubMed

Xu, Yichun; Yao, Hui; Li, Pei; Xu, Wenbin; Zhang, Junbin; Lv, Lulu; Teng, Haijun; Guo, Zhiliang; Zhao, Huiqing; Hou, Gang

2018-01-01

An adequate matrix production of nucleus pulposus (NP) cells is an important tissue engineering-based strategy to regenerate degenerative discs. Here, we mainly aimed to investigate the effects and mechanism of mechanical compression (i.e., static compression vs. dynamic compression) on the matrix synthesis of three-dimensional (3D) cultured NP cells in vitro. Rat NP cells seeded on small intestinal submucosa (SIS) cryogel scaffolds were cultured in the chambers of a self-developed, mechanically active bioreactor for 10 days. Meanwhile, the NP cells were subjected to compression (static compression or dynamic compression at a 10% scaffold deformation) for 6 hours once per day. Unloaded NP cells were used as controls. The cellular phenotype and matrix biosynthesis of NP cells were investigated by real-time PCR and Western blotting assays. Lentivirus-mediated N-cadherin (N-CDH) knockdown and an inhibitor, LY294002, were used to further investigate the role of N-CDH and the PI3K/Akt pathway in this process. Dynamic compression better maintained the expression of cell-specific markers (keratin-19, FOXF1 and PAX1) and matrix macromolecules (aggrecan and collagen II), as well as N-CDH expression and the activity of the PI3K/Akt pathway, in the 3D-cultured NP cells compared with those expression levels and activity in the cells grown under static compression. Further analysis showed that the N-CDH knockdown significantly down-regulated the expression of NP cell-specific markers and matrix macromolecules and inhibited the activation of the PI3K/Akt pathway under dynamic compression. However, inhibition of the PI3K/Akt pathway had no effects on N-CDH expression but down-regulated the expression of NP cell-specific markers and matrix macromolecules under dynamic compression. Dynamic compression increases the matrix synthesis of 3D-cultured NP cells compared with that of the cells under static compression, and the N-CDH-PI3K/Akt pathway is involved in this regulatory process. This study provides a promising strategy to promote the matrix deposition of tissue-engineered NP tissue in vitro prior to clinical transplantation. © 2018 The Author(s). Published by S. Karger AG, Basel.

Interlaboratory Comparison of Sample Preparation Methods, Database Expansions, and Cutoff Values for Identification of Yeasts by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Using a Yeast Test Panel

PubMed Central

Vlek, Anneloes; Kolecka, Anna; Khayhan, Kantarawee; Theelen, Bart; Groenewald, Marizeth; Boel, Edwin

2014-01-01

An interlaboratory study using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) to determine the identification of clinically important yeasts (n = 35) was performed at 11 clinical centers, one company, and one reference center using the Bruker Daltonics MALDI Biotyper system. The optimal cutoff for the MALDI-TOF MS score was investigated using receiver operating characteristic (ROC) curve analyses. The percentages of correct identifications were compared for different sample preparation methods and different databases. Logistic regression analysis was performed to analyze the association between the number of spectra in the database and the percentage of strains that were correctly identified. A total of 5,460 MALDI-TOF MS results were obtained. Using all results, the area under the ROC curve was 0.95 (95% confidence interval [CI], 0.94 to 0.96). With a sensitivity of 0.84 and a specificity of 0.97, a cutoff value of 1.7 was considered optimal. The overall percentage of correct identifications (formic acid-ethanol extraction method, score ≥ 1.7) was 61.5% when the commercial Bruker Daltonics database (BDAL) was used, and it increased to 86.8% by using an extended BDAL supplemented with a Centraalbureau voor Schimmelcultures (CBS)-KNAW Fungal Biodiversity Centre in-house database (BDAL+CBS in-house). A greater number of main spectra (MSP) in the database was associated with a higher percentage of correct identifications (odds ratio [OR], 1.10; 95% CI, 1.05 to 1.15; P < 0.01). The results from the direct transfer method ranged from 0% to 82.9% correct identifications, with the results of the top four centers ranging from 71.4% to 82.9% correct identifications. This study supports the use of a cutoff value of 1.7 for the identification of yeasts using MALDI-TOF MS. The inclusion of enough isolates of the same species in the database can enhance the proportion of correctly identified strains. Further optimization of the preparation methods, especially of the direct transfer method, may contribute to improved diagnosis of yeast-related infections. PMID:24920782

45 CFR Appendix A to Subpart C of... - Security Standards: Matrix

Code of Federal Regulations, 2011 CFR

2011-10-01

... C of Part 164 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES ADMINISTRATIVE DATA STANDARDS... Protected Health Information Pt. 164, Subpt. C, App. A Appendix A to Subpart C of Part 164—Security Standards: Matrix Standards Sections Implementation Specifications (R)=Required, (A)=Addressable...

45 CFR Appendix A to Subpart C of... - Security Standards: Matrix

Code of Federal Regulations, 2010 CFR

2010-10-01

... C of Part 164 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES ADMINISTRATIVE DATA STANDARDS... Protected Health Information Pt. 164, Subpt. C, App. A Appendix A to Subpart C of Part 164—Security Standards: Matrix Standards Sections Implementation Specifications (R)=Required, (A)=Addressable...

Advanced Composites: Mechanical Properties and Hardware Programs for Selected Resin Matrix Materials. [considering space shuttle applications

NASA Technical Reports Server (NTRS)

Welhart, E. K.

1976-01-01

This design note presents typical mechanical properties tabulated from industrial and governmental agencies' test programs. All data are correlated to specific products and all of the best known products are presented. The data include six epoxies, eight polyimides and one polyquinoxaline matrix material. Bron and graphite are the fiber reinforcements. Included are forty-two summaries of advanced (resin matrix) composite programs in existence in the United States. It is concluded that the selection of appropriate matrices, the geometric manner in which the fibers are incorporated in the matrix and the durability of the bond between fiber and matrix establish the end properties of the composite material and the performance of the fabricated structure.

Generating Nonnormal Multivariate Data Using Copulas: Applications to SEM.

PubMed

Mair, Patrick; Satorra, Albert; Bentler, Peter M

2012-07-01

This article develops a procedure based on copulas to simulate multivariate nonnormal data that satisfy a prespecified variance-covariance matrix. The covariance matrix used can comply with a specific moment structure form (e.g., a factor analysis or a general structural equation model). Thus, the method is particularly useful for Monte Carlo evaluation of structural equation models within the context of nonnormal data. The new procedure for nonnormal data simulation is theoretically described and also implemented in the widely used R environment. The quality of the method is assessed by Monte Carlo simulations. A 1-sample test on the observed covariance matrix based on the copula methodology is proposed. This new test for evaluating the quality of a simulation is defined through a particular structural model specification and is robust against normality violations.

Matrix-specific distribution and diastereomeric profiles of hexabromocyclododecane (HBCD) in a multimedia environment: Air, soil, sludge, sediment, and fish.

PubMed

Jo, Hyeyeong; Son, Min-Hui; Seo, Sung-Hee; Chang, Yoon-Seok

2017-07-01

Hexabromocyclododecane (HBCD) contamination and its diastereomeric profile were investigated in a multi-media environment along a river at the local scale in air, soil, sludge, sediment, and fish samples. The spatial distribution of HBCD in each matrix showed a different result. The highest concentrations of HBCD in air and soil were detected near a general industrial complex; in the sediment and sludge samples, they were detected in the down-stream region (i.e., urban area). Each matrix showed the specific distribution patterns of HBCD diastereomers, suggesting continuous inputs of contaminants, different physicochemical properties, or isomerizations. The particle phases in air, sludge, and fish matrices were dominated by α-HBCD, owing to HBCD's various isomerization processes and different degradation rate in the environment, and metabolic capabilities of the fish; in contrast, the sediment and soil matrices were dominated by γ-HBCD because of the major composition of the technical mixtures and the strong adsorption onto solid particles. Based on these results, the prevalent and matrix-specific distribution of HBCD diastereomers suggested that more careful consideration should be given to the characteristics of the matrices and their effects on the potential influence of HBCD at the diastereomeric level. Copyright © 2017 Elsevier Ltd. All rights reserved.

Targeting the extracellular matrix of ovarian cancer using functionalized, drug loaded lyophilisomes.

PubMed

van der Steen, Sophieke C H A; Raavé, René; Langerak, Sjoerd; van Houdt, Laurens; van Duijnhoven, Sander M J; van Lith, Sanne A M; Massuger, Leon F A G; Daamen, Willeke F; Leenders, William P; van Kuppevelt, Toin H

2017-04-01

Epithelial ovarian cancer is characterized by a high mortality rate and is in need for novel therapeutic avenues to improve patient outcome. The tumor's extracellular matrix ("stroma") offers new possibilities for targeted drug-delivery. Recently we identified highly sulfated chondroitin sulfate (CS-E) as a component abundantly present in the ovarian cancer extracellular matrix, and as a novel target for anti-cancer therapy. Here, we report on the functionalization of drug-loaded lyophilisomes (albumin-based biocapsules) to specifically target the stroma of ovarian carcinomas with the potential to eliminate cancer cells. To achieve specific targeting, we conjugated single chain antibodies reactive with CS-E to lyophilisomes using a two-step approach comprising sortase-mediated ligation and bioorthogonal click chemistry. Antibody-functionalized lyophilisomes specifically targeted the ovarian cancer stroma through CS-E. In a CS-E rich micro-environment in vitro lyophilisomes induced cell death by extracellular release of doxorubicin which localized to the nucleus. Immunohistochemistry identified CS-E rich stroma in a variety of solid tumors other than ovarian cancer, including breast, lung and colon cancer indicating the potential versatility of matrix therapy and the use of highly sulfated chondroitin sulfates in cancer stroma as a micro-environmental hook for targeted drug delivery. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Drug-target interaction prediction from PSSM based evolutionary information.

PubMed

Mousavian, Zaynab; Khakabimamaghani, Sahand; Kavousi, Kaveh; Masoudi-Nejad, Ali

2016-01-01

The labor-intensive and expensive experimental process of drug-target interaction prediction has motivated many researchers to focus on in silico prediction, which leads to the helpful information in supporting the experimental interaction data. Therefore, they have proposed several computational approaches for discovering new drug-target interactions. Several learning-based methods have been increasingly developed which can be categorized into two main groups: similarity-based and feature-based. In this paper, we firstly use the bi-gram features extracted from the Position Specific Scoring Matrix (PSSM) of proteins in predicting drug-target interactions. Our results demonstrate the high-confidence prediction ability of the Bigram-PSSM model in terms of several performance indicators specifically for enzymes and ion channels. Moreover, we investigate the impact of negative selection strategy on the performance of the prediction, which is not widely taken into account in the other relevant studies. This is important, as the number of non-interacting drug-target pairs are usually extremely large in comparison with the number of interacting ones in existing drug-target interaction data. An interesting observation is that different levels of performance reduction have been attained for four datasets when we change the sampling method from the random sampling to the balanced sampling. Copyright © 2015 Elsevier Inc. All rights reserved.

Patterns of Protein Food Intake Are Associated with Nutrient Adequacy in the General French Adult Population.

PubMed

Gavelle, Erwan de; Huneau, Jean-François; Mariotti, François

2018-02-17

Protein food intake appears to partially structure dietary patterns, as most current emergent diets (e.g., vegetarian and flexitarian) can be described according to their levels of specific protein sources. However, few data are available on dietary protein patterns in the general population and their association with nutrient adequacy. Based on protein food intake data concerning 1678 adults from a representative French national dietary survey, and non-negative-matrix factorization followed by cluster analysis, we were able to identify distinctive dietary protein patterns and compare their nutrient adequacy (using PANDiet probabilistic scoring). The findings revealed eight patterns that clearly discriminate protein intakes and were characterized by the intakes of one or more specific protein foods: 'Processed meat', 'Poultry', 'Pork', 'Traditional', 'Milk', 'Take-away', 'Beef' and 'Fish'. 'Fish eaters' and 'Milk drinkers' had the highest overall nutrient adequacy, whereas that of 'Pork' and 'Take-away eaters' was the lowest. Nutrient adequacy could often be accounted for by the characteristics of the food contributing to protein intake: 'Meat eaters' had high probability of adequacy for iron and zinc, for example. We concluded that protein patterns constitute strong elements in the background structure of the dietary intake and are associated with the nutrient profile that they convey.

Wechsler Adult Intelligence Scale-Third Edition short form for index and IQ scores in a psychiatric population.

PubMed

Christensen, Bruce K; Girard, Todd A; Bagby, R Michael

2007-06-01

An eight-subtest short form (SF8) of the Wechsler Adult Intelligence Scale, Third Edition (WAIS-III), maintaining equal representation of each index factor, was developed for use with psychiatric populations. Data were collected from a mixed inpatient/outpatient sample (99 men and 101 women) referred for neuropsychological assessment. Psychometric analyses revealed an optimal SF8 comprising Vocabulary, Similarities, Arithmetic, Digit Span, Picture Completion, Matrix Reasoning, Digit Symbol Coding, and Symbol Search, scored by linear scaling. Expanding on previous short forms, the current SF8 maximizes the breadth of information and reduces administration time while maintaining the original WAIS-III factor structure. (c) 2007 APA, all rights reserved

Efficacy of functional movement screening for predicting injuries in coast guard cadets.

PubMed

Knapik, Joseph J; Cosio-Lima, Ludimila M; Reynolds, Katy L; Shumway, Richard S

2015-05-01

Functional movement screening (FMS) examines the ability of individuals to perform highly specific movements with the aim of identifying individuals who have functional limitations or asymmetries. It is assumed that individuals who can more effectively accomplish the required movements have a lower injury risk. This study determined the ability of FMS to predict injuries in the United States Coast Guard (USCG) cadets. Seven hundred seventy male and 275 female USCG freshman cadets were administered the 7 FMS tests before the physically intense 8-week Summer Warfare Annual Basic (SWAB) training. Physical training-related injuries were recorded during SWAB training. Cumulative injury incidence was calculated at various FMS cutpoint scores. The ability of the FMS total score to predict injuries was examined by calculating sensitivity and specificity. Determination of the FMS cutpoint that maximized specificity and sensitivity was determined from the Youden's index (sensitivity + specificity - 1). For men, FMS scores ≤ 12 were associated with higher injury risk than scores >12; for women, FMS scores ≤ 15 were associated with higher injury risk than scores >15. The Youden's Index indicated that the optimal FMS cutpoint was ≤ 11 for men (22% sensitivity, 87% specificity) and ≤ 14 for women (60% sensitivity, 61% specificity). Functional movement screening demonstrated moderate prognostic accuracy for determining injury risk among female Coast Guard cadets but relatively low accuracy among male cadets. Attempting to predict injury risk based on the FMS test seems to have some limited promise based on the present and past investigations.

Comparative Effect of Physicomechanical and Biomolecular Cues on Zone-Specific Chondrogenic Differentiation of Mesenchymal Stem Cells

PubMed Central

Moeinzadeh, Seyedsina; Shariati, Seyed Ramin Pajoum; Jabbari, Esmaiel

2016-01-01

Current tissue engineering approaches to regeneration of articular cartilage rarely restore the tissue to its normal state because the generated tissue lacks the intricate zonal organization of the native cartilage. Zonal regeneration of articular cartilage is hampered by the lack of knowledge for the relation between physical, mechanical, and biomolecular cues and zone-specific chondrogenic differentiation of progenitor cells. This work investigated in 3D the effect of TGF-β1, zone-specific growth factors, optimum matrix stiffness, and adding nanofibers on the expression of chondrogenic markers specific to the superficial, middle, and calcified zones of articular cartilage by the differentiating human mesenchymal stem cells (hMSCs). Growth factors included BMP-7, IGF-1, and hydroxyapatite (HA) for the superficial, middle, and calcified zones, respectively; optimum matrix stiffness was 80 kPa, 2.1 MPa, and 320 MPa; and nanofibers were aligned horizontal, random, and perpendicular to the gel surface. hMSCs with zone-specific cell densities were encapsulated in engineered hydrogels and cultured with or without TGF-β1, zone-specific growth factor, optimum matrix modulus, and fiber addition and cultured in basic chondrogenic medium. The expression of encapsulated cells was measured by mRNA, protein, and biochemical analysis. Results indicated that zone-specific matrix stiffness had a dominating effect on chondrogenic differentiation of hMSCs to the superficial and calcified zone phenotypes. Addition of aligned nanofibers parallel to the direction of gel surface significantly enhanced expression of Col II in the superficial zone chondrogenic differentiation of hMSCs. Conversely, biomolecular factor IGF-1 in combination with TGF-β1 had a dominating effect on the middle zone chondrogenic differentiation of hMSCs. Results of this work could potentially lead to the development of multilayer grafts mimicking the zonal organization of articular cartilage. PMID:27038568

Assessing a Critical Aspect of Construct Continuity when Test Specifications Change or Test Forms Deviate from Specifications

ERIC Educational Resources Information Center

Liu, Jinghua; Dorans, Neil J.

2013-01-01

We make a distinction between two types of test changes: inevitable deviations from specifications versus planned modifications of specifications. We describe how score equity assessment (SEA) can be used as a tool to assess a critical aspect of construct continuity, the equivalence of scores, whenever planned changes are introduced to testing…

A novel gene expression-based prognostic scoring system to predict survival in gastric cancer

DOE PAGES

Wang, Pin; Wang, Yunshan; Hang, Bo; ...

2016-07-11

Analysis of gene expression patterns in gastric cancer (GC) can help to identify a comprehensive panel of gene biomarkers for predicting clinical outcomes and to discover potential new therapeutic targets. Here, a multi-step bioinformatics analytic approach was developed to establish a novel prognostic scoring system for GC. We first identified 276 genes that were robustly differentially expressed between normal and GC tissues, of which, 249 were found to be significantly associated with overall survival (OS) by univariate Cox regression analysis. The biological functions of 249 genes are related to cell cycle, RNA/ncRNA process, acetylation and extracellular matrix organization. A networkmore » was generated for view of the gene expression architecture of 249 genes in 265 GCs. Finally, we applied a canonical discriminant analysis approach to identify a 53-gene signature and a prognostic scoring system was established based on a canonical discriminant function of 53 genes. The prognostic scores strongly predicted patients with GC to have either a poor or good OS. Our study raises the prospect that the practicality of GC patient prognosis can be assessed by this prognostic scoring system.« less

A novel gene expression-based prognostic scoring system to predict survival in gastric cancer

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

Wang, Pin; Wang, Yunshan; Hang, Bo

Analysis of gene expression patterns in gastric cancer (GC) can help to identify a comprehensive panel of gene biomarkers for predicting clinical outcomes and to discover potential new therapeutic targets. Here, a multi-step bioinformatics analytic approach was developed to establish a novel prognostic scoring system for GC. We first identified 276 genes that were robustly differentially expressed between normal and GC tissues, of which, 249 were found to be significantly associated with overall survival (OS) by univariate Cox regression analysis. The biological functions of 249 genes are related to cell cycle, RNA/ncRNA process, acetylation and extracellular matrix organization. A networkmore » was generated for view of the gene expression architecture of 249 genes in 265 GCs. Finally, we applied a canonical discriminant analysis approach to identify a 53-gene signature and a prognostic scoring system was established based on a canonical discriminant function of 53 genes. The prognostic scores strongly predicted patients with GC to have either a poor or good OS. Our study raises the prospect that the practicality of GC patient prognosis can be assessed by this prognostic scoring system.« less

SH2 Ligand Prediction-Guidance for In-Silico Screening.

PubMed

Li, Shawn S C; Li, Lei

2017-01-01

Systematic identification of binding partners for SH2 domains is important for understanding the biological function of the corresponding SH2 domain-containing proteins. Here, we describe two different web-accessible computer programs, SMALI and DomPep, for predicting binding ligands for SH2 domains. The former was developed using a Scoring Matrix method and the latter based on the Support Vector Machine model.

The Effects of Acute Stress on Cognitive Performance. A Pilot Study

DTIC Science & Technology

2010-12-01

Correlation Matrix – Stress Response Measures. ................................ 13  Table 4. Non-significant HRV Results...validity and reliability. The State-Trait Anxiety Index (or STAI; Spielberger and Sydeman, 1994) is a popular self-report instrument of this type...and provides distinct scores for state anxiety (a property of the situation) and trait anxiety (a property of the individual) using a 4-point rating

[Diagnostic value of integral scoring systems in assessing the severity of acute pancreatitis and patient's condition].

PubMed

Vinnik, Y S; Dunaevskaya, S S; Antufrieva, D A

2015-01-01

The aim of the study was to evaluate the diagnostic value of specific and nonspecific scoring systems Tolstoy-Krasnogorov score, Ranson, BISAP, Glasgow, MODS 2, APACHE II and CTSI, which used at urgent pancreatology for estimation the severity of acute pancreatitis and status of patient. 1550 case reports of patients which had inpatient surgical treatment at Road clinical hospital at the station Krasnoyarsk from 2009 till 2013 were analyzed. Diagnosis of severe acute pancreatitis and its complications were determined based on anamnestic data, physical exami- nation, clinical indexes, ultrasonic examination and computed tomography angiography. Specific and nonspecific scores (scoring system of estimation by Tolstoy-Krasnogorov, Ranson, Glasgow, BISAP, MODS 2, APACHE II, CTSI) were used for estimation the severity of acute pancreatitis and patient's general condition. Effectiveness of these scoring systems was determined based on some parameters: accuracy (Ac), sensitivity (Se), specificity (Sp), positive predictive value (PPV) and negative predictive value (NPV). Most valuables score for estimation of acute pancreatitis's severity is BISAP (Se--98.10%), for estimation of organ failure--MODS 2 (Sp--100%, PPV--100%) and APACHE II (Sp--100%, PPV--100%), for detection of pancreatonecrosis sings--CTSI (Sp--100%, NPV--100%), for estimation of need for intensive care--MODS 2 (Sp--100%, PPV--100%, NPV--96.29%) and APACHE II (Sp--100%, PPV--100%, NPV--97.21%), for prediction of lethality--MODS 2 (Se-- 100%, Sp--98.14%, NPV--100%) and APACHE II (Se--95.00%, NPV-.99.86%). Most effective scores for estimation of acute pancreatitis's severity are Score of estimation by Tolstoy-Krasnogorov, Ranson, Glasgow and BISAP Scoring systems MODS 2, APACHE I high specificity and positive predictive value allow using it at clinical practice.

CT technology overview.

PubMed

Frazee, D

2001-01-01

I hope that you will find the product matrix to be a useful tool for making comparisons between vendors and scanners. Please keep in mind that the vendors have directly provided the specific answers to the questions within the matrix. Neither the author nor Radiology Management shall be held responsible for any misrepresented or erroneous data.

THE INFLUENCE OF MODEL TIME STEP ON THE RELATIVE SENSITIVITY OF POPULATION GROWTH TO SURVIVAL, GROWTH AND REPRODUCTION

EPA Science Inventory

Matrix population models are often used to extrapolate from life stage-specific stressor effects on survival and reproduction to population-level effects. Demographic elasticity analysis of a matrix model allows an evaluation of the relative sensitivity of population growth rate ...

The influence of extracelluar matrix on intramuscular and extramuscular adipogenesis

USDA-ARS?s Scientific Manuscript database

The extracellular matrix (ECM) and specific ECM components can have a major influence on cell growth, development and phenotype. The influence of the ECM and ECM components on adipogenesis in vivo and in vitro will be reviewed. Engelbreth-Holm-Swarm (EHS) substratum and laminin per se markedly incre...

Investigation of Laser Generation and Detection of Ultrasound in Ceramic Matrix Composites and Intermetallics

NASA Technical Reports Server (NTRS)

Ehrlich, Michael J.

1998-01-01

The goal of this program is to assess the feasibility of using laser based ultrasonic techniques for inspecting and characterizing materials of interest to NASA, specifically those used in propulsion and turbomachinery applications, such as ceramic composites, metal matrix composites, and intermetallics.

Determination of phytate in high molecular weight, charged organic matrices by two-dimensional size exclusion-ion chromatography

USDA-ARS?s Scientific Manuscript database

A two-dimensional chromatography method for analyzing anionic targets (specifically phytate) in complex matrices is described. Prior to quantification by anion exchange chromatography, the sample matrix was prepared by size exclusion chromatography, which removed the majority of matrix complexities....

A Chess-Like Game for Teaching Engineering Students to Solve Large System of Simultaneous Linear Equations

NASA Technical Reports Server (NTRS)

Nguyen, Duc T.; Mohammed, Ahmed Ali; Kadiam, Subhash

2010-01-01

Solving large (and sparse) system of simultaneous linear equations has been (and continues to be) a major challenging problem for many real-world engineering/science applications [1-2]. For many practical/large-scale problems, the sparse, Symmetrical and Positive Definite (SPD) system of linear equations can be conveniently represented in matrix notation as [A] {x} = {b} , where the square coefficient matrix [A] and the Right-Hand-Side (RHS) vector {b} are known. The unknown solution vector {x} can be efficiently solved by the following step-by-step procedures [1-2]: Reordering phase, Matrix Factorization phase, Forward solution phase, and Backward solution phase. In this research work, a Game-Based Learning (GBL) approach has been developed to help engineering students to understand crucial details about matrix reordering and factorization phases. A "chess-like" game has been developed and can be played by either a single player, or two players. Through this "chess-like" open-ended game, the players/learners will not only understand the key concepts involved in reordering algorithms (based on existing algorithms), but also have the opportunities to "discover new algorithms" which are better than existing algorithms. Implementing the proposed "chess-like" game for matrix reordering and factorization phases can be enhanced by FLASH [3] computer environments, where computer simulation with animated human voice, sound effects, visual/graphical/colorful displays of matrix tables, score (or monetary) awards for the best game players, etc. can all be exploited. Preliminary demonstrations of the developed GBL approach can be viewed by anyone who has access to the internet web-site [4]!

Assessment of the Speech Intelligibility Performance of Post Lingual Cochlear Implant Users at Different Signal-to-Noise Ratios Using the Turkish Matrix Test.

PubMed

Polat, Zahra; Bulut, Erdoğan; Ataş, Ahmet

2016-09-01

Spoken word recognition and speech perception tests in quiet are being used as a routine in assessment of the benefit which children and adult cochlear implant users receive from their devices. Cochlear implant users generally demonstrate high level performances in these test materials as they are able to achieve high level speech perception ability in quiet situations. Although these test materials provide valuable information regarding Cochlear Implant (CI) users' performances in optimal listening conditions, they do not give realistic information regarding performances in adverse listening conditions, which is the case in the everyday environment. The aim of this study was to assess the speech intelligibility performance of post lingual CI users in the presence of noise at different signal-to-noise ratio with the Matrix Test developed for Turkish language. Cross-sectional study. The thirty post lingual implant user adult subjects, who had been using implants for a minimum of one year, were evaluated with Turkish Matrix test. Subjects' speech intelligibility was measured using the adaptive and non-adaptive Matrix Test in quiet and noisy environments. The results of the study show a correlation between Pure Tone Average (PTA) values of the subjects and Matrix test Speech Reception Threshold (SRT) values in the quiet. Hence, it is possible to asses PTA values of CI users using the Matrix Test also. However, no correlations were found between Matrix SRT values in the quiet and Matrix SRT values in noise. Similarly, the correlation between PTA values and intelligibility scores in noise was also not significant. Therefore, it may not be possible to assess the intelligibility performance of CI users using test batteries performed in quiet conditions. The Matrix Test can be used to assess the benefit of CI users from their systems in everyday life, since it is possible to perform intelligibility test with the Matrix test using a material that CI users experience in their everyday life and it is possible to assess their difficulty in speech discrimination in noisy conditions they have to cope with.

Diagnostic Accuracy, Sensitivity, and Specificity of Executive Function Tests in Moderate Traumatic Brain Injury in Ghana.

PubMed

Adjorlolo, Samuel

2018-06-01

The sociocultural differences between Western and sub-Saharan African countries make it imperative to standardize neuropsychological tests in the latter. However, Western-normed tests are frequently administered in sub-Saharan Africa because of challenges hampering standardization efforts. Yet a salient topical issue in the cross-cultural neuropsychology literature relates to the utility of Western-normed neuropsychological tests in minority groups, non-Caucasians, and by extension Ghanaians. Consequently, this study investigates the diagnostic accuracy, sensitivity, and specificity of executive function (EF) tests (The Stroop Test, Trail Making Test, and Controlled Oral Word Association Test), and a Revised Quick Cognitive Screening Test (RQCST) in a sample of 50 patients diagnosed with moderate traumatic brain injury and 50 healthy controls in Ghana. The EF test scores showed good diagnostic accuracy, with area under the curve (AUC) values of the Trail Making Test scores ranging from .746 to .902. With respect to the Stroop Test scores, the AUC values ranged from .793 to .898, while Controlled Oral Word Association Test had AUC value of .787. The RQCST scores discriminated between the groups, with AUC values ranging from .674 to .912. The AUC values of composite EF score and a neuropsychological score created from EF and RQCST scores were .936 and. 942, respectively. Additionally, the Stroop Test, Trail Making Test, EF composite score, and RQCST scores showed good to excellent sensitivities and specificities. In general, this study has shown that commonly used EF tests in Western countries have diagnostic accuracy, sensitivity, and specificity when administered in Ghanaian samples. The findings and implications of the study are discussed.

Pediatric trauma BIG score: Predicting mortality in polytraumatized pediatric patients.

PubMed

El-Gamasy, Mohamed Abd El-Aziz; Elezz, Ahmed Abd El Basset Abo; Basuni, Ahmed Sobhy Mohamed; Elrazek, Mohamed El Sayed Ali Abd

2016-11-01

Trauma is a worldwide health problem and the major cause of death and disability, particularly affecting the young population. It is important to remember that pediatric trauma care has made a significant improvement in the outcomes of these injured children. This study aimed at evaluation of pediatric trauma BIG score in comparison with New Injury Severity Score (NISS) and Pediatric Trauma Score (PTS) in Tanta University Emergency Hospital. The study was conducted in Tanta University Emergency Hospital to all multiple trauma pediatric patients attended to the Emergency Department for 1 year. Pediatric trauma BIG score, PTS, and NISS scores were calculated and results compared to each other and to observed mortality. BIG score ≥12.7 has sensitivity 86.7% and specificity 71.4%, whereas PTS at value ≤3.5 has sensitivity 63.3% and specificity 68.6% and NISS at value ≥39.5 has sensitivity 53.3% and specificity 54.3%. There was a significant positive correlation between BIG score value and mortality rate. The pediatric BIG score is a reliable mortality-prediction score for children with traumatic injuries; it uses international normalization ratio (INR), Base Excess (BE), and Glasgow Coma Scale (GCS) values that can be measured within a few minutes of sampling, so it can be readily applied in the Pediatric Emergency Department, but it cannot be applied on patients with chronic diseases that affect INR, BE, or GCS.

Acellular dermal matrix seeded with autologous gingival fibroblasts for the treatment of gingival recession: a proof-of-concept study.

PubMed

Jhaveri, Hiral M; Chavan, Mahesh S; Tomar, Geetanjali B; Deshmukh, Vijay L; Wani, Mohan R; Miller, Preston D

2010-04-01

One of the most common esthetic concerns associated with periodontal tissues is gingival recession. There are multiple periodontal plastic surgery approaches documented in the literature for the treatment of such defects. With the tremendous advances being made in periodontal science and technology, tissue engineering could be considered among the latest exciting techniques for recession management. In this split-mouth, controlled, double-masked clinical case series, 20 sites from 10 patients with Miller Class I or II recessions affecting canines or premolars in the maxillary arch were selected. One tooth in each patient was randomized to receive either a subepithelial connective tissue graft (SCTG) (control group) or an acellular dermal matrix allograft (ADMA) seeded with autologous gingival fibroblasts (test group) under a coronally positioned flap. Clinical parameters, including recession depth, probing depth, clinical attachment level, width of keratinized tissue, attached gingiva, and plaque scores, were recorded by a calibrated examiner at baseline and 3 and 6 months. The inflammation of grafted sites was scored, and the healing time was calculated. The final esthetic outcome of treated sites was assessed by the root coverage esthetic score at the end of 6 months. There were no significant differences between test and control sites for all measured clinical parameters. However, the test sites demonstrated less inflammation in the early postoperative period. Within the limits of this case series, the results indicate that an ADMA seeded with autologous gingival fibroblasts by tissue-engineering technology may be explored as a substitute to an SCTG for the treatment of Miller Class I and II recession defects.

Ranking of small scale proposals for water system repair using the Rapid Impact Assessment Matrix (RIAM)

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

Shakib-Manesh, T.E.; Hirvonen, K.O.; Jalava, K.J.

2014-11-15

Environmental impacts of small scale projects are often assessed poorly, or not assessed at all. This paper examines the usability of the Rapid Impact Assessment Matrix (RIAM) as a tool to prioritize project proposals for small scale water restoration projects in relation to proposals' potential to improve the environment. The RIAM scoring system was used to assess and rank the proposals based on their environmental impacts, the costs of the projects to repair the harmful impacts, and the size of human population living around the sites. A four-member assessment group (The expert panel) gave the RIAM-scores to the proposals. Themore » assumed impacts of the studied projects at the Eastern Finland water systems were divided into the ecological and social impacts. The more detailed assessment categories of the ecological impacts in this study were impacts on landscape, natural state, and limnology. The social impact categories were impacts to recreational use of the area, fishing, industry, population, and economy. These impacts were scored according to their geographical and social significance, their magnitude of change, their character, permanence, reversibility, and cumulativeness. The RIAM method proved to be an appropriate and recommendable method for the small-scale assessment and prioritizing of project proposals. If the assessments are well documented, the RIAM can be a method for easy assessing and comparison of the various kinds of projects. In the studied project proposals there were no big surprises in the results: the best ranks were received by the projects, which were assumed to return watersheds toward their original state.« less

The use of Gram stain and matrix-assisted laser desorption ionization time-of-flight mass spectrometry on positive blood culture: synergy between new and old technology.

PubMed

Fuglsang-Damgaard, David; Nielsen, Camilla Houlberg; Mandrup, Elisabeth; Fuursted, Kurt

2011-10-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is promising as an alternative to more costly and cumbersome methods for direct identifications in blood cultures. We wanted to evaluate a simplified pre-treatment method for using MALDI-TOF-MS directly on positive blood cultures using BacT/Alert blood culture system, and to test an algorithm combining the result of the initial microscopy with the result suggested by MALDI-TOF-MS. Using the recommended cut-off score of 1.7 the best results were obtained among Gram-negative rods with correct identifications in 91% of Enterobacteriaceae, 83% in aerobic/non-fermentative Gram-negative rods, whereas results were more modest among Gram-positive cocci with correct identifications in 52% of Staphylococci, 54% in Enterococci and only 20% in Streptococci. Combining the results of Gram stain with the top reports by MALDI-TOF-MS, increased the sensitivity from 91% to 93% in the score range from 1.5 to 1.7 and from 48% to 85% in the score range from 1.3 to 1.5. Thus, using this strategy and accepting a cut-off at 1.3 instead of the suggested 1.7, overall sensitivity could be increased from 88.1% to 96.3%. MALDI-TOF-MS is an efficient method for direct routine identification of bacterial isolates in blood culture, especially when combined with the result of the Gram stain. © 2011 The Authors. APMIS © 2011 APMIS.

The efficacy of different commercially available demineralized bone matrix substances in an athymic rat model.

PubMed

Lee, Yu-Po; Jo, Mark; Luna, Mario; Chien, Bobby; Lieberman, Jay R; Wang, Jeffrey C

2005-10-01

Bone graft substitutes have been developed because there is a limited supply of autogenous graft and the harvesting of iliac crest bone graft is associated with significant morbidity. Currently, there are a number of different commercially available demineralized bone matrix (DBM) products available that have been prepared by different methods and have different carriers. The objective of this study was to compare eight different commercially available DBM products. Eight different DBMs were used to attempt a spinal fusion between the L4-L5 transverse processes in athymic rats. There were 10 rats in each group, and 5 rats were killed at both 4 and 8 weeks. Radiographic and histologic analyses were performed. Manual palpation testing was also performed. At 4 weeks, Osteofil Paste had the highest radiographic scores, whereas Grafton Putty had the best radiographic scores at 8 weeks. Conversely, the spines implanted with Allomatrix had the lowest radiographic scores at both 4 and 8 weeks. In regard to forming a spinal fusion confirmed by manual palpation, Osteofil Paste was the most effective at 4 weeks, whereas Grafton Flex and Grafton Putty had the highest rate of fusion at 8 weeks. Conversely, the lowest rates of fusion were seen in the Allomatrix and Grafton Crunch groups. Statistical analysis showed that there were significant differences among the groups seen on radiographs and by manual palpation. Qualitative differences could be appreciated between the groups histologically. Significant differences exist among commercially available DBMs in forming a spinal fusion in an athymic rat.

Immunohistochemical expression of TGF-β1 and MMP-9 in periapical lesions.

PubMed

Álvares, Pâmella Recco; Arruda, José Alcides Almeida de; Silva, Leorik Pereira da; Nascimento, George João Ferreira do; Silveira, Maria Fonseca da; Sobral, Ana Paula Veras

2017-07-03

The objective of this study was to evaluate the expression of matrix metalloproteinase 9 (MMP-9) and transforming growth factor beta (TGF-β1) in periapical lesion samples correlated with the intensity of the inflammatory infiltrate and thickness of the epithelial lining. Forty-five cases of periapical lesions (23 periapical granulomas and 22 radicular cysts) were subjected to morphological and immunohistochemical analyses using anti-MMP-9 and anti-TGF-β1 antibodies. The data were analyzed using the following tests: non-parametric Mann-Whitney, chi-square, Fisher's exact test and Spearman's correlation test (P<0.05). Analysis of inflammatory infiltrate revealed that 78% of periapical granulomas presented infiltrate grade III, in contrast with 32% of radicular cysts (P<0.001). Morphological evaluation of the epithelial thickness in radicular cysts revealed the presence of atrophic epithelium in 86% of the cysts. The immunostaining of MMP-9 was score 2 in 67% of the granulomas and 77% of the cysts. Both lesions were predominantly score 1 for TGF-β1. Significant differences were confirmed between the expression scores of TGF-β1 and MMP-9 in periapical granulomas (p = 0.004) and in radicular cysts (p < 0.001). Expression of TGF-β1 was different for periapical granulomas and radicular cysts. This immunoregulatory cytokine seems more representative in asymptomatic lesions. The extracellular matrix remodeling process dependent on MMP-9 seems to be similar for both periapical granulomas and radicular cysts. TGF-β1 and MMP-9 may play an important role in the maintenance of periapical lesions.

MMX Multi Matrix System mesalazine for the induction of remission in patients with mild-to-moderate ulcerative colitis: a combined analysis of two randomized, double-blind, placebo-controlled trials.

PubMed

Sandborn, W J; Kamm, M A; Lichtenstein, G R; Lyne, A; Butler, T; Joseph, R E

2007-07-15

MMX mesalazine [LIALDA (US), MEZAVANT XL (UK and Ireland) MEZAVANT (elsewhere)] utilizes MMX Multi Matrix System (MMX) technology which delivers mesalazine throughout the colon. Two phase III studies have already evaluated MMX mesalazine in patients with active, mild-to-moderate ulcerative colitis. Aim To provide more precise estimates of the efficacy of MMX mesalazine over placebo by combining the patient populations from the two phase III studies. Methods Combined data from two 8-week, double-blind, placebo-controlled trials were analyzed. Patients randomized to MMX mesalazine 2.4 g/day (once daily or 1.2 g twice daily), 4.8 g/day (once daily) or placebo were reviewed. The primary end point was clinical and endoscopic remission (modified Ulcerative Colitis-Disease Activity Index of /=1-point reduction in sigmoidoscopy score from week 0). Results Data from 517 patients were analysed. 8-week remission rates were 37.2% and 35.1% in the MMX mesalazine 2.4 g/day and 4.8 g/day groups, vs. 17.5% on placebo (P < 0.001, both comparisons). 8-week complete mucosal healing rates were 32% in both MMX mesalazine groups compared with 16% on placebo. Adverse event frequency was similar in all groups. Conclusion MMX mesalazine is effective and generally well tolerated for inducing clinical and endoscopic remission of active, mild-to-moderate ulcerative colitis.

Identification of Weissella species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Lee, Meng-Rui; Tsai, Chia-Jung; Teng, Shih-Hua; Hsueh, Po-Ren

2015-01-01

Although some Weissella species play beneficial roles in food fermentation and in probiotic products, others such as Weissella confusa are emerging Gram-positive pathogens in immunocompromised hosts. Weissella species are difficult to identify by conventional biochemical methods and commercial automated systems and are easily misidentified as Lactobacillus and Leuconostoc species. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly being used for bacterial identification. Little, however, is known about the effectiveness of MALDI-TOF MS in identifying clinical isolates of Weissella to the species level. In this study, we evaluated whether the MALDI-TOF MS Bruker Biotyper system could accurately identify a total of 20 W. confusa and 2 W. cibaria blood isolates that had been confirmed by 16s rRNA sequencing analysis. The MALDI-TOF Biotyper system yielded no reliable identification results based on the current reference spectra for the two species (all score values <1.7). New W. confusa spectra were created by randomly selecting 3 W. confusa isolates and external validation was performed by testing the remaining 17 W. confusa isolates using the new spectra. The new main spectra projection (MSP) yielded reliable score values of >2 for all isolates with the exception of one (score value, 1.963). Our results showed that the MSPs in the current database are not sufficient for correctly identifying W. confusa or W. cibaria. Further studies including more Weissella isolates are warranted to further validate the performance of MALDI-TOF in identifying Weissella species.

The Association Between Dietary Quality and Overall and Cancer-Specific Mortality Among Cancer Survivors, NHANES III

PubMed Central

Deshmukh, Ashish A; Shirvani, Shervin M; Likhacheva, Anna; Chhatwal, Jagpreet; Chiao, Elizabeth Y; Sonawane, Kalyani

2018-01-01

Abstract Given the recent emphasis on the totality of the diet by national guidelines, we examined the relationship between the quality of diet and overall and cancer-specific mortality among cancer survivors. From the Third National Health and Nutrition Examination Survey (NHANES III), 1191 participants diagnosed with cancer were identified. Healthy Eating Index (HEI) scores were utilized; higher HEI score indicated better adherence to dietary recommendations. During a median follow-up of 17.2 years, a total of 607 cancer-specific deaths occurred. A high-quality diet (highest-quartile HEI score) was associated with decreased risk of overall (hazard ratio [HR] = 0.59, 95% confidence interval [CI] = 0.45 to 0.77) and cancer-specific (HR = 0.35, 95% CI = 0.19 to 0.63) mortality when compared with a poor-quality diet (lowest-quartile HEI score). Among individual dietary components, the highest-quartile score for saturated fat intake was associated decreased cancer-specific mortality (HR = 0.55, 95% CI = 0.36 to 0.86). Our results highlight the importance of a “total diet” approach to improving survival among cancer patients. PMID:29905226

RBAC-Matrix-based EMR right management system to improve HIPAA compliance.

PubMed

Lee, Hung-Chang; Chang, Shih-Hsin

2012-10-01

Security control of Electronic Medical Record (EMR) is a mechanism used to manage electronic medical records files and protect sensitive medical records document from information leakage. Researches proposed the Role-Based Access Control(RBAC). However, with the increasing scale of medical institutions, the access control behavior is difficult to have a detailed declaration among roles in RBAC. Furthermore, with the stringent specifications such as the U.S. HIPAA and Canada PIPEDA etc., patients are encouraged to have the right in regulating the access control of his EMR. In response to these problems, we propose an EMR digital rights management system, which is a RBAC-based extension to a matrix organization of medical institutions, known as RBAC-Matrix. With the aim of authorizing the EMR among roles in the organization, RBAC-Matrix also allow patients to be involved in defining access rights of his records. RBAC-Matrix authorizes access control declaration among matrix organizations of medical institutions by using XrML file in association with each EMR. It processes XrML rights declaration file-based authorization of behavior in the two-stage design, called master & servant stage, thus makes the associated EMR to be better protected. RBAC-Matrix will also make medical record file and its associated XrML declaration to two different EMRA(EMR Authorization)roles, namely, the medical records Document Creator (DC) and the medical records Document Right Setting (DRS). Access right setting, determined by the DRS, is cosigned by the patient, thus make the declaration of rights and the use of EMR to comply with HIPAA specifications.

Direct analysis and identification of pathogenic Lichtheimia species by matrix-assisted laser desorption ionization-time of flight analyzer-mediated mass spectrometry.

PubMed

Schrödl, Wieland; Heydel, Tilo; Schwartze, Volker U; Hoffmann, Kerstin; Grosse-Herrenthey, Anke; Walther, Grit; Alastruey-Izquierdo, Ana; Rodriguez-Tudela, Juan Luis; Olias, Philipp; Jacobsen, Ilse D; de Hoog, G Sybren; Voigt, Kerstin

2012-02-01

Zygomycetes of the order Mucorales can cause life-threatening infections in humans. These mucormycoses are emerging and associated with a rapid tissue destruction and high mortality. The resistance of Mucorales to antimycotic substances varies between and within clinically important genera such as Mucor, Rhizopus, and Lichtheimia. Thus, an accurate diagnosis before onset of antimycotic therapy is recommended. Matrix-assisted laser desorption ionization (MALDI)-time of flight (TOF) mass spectrometry (MS) is a potentially powerful tool to rapidly identify infectious agents on the species level. We investigated the potential of MALDI-TOF MS to differentiate Lichtheimia species, one of the most important agents of mucormycoses. Using the Bruker Daltonics FlexAnalysis (version 3.0) software package, a spectral database library with m/z ratios of 2,000 to 20,000 Da was created for 19 type and reference strains of clinically relevant Zygomycetes of the order Mucorales (12 species in 7 genera). The database was tested for accuracy by use of 34 clinical and environmental isolates of Lichtheimia comprising a total of five species. Our data demonstrate that MALDI-TOF MS can be used to clearly discriminate Lichtheimia species from other pathogenic species of the Mucorales. Furthermore, the method is suitable to discriminate species within the genus. The reliability and robustness of the MALDI-TOF-based identification are evidenced by high score values (above 2.3) for the designation to a certain species and by moderate score values (below 2.0) for the discrimination between clinically relevant (Lichtheimia corymbifera, L. ramosa, and L. ornata) and irrelevant (L. hyalospora and L. sphaerocystis) species. In total, all 34 strains were unequivocally identified by MALDI-TOF MS with score values of >1.8 down to the generic level, 32 out of 34 of the Lichtheimia isolates (except CNM-CM 5399 and FSU 10566) were identified accurately with score values of >2 (probable species identification), and 25 of 34 isolates were identified to the species level with score values of >2.3 (highly probable species identification). The MALDI-TOF MS-based method reported here was found to be reproducible and accurate, with low consumable costs and minimal preparation time.

Breaking Megrelishvili protocol using matrix diagonalization

NASA Astrophysics Data System (ADS)

Arzaki, Muhammad; Triantoro Murdiansyah, Danang; Adi Prabowo, Satrio

2018-03-01

In this article we conduct a theoretical security analysis of Megrelishvili protocol—a linear algebra-based key agreement between two participants. We study the computational complexity of Megrelishvili vector-matrix problem (MVMP) as a mathematical problem that strongly relates to the security of Megrelishvili protocol. In particular, we investigate the asymptotic upper bounds for the running time and memory requirement of the MVMP that involves diagonalizable public matrix. Specifically, we devise a diagonalization method for solving the MVMP that is asymptotically faster than all of the previously existing algorithms. We also found an important counterintuitive result: the utilization of primitive matrix in Megrelishvili protocol makes the protocol more vulnerable to attacks.

The effect of group-exercising on females with non-specific chronic low back pain in a sitting position: a pilot study.

PubMed

Beladev, Noa; Masharawi, Youssef

2011-01-01

The aim of this study was to investigate the effect of active group-exercising on women with non specific chronic low back pain (NSCLBP) in a sitting position. 25 females with NSCLBP underwent 8 group sitting-exercise sessions of a 45 minute duration, over an 8 week period. Pain intensity (VAS), back specific disability (Rolland Morris questionnaire-RMQ), and lumbar flexion and extension ranges of motion were measured twice, for reliability tests and cut-off score values, with a 1 week interval between measurements, prior to intervention and subsequently, six weeks following intervention. Several significant changes in outcome measures were indicated following intervention compared with baseline (p < 0.001): an increase in lumbar flexion and extension (mean differences of 6° for flexion and 4° for extension, cutoff score = 5.91°); reduction in VAS score (mean difference=4.21, cutoff score =4.48); an increase in RMQ total score (mean difference=10.76, cutoff score=8.15). Changes in the VAS score was highly correlated with changes in the RMQ score (r=- 6.35). A functional program of group-exercising conducted in a sitting position, improved the functional, painful status and lumbar ranges of motion in the sagittal plane of women suffering from non specific chronic low back pain. As sitting is considered the most common posture in today's workplace, applying this protocol during working hours would be very effective.

Outcome of Large to Massive Rotator Cuff Tears Repaired With and Without Extracellular Matrix Augmentation: A Prospective Comparative Study.

PubMed

Gilot, Gregory J; Alvarez-Pinzon, Andres M; Barcksdale, Leticia; Westerdahl, David; Krill, Michael; Peck, Evan

2015-08-01

To compare the results of arthroscopic repair of large to massive rotator cuff tears (RCTs) with or without augmentation using an extracellular matrix (ECM) graft and to present ECM graft augmentation as a valuable surgical alternative used for biomechanical reinforcement in any RCT repair. We performed a prospective, blinded, single-center, comparative study of patients who underwent arthroscopic repair of a large to massive RCT with or without augmentation with ECM graft. The primary outcome was assessed by the presence or absence of a retear of the previously repaired rotator cuff, as noted on ultrasound examination. The secondary outcomes were patient satisfaction evaluated preoperatively and postoperatively using the 12-item Short Form Health Survey, the American Shoulder and Elbow Surgeons shoulder outcome score, a visual analog scale score, the Western Ontario Rotator Cuff index, and a shoulder activity level survey. We enrolled 35 patients in the study: 20 in the ECM-augmented rotator cuff repair group and 15 in the control group. The follow-up period ranged from 22 to 26 months, with a mean of 24.9 months. There was a significant difference between the groups in terms of the incidence of retears: 26% (4 retears) in the control group and 10% (2 retears) in the ECM graft group (P = .0483). The mean pain level decreased from 6.9 to 4.1 in the control group and from 6.8 to 0.9 in the ECM graft group (P = .024). The American Shoulder and Elbow Surgeons score improved from 62.1 to 72.6 points in the control group and from 63.8 to 88.9 points (P = .02) in the treatment group. The mean Short Form 12 scores improved in the 2 groups, with a statistically significant difference favoring graft augmentation (P = .031), and correspondingly, the Western Ontario Rotator Cuff index scores improved in both arms, favoring the treatment group (P = .0412). The use of ECM for augmentation of arthroscopic repairs of large to massive RCTs reduces the incidence of retears, improves patient outcome scores, and is a viable option during complicated cases in which a significant failure rate is anticipated. Level III, prospective, blinded, nonrandomized, comparative study. Copyright © 2015 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Heat exchanger and method of making. [bonding rocket chambers with a porous metal matrix

NASA Technical Reports Server (NTRS)

Fortini, A.; Kazaroff, J. M. (Inventor)

1978-01-01

A heat exchanger of increased effectiveness is disclosed. A porous metal matrix is disposed in a metal chamber or between walls through which a heat-transfer fluid is directed. The porous metal matrix has internal bonds and is bonded to the chamber in order to remove all thermal contact resistance within the composite structure. Utilization of the invention in a rocket chamber is disclosed as a specific use. Also disclosed is a method of constructing the heat exchanger.

Metal- and intermetallic-matrix composites for aerospace propulsion and power systems

NASA Technical Reports Server (NTRS)

Doychak, J.

1992-01-01

The requirements for high specific strength refractory materials of prospective military, civil, and space propulsion systems are presently addressed in the context of emerging capabilities in metal- and intermetallic-matrix composites. The candidate systems encompass composite matrix compositions of superalloy, Nb-Zr refractory alloy, Cu-base, and Ti-base alloy types, as well as such intermetallics as TiAl, Ti3Al, NiAl, and MoSi2. The brittleness of intermetallic matrices remains a major consideration, as does their general difficulty of fabrication.

Detecting epilepsy-related cognitive problems in clinically referred children with epilepsy: is the WISC-IV a useful tool?

PubMed

Sherman, Elisabeth M S; Brooks, Brian L; Fay-McClymont, Taryn B; MacAllister, William S

2012-06-01

The Wechsler Intelligence Scale for Children - Fourth Edition is the most widely used intelligence quotient (IQ) test in use today. However, despite numerous studies on IQ in childhood epilepsy, data exist almost exclusively from prior editions of the test, and no studies to date provide information on the sensitivity of specific WISC-IV scores (full-scale IQ [FSIQ], index, and subtest scores) to epilepsy-related cognitive impairments. The goal of this study was to determine the relative sensitivity of WISC-IV index and subscale scores in detecting cognitive problems in a group of clinically referred children with epilepsy compared to matched controls, and to define the relationship among WISC-IV scales, demographic factors, and epilepsy-related variables. WISC-IV data for children with epilepsy and high seizure burden were obtained from the Alberta Children's Hospital (ACH) and the New York University Comprehensive Epilepsy Center (NYU), two tertiary care medical centers for pediatric epilepsy. All children were clinically referred and received a standard assessment including WISC-IV. Matched controls were obtained from the WISC-IV Canadian and American standardization samples. WISC-IV scores from 212 children were included: 106 children with epilepsy (46 girls, 60 boys; mean age 11.0 years, standard deviation [SD] 3.1; parental education 14.5 years, SD 2.8), and 106 controls matched for age, gender, ethnicity, and parental education. Of the children with epilepsy, 44 had a clearly lateralized focus on electroencephalography (EEG) involving either the right or left hemisphere (26 left, 18 right). FSIQ for the epilepsy group was significantly lower than for controls, and 36.8% of children had IQs compatible with intellectual disability (FSIQ < 70), versus <1% of controls. In children with epilepsy, Working Memory and Processing Speed Index scores were lower than those for Verbal Comprehension and Perceptual Reasoning (p < 0.01). At the subtest level, scores for children with epilepsy were highest on visual and verbal subtests measuring reasoning skills such as Matrix Reasoning, and lowest on Coding (mean 5.93, SD 3.6). In terms of percentage of children on each subtest with low scores (i.e., scores below 2 SDs from the expected normative mean of 10), the Coding subtest identified the most children (28.3%) with low scores, and the Similarities subtest identified the fewest (16%). Later age at onset and shorter epilepsy duration were both correlated with higher WISC-IV FSIQ and index scores (r correlation coefficient values ranging from 0.36 to 0.44, p < 0.0001), and number of current and previous antiepileptic drug trials were both inversely correlated with FSIQ and index scores (r -0.27 to -0.47, all p-values < 0.01). Neither the FSIQ nor the index scores were significantly related to seizure frequency. A similar pattern was found for subtest scores. No differences in FSIQ, index scores, or subtest scores were found between children with left- and right-hemisphere seizure foci, or between those with positive or negative magnetic resonance imaging (MRI) findings. The WISC-IV is sensitive to epilepsy-related cognitive problems in clinically referred children with high seizure burden, particularly problems relating to expressive verbal, working memory, and processing speed difficulties. Compared to healthy children, these children have a very high rate of cognitive difficulties as assessed by the WISC-IV. The usefulness of the WISC-IV in detecting cognitive deficits in children with milder forms of epilepsy remains to be determined. Wiley Periodicals, Inc. © 2012 International League Against Epilepsy.

Development and Justification of a Risk Evaluation Matrix To Guide Chemical Testing Necessary To Select and Qualify Plastic Components Used in Production Systems for Pharmaceutical Products.

PubMed

Jenke, Dennis

2015-01-01

An accelerating trend in the pharmaceutical industry is the use of plastic components in systems used to produce an active pharmaceutical ingredient or a finished drug product. If the active pharmaceutical ingredient, the finished drug product, or any solution used to generate them (for example, a process stream such as media, buffers, eluents, and the like) is contacted by a plastic component at any time during the production process, substances leached from the component may accumulate in the active pharmaceutical ingredient or finished drug product, affecting its safety and/or efficacy. In this article the author develops and justifies a semi-quantitative risk evaluation matrix that is used to determine the amount and rigor of component testing necessary and appropriate to establish that the component is chemically suitable for its intended use. By considering key properties of the component, the contact medium, the contact conditions, and the active pharmaceutical ingredient's or finished drug product's clinical conditions of use, use of the risk evaluation matrix produces a risk score whose magnitude reflects the accumulated risk that the component will interact with the contact solution to such an extent that component-related extractables will accumulate in the active pharmaceutical ingredient or finished drug product as leachables at levels sufficiently high to adversely affect user safety. The magnitude of the risk score establishes the amount and rigor of the testing that is required to select and qualify the component, and such testing is broadly grouped into three categories: baseline assessment, general testing, and full testing (extractables profiling). Production suites used to generate pharmaceuticals can include plastic components. It is possible that substances in the components could leach into manufacturing solutions and accumulate in the pharmaceutical product. In this article the author develops and justifies a semi-quantitative risk evaluation matrix that can be used to determine the amount and rigor of component testing that may be necessary and appropriate to establish that the component is suitable for its intended use. Use of the risk evaluation matrix allows a user of a component to determine the type and amount of testing that should be performed to establish the patient safety risk associated with using that component in order to manufacture an active pharmaceutical ingredient or a finished drug product. © PDA, Inc. 2015.

Utility of the Spelling Sensitivity Score to Analyze Spellings of Children with Specific Language Impairment

PubMed Central

Werfel, Krystal L.; Krimm, Hannah

2015-01-01

The purpose of this study was to examine the utility of the Spelling Sensitivity Score (SSS) beyond percentage correct scoring in analysing the spellings of children with specific language impairment (SLI). Participants were 31 children with SLI and 28 children with typical language in grades 2 through 4. Spellings of individual words were scored using two methods: (a) percentage correct and (b) SSS. Children with SLI scored lower than children with typical language when spelling was analysed with percentage correct scoring and with SSS scoring. Additionally, SSS scoring highlighted group differences in the nature of spelling errors. Children with SLI were more likely than children with typical language to omit elements and to represent elements with an illegal grapheme in words, whereas children with typical language were more likely than children with SLI to represent all elements with correct letters. PMID:26413194

Occupational exposures and chronic obstructive pulmonary disease (COPD): comparison of a COPD-specific job exposure matrix and expert-evaluated occupational exposures

PubMed Central

Kurth, Laura; Doney, Brent; Weinmann, Sheila

2017-01-01

Objectives To compare the occupational exposure levels assigned by our National Institute for Occupational Safety and Health chronic obstructive pulmonary disease-specific job exposure matrix (NIOSH COPD JEM) and by expert evaluation of detailed occupational information for various jobs held by members of an integrated health plan in the Northwest USA. Methods We analysed data from a prior study examining COPD and occupational exposures. Jobs were assigned exposure levels using 2 methods: (1) the COPD JEM and (2) expert evaluation. Agreement (Cohen’s κ coefficients), sensitivity and specificity were calculated to compare exposure levels assigned by the 2 methods for 8 exposure categories. Results κ indicated slight to moderate agreement (0.19–0.51) between the 2 methods and was highest for organic dust and overall exposure. Sensitivity of the matrix ranged from 33.9% to 68.5% and was highest for sensitisers, diesel exhaust and overall exposure. Specificity ranged from 74.7% to 97.1% and was highest for fumes, organic dust and mineral dust. Conclusions This COPD JEM was compared with exposures assigned by experts and offers a generalisable approach to assigning occupational exposure. PMID:27777373

An efficient matrix product operator representation of the quantum chemical Hamiltonian

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

Keller, Sebastian, E-mail: sebastian.keller@phys.chem.ethz.ch; Reiher, Markus, E-mail: markus.reiher@phys.chem.ethz.ch; Dolfi, Michele, E-mail: dolfim@phys.ethz.ch

We describe how to efficiently construct the quantum chemical Hamiltonian operator in matrix product form. We present its implementation as a density matrix renormalization group (DMRG) algorithm for quantum chemical applications. Existing implementations of DMRG for quantum chemistry are based on the traditional formulation of the method, which was developed from the point of view of Hilbert space decimation and attained higher performance compared to straightforward implementations of matrix product based DMRG. The latter variationally optimizes a class of ansatz states known as matrix product states, where operators are correspondingly represented as matrix product operators (MPOs). The MPO construction schememore » presented here eliminates the previous performance disadvantages while retaining the additional flexibility provided by a matrix product approach, for example, the specification of expectation values becomes an input parameter. In this way, MPOs for different symmetries — abelian and non-abelian — and different relativistic and non-relativistic models may be solved by an otherwise unmodified program.« less

Micro-mechanics modelling of smart materials

NASA Astrophysics Data System (ADS)

Shah, Syed Asim Ali

Metal Matrix ceramic-reinforced composites are rapidly becoming strong candidates as structural materials for many high temperature and engineering applications. Metal matrix composites (MMC) combine the ductile properties of the matrix with a brittle phase of the reinforcement, leading to high stiffness and strength with a reduction in structural weight. The main objective of using a metal matrix composite system is to increase service temperature or improve specific mechanical properties of structural components by replacing existing super alloys.The purpose of the study is to investigate, develop and implement second phase reinforcement alloy strengthening empirical model with SiCp reinforced A359 aluminium alloy composites on the particle-matrix interface and the overall mechanical properties of the material.To predict the interfacial fracture strength of aluminium, in the presence of silicon segregation, an empirical model has been modified. This model considers the interfacial energy caused by segregation of impurities at the interface and uses Griffith crack type arguments to predict the formation energies of impurities at the interface. Based on this, model simulations were conducted at nano scale specifically at the interface and the interfacial strengthening behaviour of reinforced aluminium alloy system was expressed in terms of elastic modulus.The numerical model shows success in making prediction possible of trends in relation to segregation and interfacial fracture strength behaviour in SiC particle-reinforced aluminium matrix composites. The simulation models using various micro scale modelling techniques to the aluminum alloy matrix composite, strengthenedwith varying amounts of silicon carbide particulate were done to predict the material state at critical points with properties of Al-SiC which had been heat treated.In this study an algorithm is developed to model a hard ceramic particle in a soft matrix with a clear distinct interface and a strain based relationship has been proposed for the strengthening behaviour of the MMC at the interface rather than stress based, by successfully completing the numerical modelling of particulate reinforced metal matrix composites.

The Connectivity Between Site-Specific Life Cycle Impact Assessment and Site-Specific Weighting

EPA Science Inventory

The goal of many LCIAs is to come to a single score with all of the impacts from a wide variety of impact assessments weighted to form this single score. My past experiences with developing site-specific impact assessment methodologies and how this can change the valuation porti...

Analytical Micromechanics Modeling Technique Developed for Ceramic Matrix Composites Analysis

NASA Technical Reports Server (NTRS)

Min, James B.

2005-01-01

Ceramic matrix composites (CMCs) promise many advantages for next-generation aerospace propulsion systems. Specifically, carbon-reinforced silicon carbide (C/SiC) CMCs enable higher operational temperatures and provide potential component weight savings by virtue of their high specific strength. These attributes may provide systemwide benefits. Higher operating temperatures lessen or eliminate the need for cooling, thereby reducing both fuel consumption and the complex hardware and plumbing required for heat management. This, in turn, lowers system weight, size, and complexity, while improving efficiency, reliability, and service life, resulting in overall lower operating costs.

Crawling from soft to stiff matrix polarizes the cytoskeleton and phosphoregulates myosin-II heavy chain

PubMed Central

Raab, Matthew; Swift, Joe; P. Dingal, P.C. Dave; Shah, Palak; Shin, Jae-Won

2012-01-01

On rigid surfaces, the cytoskeleton of migrating cells is polarized, but tissue matrix is normally soft. We show that nonmuscle MIIB (myosin-IIB) is unpolarized in cells on soft matrix in 2D and also within soft 3D collagen, with rearward polarization of MIIB emerging only as cells migrate from soft to stiff matrix. Durotaxis is the tendency of cells to crawl from soft to stiff matrix, and durotaxis of primary mesenchymal stem cells (MSCs) proved more sensitive to MIIB than to the more abundant and persistently unpolarized nonmuscle MIIA (myosin-IIA). However, MIIA has a key upstream role: in cells on soft matrix, MIIA appeared diffuse and mobile, whereas on stiff matrix, MIIA was strongly assembled in oriented stress fibers that MIIB then polarized. The difference was caused in part by elevated phospho-S1943–MIIA in MSCs on soft matrix, with site-specific mutants revealing the importance of phosphomoderated assembly of MIIA. Polarization is thus shown to be a highly regulated compass for mechanosensitive migration. PMID:23128239

Development of a Pediatric Ebola Predictive Score, Sierra Leone1.

PubMed

Fitzgerald, Felicity; Wing, Kevin; Naveed, Asad; Gbessay, Musa; Ross, J C G; Checchi, Francesco; Youkee, Daniel; Jalloh, Mohamed Boie; Baion, David E; Mustapha, Ayeshatu; Jah, Hawanatu; Lako, Sandra; Oza, Shefali; Boufkhed, Sabah; Feury, Reynold; Bielicki, Julia; Williamson, Elizabeth; Gibb, Diana M; Klein, Nigel; Sahr, Foday; Yeung, Shunmay

2018-02-01

We compared children who were positive for Ebola virus disease (EVD) with those who were negative to derive a pediatric EVD predictor (PEP) score. We collected data on all children <13 years of age admitted to 11 Ebola holding units in Sierra Leone during August 2014-March 2015 and performed multivariable logistic regression. Among 1,054 children, 309 (29%) were EVD positive and 697 (66%) EVD negative, with 48 (5%) missing. Contact history, conjunctivitis, and age were the strongest positive predictors for EVD. The PEP score had an area under receiver operating characteristics curve of 0.80. A PEP score of 7/10 was 92% specific and 44% sensitive; 3/10 was 30% specific, 94% sensitive. The PEP score could correctly classify 79%-90% of children and could be used to facilitate triage into risk categories, depending on the sensitivity or specificity required.

Based on Real Time Remote Health Monitoring Systems: A New Approach for Prioritization "Large Scales Data" Patients with Chronic Heart Diseases Using Body Sensors and Communication Technology.

PubMed

Kalid, Naser; Zaidan, A A; Zaidan, B B; Salman, Omar H; Hashim, M; Albahri, O S; Albahri, A S

2018-03-02

This paper presents a new approach to prioritize "Large-scale Data" of patients with chronic heart diseases by using body sensors and communication technology during disasters and peak seasons. An evaluation matrix is used for emergency evaluation and large-scale data scoring of patients with chronic heart diseases in telemedicine environment. However, one major problem in the emergency evaluation of these patients is establishing a reasonable threshold for patients with the most and least critical conditions. This threshold can be used to detect the highest and lowest priority levels when all the scores of patients are identical during disasters and peak seasons. A practical study was performed on 500 patients with chronic heart diseases and different symptoms, and their emergency levels were evaluated based on four main measurements: electrocardiogram, oxygen saturation sensor, blood pressure monitoring, and non-sensory measurement tool, namely, text frame. Data alignment was conducted for the raw data and decision-making matrix by converting each extracted feature into an integer. This integer represents their state in the triage level based on medical guidelines to determine the features from different sources in a platform. The patients were then scored based on a decision matrix by using multi-criteria decision-making techniques, namely, integrated multi-layer for analytic hierarchy process (MLAHP) and technique for order performance by similarity to ideal solution (TOPSIS). For subjective validation, cardiologists were consulted to confirm the ranking results. For objective validation, mean ± standard deviation was computed to check the accuracy of the systematic ranking. This study provides scenarios and checklist benchmarking to evaluate the proposed and existing prioritization methods. Experimental results revealed the following. (1) The integration of TOPSIS and MLAHP effectively and systematically solved the patient settings on triage and prioritization problems. (2) In subjective validation, the first five patients assigned to the doctors were the most urgent cases that required the highest priority, whereas the last five patients were the least urgent cases and were given the lowest priority. In objective validation, scores significantly differed between the groups, indicating that the ranking results were identical. (3) For the first, second, and third scenarios, the proposed method exhibited an advantage over the benchmark method with percentages of 40%, 60%, and 100%, respectively. In conclusion, patients with the most and least urgent cases received the highest and lowest priority levels, respectively.

The tissue microarray data exchange specification: Extending TMA DES to provide flexible scoring and incorporate virtual slides

PubMed Central

Wright, Alexander; Lyttleton, Oliver; Lewis, Paul; Quirke, Philip; Treanor, Darren

2011-01-01

Background: Tissue MicroArrays (TMAs) are a high throughput technology for rapid analysis of protein expression across hundreds of patient samples. Often, data relating to TMAs is specific to the clinical trial or experiment it is being used for, and not interoperable. The Tissue Microarray Data Exchange Specification (TMA DES) is a set of eXtensible Markup Language (XML)-based protocols for storing and sharing digitized Tissue Microarray data. XML data are enclosed by named tags which serve as identifiers. These tag names can be Common Data Elements (CDEs), which have a predefined meaning or semantics. By using this specification in a laboratory setting with increasing demands for digital pathology integration, we found that the data structure lacked the ability to cope with digital slide imaging in respect to web-enabled digital pathology systems and advanced scoring techniques. Materials and Methods: By employing user centric design, and observing behavior in relation to TMA scoring and associated data, the TMA DES format was extended to accommodate the current limitations. This was done with specific focus on developing a generic tool for handling any given scoring system, and utilizing data for multiple observations and observers. Results: DTDs were created to validate the extensions of the TMA DES protocol, and a test set of data containing scores for 6,708 TMA core images was generated. The XML was then read into an image processing algorithm to utilize the digital pathology data extensions, and scoring results were easily stored alongside the existing multiple pathologist scores. Conclusions: By extending the TMA DES format to include digital pathology data and customizable scoring systems for TMAs, the new system facilitates the collaboration between pathologists and organizations, and can be used in automatic or manual data analysis. This allows complying systems to effectively communicate complex and varied scoring data. PMID:21572508

Modeling CO2 Storage in Fractured Reservoirs: Fracture-Matrix Interactions of Free-Phase and Dissolved CO2

NASA Astrophysics Data System (ADS)

Oldenburg, C. M.; Zhou, Q.; Birkholzer, J. T.

2017-12-01

The injection of supercritical CO2 (scCO2) in fractured reservoirs has been conducted at several storage sites. However, no site-specific dual-continuum modeling for fractured reservoirs has been reported and modeling studies have generally underestimated the fracture-matrix interactions. We developed a conceptual model for enhanced CO2 storage to take into account global scCO2 migration in the fracture continuum, local storage of scCO2 and dissolved CO2 (dsCO2) in the matrix continuum, and driving forces for scCO2 invasion and dsCO2 diffusion from fractures. High-resolution discrete fracture-matrix models were developed for a column of idealized matrix blocks bounded by vertical and horizontal fractures and for a km-scale fractured reservoir. The column-scale simulation results show that equilibrium storage efficiency strongly depends on matrix entry capillary pressure and matrix-matrix connectivity while the time scale to reach equilibrium is sensitive to fracture spacing and matrix flow properties. The reservoir-scale modeling results shows that the preferential migration of scCO2 through fractures is coupled with bulk storage in the rock matrix that in turn retards the fracture scCO2 plume. We also developed unified-form diffusive flux equations to account for dsCO2 storage in brine-filled matrix blocks and found solubility trapping is significant in fractured reservoirs with low-permeability matrix.

Immunoexpression of EGFR and EMMPRIN in a series of cases of head and neck squamous cell carcinoma.

PubMed

de Andrade, Ana Luiza Dias Leite; Ferreira, Stefânia Jeronimo; Ferreira, Sonia Maria Soares; Ribeiro, Camila Maria Beder; Freitas, Roseana de Almeida; Galvão, Hébel Cavalcanti

2015-10-01

The epidermal growth factor receptor (EGFR) and the extracellular matrix metalloproteinase inducer (EMMPRIN) have been identified as oncologically important targets. This study aimed to evaluate the immunoexpression of EGFR and EMMPRIN in a series of cases of head and neck squamous cell carcinoma (HNSCC). Forty-five cases of HNSCC were selected for this study and evaluated with anti-EGFR and anti-EMMPRIN antibodies. The percentage of positive cells was determined assessing to the following categories: score 1 (staining in 0-50% of cells), score 2 (staining in 51-75% of cells), and score 3 (staining in >75% of cells). Immunostaining intensity was graded according to the following parameters: score 1 (absent/weak expression) and score 2 (strong expression). For EGFR, a predominance of high median scores was observed in cases of both histological grades of malignancy and in different clinical stages (p>0.05). For EMMPRIN, a statistically significant difference was observed between the histological grades of malignancy (p=0.030). Regarding the immunostaining intensity of EMMPRIN, it was observed a predominance of score 1 in cases with stages I/II, whereas most cases with stages III/IV presented score 2 (p=0.032). Considering the anatomical location, most cases of buccal floor presented higher median score of EMMPRIN in comparison with the other sites (p=0.015). These findings suggest that both proteins are potential targets for cancer therapy and EMMPRIN can be used as a prognostic marker of a more aggressive biological behavior in patients with HNSCC. Copyright © 2015 Elsevier GmbH. All rights reserved.

Which family physician should I choose? The analytic hierarchy process approach for ranking of criteria in the selection of a family physician.

PubMed

Kuruoglu, Emel; Guldal, Dilek; Mevsim, Vildan; Gunvar, Tolga

2015-08-05

Choosing the most appropriate family physician (FP) for the individual, plays a fundamental role in primary care. The aim of this study is to determine the selection criteria for the patients in choosing their family doctors and priority ranking of these criteria by using the multi-criteria decision-making method of the Analytic Hierarchy Process (AHP) model. The study was planned and conducted in two phases. In the first phase, factors affecting the patients' decisions were revealed with a qualitative research. In the next phase, the priorities of FP selection criteria were determined by using AHP model. Criteria were compared in pairs. 96 patient were asked to fill the information forms which contains comparison scores in the Family Health Centres. According to the analysis of focus group discussions FP selection criteria were congregated in to five groups: Individual Characteristics, Patient-Doctor relationship, Professional characteristics, the Setting, and Ethical Characteristics. For each of the 96 participants, comparison matrixes were formed based on the scores of their information forms. Of these, models of only 5 (5.2 %) of the participants were consistent, in other words, they have been able to score consistent ranking. The consistency ratios (CR) were found to be smaller than 0.10. Therefore the comparison matrix of this new model, which was formed based on the medians of scores only given by these 5 participants, was consistent (CR = 0.06 < 0.10). According to comparison results; with a 0.467 value-weight, the most important criterion for choosing a family physician is his/her 'Professional characteristics'. Selection criteria for choosing a FP were put in a priority order by using AHP model. These criteria can be used as measures for selecting alternative FPs in further researches.

PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations.

PubMed

Li, Liqi; Cui, Xiang; Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

2014-01-01

Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets.

A family-specific use of the Measure of Processes of Care for Service Providers (MPOC-SP).

PubMed

Siebes, R C; Nijhuis, B J G; Boonstra, A M; Ketelaar, M; Wijnroks, L; Reinders-Messelink, H A; Postema, K; Vermeer, A

2008-03-01

To examine the validity and utility of the Dutch Measure of Processes of Care for Service Providers (MPOC-SP) as a family-specific measure. A validation study. Five paediatric rehabilitation settings in the Netherlands. The MPOC-SP was utilized in a general (reflecting on services provided for all clients and clients' families) and family-specific way (filled out in reference to a particular child and his or her family). Professionals providing rehabilitation and educational services to children with cerebral palsy. For construct validity, Pearson's product-moment correlation coefficients (r ) between the scales were calculated. The ability of service providers to discriminate between general and family-specific ratings was examined by exploration of absolute difference scores. One hundred and sixteen service professionals filled out 240 family-specific MPOC-SPs. In addition, a subgroup of 81 professionals filled out a general MPOC-SP. For each professional, family-specific and general scores were paired, resulting in 151 general-family-specific MPOC-SP pairs. The construct validity analyses confirmed the scale structure: 21 items (77.8%) loaded highest in the original MPOC-SP factors, and all items correlated best and significantly with their own scale score (r 0.565 to 0.897; P<0.001). Intercorrelations between the scales ranged from r = 0.159 to r = 0.522. In total, 94.4% of the mean absolute difference scores between general and family-specific scale scores were larger than the expected difference. Service providers were able to discriminate between general and family-specific MPOC-SP item ratings. The family-specific MPOC-SP is a valid measure that can be used for individual evaluation of family-centred services and can be the impetus for family-related quality improvement.

Are vision-specific quality of life questionnaires important in assessing rehabilitation for patients with hemianopia post stroke?

PubMed

George, Stacey; Hayes, Allison; Chen, Celia; Crotty, Maria

2011-01-01

To explore the relationship between disability and functional measures with vision-specific quality of life (QoL) measures for people with hemianopia and stroke. The Behavioral Inattention Test (BIT) and the Mayo-Portland Adaptability Inventory (MPAI) were compared with scores on 2 vision-specific QoL measures, the National Eye Institute Visual Function Questionnaire (NEI VFQ-25) and Veteran Low Vision Visual Function Questionnaire (VA LV VFQ-48). Rehabilitation hospitals in Adelaide, South Australia. Stroke patients (n = 24) with homonymous hemianopia. Most of the BIT and MPAI scores were significantly associated with the NEI VFQ-25 and VA LV VFQ-48 scores. Behavioral test scores of the BIT and the MPAI total score correlated with more aspects of the QoL measures than the other components of the BIT and the MPAI. BIT and MPAI measure constructs associated with QoL for people with hemianopia following stroke. Vision-specific QoL questionnaires can complement the functional instruments by identifying the domains of difficulty, based on the instrument's subscale, that can guide rehabilitation therapists to address the person's deficit.

Differential effect of extracellular matrix derived from papillary and reticular fibroblasts on epidermal development in vitro.

PubMed

Janson, David; Rietveld, Marion; Mahé, Christian; Saintigny, Gaëlle; El Ghalbzouri, Abdoelwaheb

2017-06-01

Papillary and reticular fibroblasts have different effects on keratinocyte proliferation and differentiation. The aim of this study was to investigate whether these effects are caused by differential secretion of soluble factors or by differential generation of extracellular matrix from papillary and reticular fibroblasts. To study the effect of soluble factors, keratinocyte monolayer cultures were grown in papillary or reticular fibroblast-conditioned medium. To study the effect of extracellular matrix, keratinocytes were grown on papillary or reticular-derived matrix. Conditioned medium from papillary or reticular fibroblasts did not differentially affect keratinocyte viability or epidermal development. However, keratinocyte viability was increased when grown on matrix derived from papillary, compared with reticular, fibroblasts. In addition, the longevity of the epidermis was increased when cultured on papillary fibroblast-derived matrix skin equivalents compared with reticular-derived matrix skin equivalents. The findings indicate that the matrix secreted by papillary and reticular fibroblasts is the main causal factor to account for the differences in keratinocyte growth and viability observed in our study. Differences in response to soluble factors between both populations were less significant. Matrix components specific to the papillary dermis may account for the preferential growth of keratinocytes on papillary dermis.

Novel hydrophobic interaction chromatography matrix for specific isolation and simple elution of immunoglobulins (A, G, and M) from porcine serum.

PubMed

Ramos-Clamont, Gabriela; del Carmen Candia-Plata, Maria; Zamudio, Roberto Guzman; Vazquez-Moreno, Luz

2006-07-28

A new, highly acetylated agarose matrix (HA-Sepharose) was synthesized and used as a hydrophobic interaction chromatography (HIC) medium to specifically isolate immunoglobulins (Igs) from porcine serum. Recovery of Igs was in a single step and under mild conditions. HA-Sepharose adsorption was studied in terms of salt, gel acetylation time, flow rate, and protein concentration on the loading buffer. At 0.5 M Na2SO4, control with unmodified Sepharose retained a small fraction (0.70 mg/mL of matrix) of serum albumin. On the contrary HA-Sepharose retained primary Igs (IgA, IgG, and 53% of IgM) as revealed by sodium dodecyl sulphate 10% polyacrylamide gel electrophoresis (SDS-PAGE), quantitative radial immunodiffusion and immunodetection. At a flow rate of 1 mL/min, the HA-Sepharose column capacity (3.9 mg/mL of matrix) was similar to the reported capacity for the commercial thiophilic T-gel. However, HA-Sepharose showed higher recovery of IgA and IgM than the T-gel in the same salt conditions, clearly an advantage in terms of immunoglobulin recovery strategies. Acetylation changed the matrix adsorption from albumin to immunoglobulins; thus, the highly acetylated gel rendered recoveries of Igs from unprocessed porcine serum practically free of albumin.

Increasing number of small hole diameter microfracture compared with traditional microfracture in same size cartilage defects and effect of HA based aselluler scaffold. An animal study

PubMed Central

Uzer, Gökçer; Elmadağ, Nuh Mehmet; Yıldız, Fatih; Güzel, Yunus; Tok, Olgu Enis

2017-01-01

Purpose: The purpose of this study is small hole microfracure method comparing with traditional microfracture method and investigation of effect of HA based acellular matrix scaffold on microfracture area. Materials-Methods: 21 Twenty-one New Zealand white rabbits were used for the in vitro portion of this study, bilateral knee joint from the same rabbit were same technic. An articular cartilage defect was established in the femoral trochlear groove about 5 mm. Control group was established alone microfracture (MF). 6 groups were formed in this study and each group has 3 rabbits and their six knees. In 3 groups were applied different number of small diameter hole microfracture (4,5,6 small holes microfracture respectively)and the other 3 groups were applied different number of small diameter hole microfracture (4,5,6 small holes micro fracture respectively added HA based acellular matrix scaffold in the same size ostechondral lesion. The regenerated tissues were harvested for gross morphology, histology at 12 weeks postoperatively. Results: Cartilage were regenerated, maintaining a constant thickness of cartilage. MF group has worse Wakitani scores than 6 small diameter holes mıcrofracture groups(group 6 and group 7) in either parameter of the score. (p=0,043, p=0,016) Matrix addition did not contribute to healing. (p=1,000) Conclusions: Increasing number of the small diameter holes microfracture (minimum %15 of defect size) improves cartilage repair compared with traditional MF in the same size ostechondral lesion. Also small diameter holes microfracture combined with HA-based AM implantation didn’t result in improved quality of the regenerated cartilage tissue.

Matrix metalloproteinase-9 expression correlated with tumor response in patients with locally advanced rectal cancer undergoing preoperative chemoradiotherapy

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

Unsal, Diclehan; Uner, Aytug; Akyurek, Nalan

2007-01-01

Purpose: To analyze whether the expression of matrix metalloproteinases (MMPs) and their tissue inhibitors are associated with tumor response to preoperative chemoradiotherapy in rectal cancer patients. Methods and Materials: Forty-four patients who had undergone preoperative chemoradiotherapy were evaluated retrospectively. Treatment consisted of pelvic radiotherapy and two cycles of 5-fluorouracil plus leucovorin. Surgery was performed 6-8 weeks later. MMP-2, MMP-9, and tissue inhibitors of metalloproteinase-1 and -2 expression was analyzed by immunohistochemistry of the preradiation biopsy and surgical specimens. The intensity and extent of staining were evaluated separately, and a final score was calculated by multiplying the two scores. The primarymore » endpoint was the correlation of expression with tumor response, with the secondary endpoint the effect of chemoradiotherapy on the expression. Results: Preoperative treatment resulted in downstaging in 20 patients (45%) and no clinical response in 24 (55%). The pathologic tumor response was complete in 11 patients (25%), partial in 23 (52%), and none in 10 (23%). Positive MMP-9 staining was observed in 20 tumors (45%) and was associated with the clinical nodal stage (p = 0.035) and the pathologic and clinical response (p < 0.0001). The staining status of the other markers was associated with neither stage nor response. The overall pathologic response rate was 25% in MMP-9-positive patients vs. 52% in MMP-9-negative patients (p = 0.001). None of the 11 patients with pathologic complete remission was MMP-9 positive. Conclusions: Matrix metalloproteinase-9 expression correlated with a poor tumor response to preoperative chemoradiotherapy in rectal carcinoma patients.« less

Role of segregation and precipitates on interfacial strengthening mechanisms in metal matrix composites when subjected to thermo-mechanical processing

NASA Astrophysics Data System (ADS)

Myriounis, Dimitrios

Metal Matrix ceramic-reinforced composites are rapidly becoming strong candidates as structural materials for many high temperatures and aerospace applications. Metal matrix composites combine the ductile properties of the matrix with a brittle phase of the reinforcement, leading to high stiffness and strength with a reduction in structural weight. The main objective of using a metal matrix composite system is to increase service temperature or improve specific mechanical properties of structural components by replacing existing superalloys.The satisfactory performance of metal matrix composites depends critically on their integrity, the heart of which is the quality of the matrix-reinforcement interface. The nature of the interface depends on the processing of the metal matrix composite component. At the micro-level the development of local stress concentration gradients around the ceramic reinforcement, as the metal matrix attempts to deform during processing, can be very different to the nominal conditions and play a crucial role in important microstructural events such as segregation and precipitation at the matrix-reinforcement interface. These events dominate the cohesive strength and subsequent mechanical properties of the interface.At present the relationship between the strength properties of metal matrix composites and the details of the thermo-mechanical forming processes is not well understood.The purpose of the study is to investigate several strengthening mechanisms and the effect of thermo-mechanical processing of SiCp reinforced A359 aluminium alloy composites on the particle-matrix interface and the overall mechanical properties of the material. From experiments performed on composite materials subjected to various thermo-mechanical conditions and by observation using SEM microanalysis and mechanical testing, data were obtained, summarised and mathematically/statistically analysed upon their significance.The Al/SiCp composites studied, processed in specific thermo-mechanical conditions in order to attain higher values of interfacial fracture strength, due to precipitation hardening and segregation mechanisms, also exhibited enhanced bulk mechanical and fracture resistant properties.An analytical model to predict the interfacial fracture strength in the presence of material segregation was also developed during this research effort. Its validity was determined based on the data gathered from the experiments.The tailoring of the properties due to the microstructural modification of the composites was examined in relation to the experimental measurements obtained, which define the macroscopical behaviour of the material.

Pre-release biological control agent recommendations for swallow-wort (Vincetoxicum spp.) informed by demographic matrix models

USDA-ARS?s Scientific Manuscript database

Weed biological control workers have advocated for the advance assessment of agent efficacy in order to minimize the release of host-specific but ineffective agents. One method involves demographic matrix modeling of target weed populations in order to identify plant life stage transitions that cont...

Generating Nonnormal Multivariate Data Using Copulas: Applications to SEM

ERIC Educational Resources Information Center

Mair, Patrick; Satorra, Albert; Bentler, Peter M.

2012-01-01

This article develops a procedure based on copulas to simulate multivariate nonnormal data that satisfy a prespecified variance-covariance matrix. The covariance matrix used can comply with a specific moment structure form (e.g., a factor analysis or a general structural equation model). Thus, the method is particularly useful for Monte Carlo…

An Alternating Least Squares Method for the Weighted Approximation of a Symmetric Matrix.

ERIC Educational Resources Information Center

ten Berge, Jos M. F.; Kiers, Henk A. L.

1993-01-01

R. A. Bailey and J. C. Gower explored approximating a symmetric matrix "B" by another, "C," in the least squares sense when the squared discrepancies for diagonal elements receive specific nonunit weights. A solution is proposed where "C" is constrained to be positive semidefinite and of a fixed rank. (SLD)

Interactions between the nuclear matrix and an enhancer of the tryptophan oxygenase gene

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

Kaneoka, Hidenori; Miyake, Katsuhide, E-mail: miyake@nubio.nagoya-u.ac.jp; Iijima, Shinji

2009-10-02

The gene for tryptophan oxygenase (TO) is expressed in adult hepatocytes in a tissue- and differentiation-specific manner. The TO promoter has two glucocorticoid-responsive elements (GREs), and its expression is regulated by glucocorticoid hormone in the liver. We found a novel GRE in close proximity to a scaffold/matrix attachment region (S/MAR) that was located around -8.5 kb from the transcriptional start site of the TO gene by electrophoretic mobility shift and chromatin immunoprecipitation (ChIP) assays. A combination of nuclear fractionation and quantitative PCR analysis showed that the S/MAR was tethered to the nuclear matrix in both fetal and adult hepatocytes. ChIPmore » assay showed that, in adult hepatocytes, the S/MAR-GRE and the promoter proximal regions interacted with lamin and heterogeneous nuclear ribonucleoprotein U in a dexamethasone dependent manner, but this was not the case in fetal cells, suggesting that developmental stage-specific expression of the TO gene might rely on the binding of the enhancer (the -8.5 kb S/MAR-GRE) and the promoter to the inner nuclear matrix.« less

Staphylococcal Bap Proteins Build Amyloid Scaffold Biofilm Matrices in Response to Environmental Signals

PubMed Central

Taglialegna, Agustina; Navarro, Susanna; Ventura, Salvador; Garnett, James A.; Matthews, Steve; Penades, José R.; Lasa, Iñigo; Valle, Jaione

2016-01-01

Biofilms are communities of bacteria that grow encased in an extracellular matrix that often contains proteins. The spatial organization and the molecular interactions between matrix scaffold proteins remain in most cases largely unknown. Here, we report that Bap protein of Staphylococcus aureus self-assembles into functional amyloid aggregates to build the biofilm matrix in response to environmental conditions. Specifically, Bap is processed and fragments containing at least the N-terminus of the protein become aggregation-prone and self-assemble into amyloid-like structures under acidic pHs and low concentrations of calcium. The molten globule-like state of Bap fragments is stabilized upon binding of the cation, hindering its self-assembly into amyloid fibers. These findings define a dual function for Bap, first as a sensor and then as a scaffold protein to promote biofilm development under specific environmental conditions. Since the pH-driven multicellular behavior mediated by Bap occurs in coagulase-negative staphylococci and many other bacteria exploit Bap-like proteins to build a biofilm matrix, the mechanism of amyloid-like aggregation described here may be widespread among pathogenic bacteria. PMID:27327765

Differences of wells scores accuracy, caprini scores and padua scores in deep vein thrombosis diagnosis

NASA Astrophysics Data System (ADS)

Gatot, D.; Mardia, A. I.

2018-03-01

Deep Vein Thrombosis (DVT) is the venous thrombus in lower limbs. Diagnosis is by using venography or ultrasound compression. However, these examinations are not available yet in some health facilities. Therefore many scoring systems are developed for the diagnosis of DVT. The scoring method is practical and safe to use in addition to efficacy, and effectiveness in terms of treatment and costs. The existing scoring systems are wells, caprini and padua score. There have been many studies comparing the accuracy of this score but not in Medan. Therefore, we are interested in comparative research of wells, capriniand padua score in Medan.An observational, analytical, case-control study was conducted to perform diagnostic tests on the wells, caprini and padua score to predict the risk of DVT. The study was at H. Adam Malik Hospital in Medan.From a total of 72 subjects, 39 people (54.2%) are men and the mean age are 53.14 years. Wells score, caprini score and padua score has a sensitivity of 80.6%; 61.1%, 50% respectively; specificity of 80.65; 66.7%; 75% respectively, and accuracy of 87.5%; 64.3%; 65.7% respectively.Wells score has better sensitivity, specificity and accuracy than caprini and padua score in diagnosing DVT.

Beyond the Dirty Dozen: A Proposed Methodology for Assessing Future Bioweapon Threats.

PubMed

Cieslak, Theodore J; Kortepeter, Mark G; Wojtyk, Ronald J; Jansen, Hugo-Jan; Reyes, Ricardo A; Smith, James O

2018-01-01

Defense policy planners and countermeasure developers are often faced with vexing problems involving the prioritization of resources and efforts. This is especially true in the area of Biodefense, where each new emerging infectious disease outbreak brings with it questions regarding the causative agent's potential for weaponization. Recent experience with West Nile Virus, Severe Acute Respiratory Syndrome, Monkeypox, and H1N1 Influenza highlights this problem. Appropriately, in each of these cases, the possibility of bioterrorism was raised, although each outbreak ultimately proved to have a natural origin. In fact, determining whether an outbreak has an unnatural origin can be quite difficult. Thus, the questions remain: could the causative agents of these and other emerging infectious disease outbreaks pose a future weaponization threat? And how great is that threat? Should precious resources be diverted from other defense efforts in order to prepare for possible hostile employment of novel diseases by belligerents? Answering such critical questions requires some form of systematic threat assessment. Through extensive collaborative work conducted within NATO's Biomedical Advisory Council, we developed a scoring matrix for evaluating the weaponization potential of the causative agents of such diseases and attempted to validate our matrix by examining the reproducibility of data using known threat agents. Our matrix included 12 attributes of a potential weapon and was provided, along with detailed scoring instructions, to 12 groups of biodefense experts in 6 NATO nations. Study participants were asked to score each of these 12 attributes on a scale of 0-3: Infectivity, Infection-to-Disease Ratio (Reliability), Predictability (& Incubation Period), Morbidity & Mortality (Virulence), Ease of Large-Scale Production & Storage, Aerosol Stability, Atmospheric Stability, Ease of Dispersal, Communicability, Prophylactic Countermeasure Availability, Therapeutic Countermeasure Availability, and Ease of Detection. Reproducibility of scoring data was assessed by examining the standard deviations (SD) of mean scores. Our results were unexpected. Several familiar biothreat diseases such as anthrax and tularemia were judged, by our experts, to be less threatening than many others owing to a number of factors including ease of detection, lack of communicability, and the ready availability of countermeasures. Conversely, several toxins were judged by experts to have very high potential as threat agents owing, in part, to their reliability, virulence, and a lack of available countermeasures. Agreement among experts, as determined by lower SD about a mean score, was greater for more familiar threats. Our study was designed to provide a concise and east-to-apply set of criteria that could be used by NATO nations to evaluate emerging infectious disease threats with respect to their weaponization potential. Our results were unexpected. We believe that a lack of appropriate weighting factors may explain these results and suggest that future studies weigh each of the 12 proposed criteria based on the intended use of the assessment data and other situational factors. We believe that the greatest value of our study lies in a codification of the attributes of a biological weapon. © Association of Military Surgeons of the United States 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Automatic segmentation of right ventricle on ultrasound images using sparse matrix transform and level set

NASA Astrophysics Data System (ADS)

Qin, Xulei; Cong, Zhibin; Halig, Luma V.; Fei, Baowei

2013-03-01

An automatic framework is proposed to segment right ventricle on ultrasound images. This method can automatically segment both epicardial and endocardial boundaries from a continuous echocardiography series by combining sparse matrix transform (SMT), a training model, and a localized region based level set. First, the sparse matrix transform extracts main motion regions of myocardium as eigenimages by analyzing statistical information of these images. Second, a training model of right ventricle is registered to the extracted eigenimages in order to automatically detect the main location of the right ventricle and the corresponding transform relationship between the training model and the SMT-extracted results in the series. Third, the training model is then adjusted as an adapted initialization for the segmentation of each image in the series. Finally, based on the adapted initializations, a localized region based level set algorithm is applied to segment both epicardial and endocardial boundaries of the right ventricle from the whole series. Experimental results from real subject data validated the performance of the proposed framework in segmenting right ventricle from echocardiography. The mean Dice scores for both epicardial and endocardial boundaries are 89.1%+/-2.3% and 83.6+/-7.3%, respectively. The automatic segmentation method based on sparse matrix transform and level set can provide a useful tool for quantitative cardiac imaging.

High-performance sparse matrix-matrix products on Intel KNL and multicore architectures

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

Nagasaka, Y; Matsuoka, S; Azad, A

Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is widely used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. Although many SpGEMM algorithms have been proposed, hardware specific optimizations for multi- and many-core processors are lacking and a detailed analysis of their performance under various use cases and matrices is not available. We firstly identify and mitigate multiple bottlenecks with memory management and thread scheduling on Intel Xeon Phi (Knights Landing or KNL). Specifically targeting multi- and many-core processors, we develop a hash-table-based algorithm and optimize a heap-based shared-memory SpGEMM algorithm. Wemore » examine their performance together with other publicly available codes. Different from the literature, our evaluation also includes use cases that are representative of real graph algorithms, such as multi-source breadth-first search or triangle counting. Our hash-table and heap-based algorithms are showing significant speedups from libraries in the majority of the cases while different algorithms dominate the other scenarios with different matrix size, sparsity, compression factor and operation type. We wrap up in-depth evaluation results and make a recipe to give the best SpGEMM algorithm for target scenario. A critical finding is that hash-table-based SpGEMM gets a significant performance boost if the nonzeros are not required to be sorted within each row of the output matrix.« less

Histopathological Validation of the Surface-Intermediate-Base Margin Score for Standardized Reporting of Resection Technique during Nephron Sparing Surgery.

PubMed

Minervini, Andrea; Campi, Riccardo; Kutikov, Alexander; Montagnani, Ilaria; Sessa, Francesco; Serni, Sergio; Raspollini, Maria Rosaria; Carini, Marco

2015-10-01

The surface-intermediate-base margin score is a novel standardized reporting system of resection techniques during nephron sparing surgery. We validated the surgeon assessed surface-intermediate-base score with microscopic histopathological assessment of partial nephrectomy specimens. Between June and August 2014 data were prospectively collected from 40 consecutive patients undergoing nephron sparing surgery. The surface-intermediate-base score was assigned to all cases. The score specific areas were color coded with tissue margin ink and sectioned for histological evaluation of healthy renal margin thickness. Maximum, minimum and mean thickness of healthy renal margin for each score specific area grade (surface [S] = 0, S = 1 ; intermediate [I] or base [B] = 0, I or B = 1, I or B = 2) was reported. The Mann-Whitney U and Kruskal-Wallis tests were used to compare the thickness of healthy renal margin in S = 0 vs 1 and I or B = 0 vs 1 vs 2 grades, respectively. Maximum, minimum and mean thickness of healthy renal margin was significantly different among score specific area grades S = 0 vs 1, and I or B = 0 vs 1, 0 vs 2 and 1 vs 2 (p <0.001). The main limitations of the study are the low number of the I or B = 1 and I or B = 2 samples and the assumption that each microscopic slide reflects the entire score specific area for histological analysis. The surface-intermediate-base scoring method can be readily harnessed in real-world clinical practice and accurately mirrors histopathological analysis for quantification and reporting of healthy renal margin thickness removed during tumor excision. Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Sensitivity and specificity of the Beck Depression Inventory in cardiologic inpatients: how useful is the conventional cut-off score?

PubMed

Forkmann, Thomas; Vehren, Thomas; Boecker, Maren; Norra, Christine; Wirtz, Markus; Gauggel, Siegfried

2009-10-01

The Beck Depression Inventory (BDI) is widely used for depression screening in various patient populations. However, there are still insufficient data about its sensitivity and specificity in nonpsychiatric patients. Furthermore, some research suggests that somatic BDI items heighten its sum score artificially in physically ill patients. The aim of the present study was to validate the conventional BDI cut-off score by examination of its sensitivity and specificity in a mixed sample of cardiac inpatients and compare it to a modified "cognitive-emotional" BDI (BDI(c/e)) after exclusion of somatic items. A total of 126 cardiologic inpatients were assessed. Receiver operating characteristic curves (ROC) were calculated for total BDI (BDI(t)) and BDI(c/e). Screening performance of cut-off scores was evaluated using the Youden Index (Y). With the application of the conventional BDI cut-off score, ROC analysis revealed a moderate overall screening performance with Y=52.6 and an area under the curve (AUC) of 0.83. In contrast, Y improved to 57.5 at a cut-off score of >9, but screening performance was still not optimal. BDI(c/e) showed also a moderate screening performance (AUC=.82); Y was maximized at a cut-off score of >8 (Y=0.53.5). Again, no cut-off score provided optimal screening performance. The BDI cannot be recommended as a formal screening instrument in cardiac inpatients since no cut-off score for either BDI(t) or BDI(c/e) combined both sufficiently high sensitivity and specificity. However, the shorter BDI(c/e) could be used as alternative to BDI(t) which may be confounded in physically ill patients. Generally, researchers should consider using alternative screening instruments (e.g., the Hospital Anxiety and Depression Scale) instead.

Japanese scoring systems to predict resistance to intravenous immunoglobulin in Kawasaki disease were unreliable for Caucasian Israeli children.

PubMed

Arane, Karen; Mendelsohn, Kerry; Mimouni, Michael; Mimouni, Francis; Koren, Yael; Simon, Dafna Brik; Bahat, Hilla; Helou, Mona Hanna; Mendelson, Amir; Hezkelo, Nofar; Glatstein, Miguel; Berkun, Yackov; Eisenstein, Eli; Aviel, Yonatan Butbul; Brik, Riva; Hashkes, Philip J; Uziel, Yosef; Harel, Liora; Amarilyo, Gil

2018-05-24

This study assessed the validity of using established Japanese risk scoring methods to predict intravenous immunoglobulin (IVIG) resistance to Kawasaki disease in Israeli children. We reviewed the medical records of 282 patients (70% male) with Kawasaki disease from six Israeli medical centres between 2004-2013. Their mean age was 2.5 years. The risk scores were calculated using the Kobayashi, Sano and Egami scoring methods and analysed to determine if a higher risk score predicted IVIG resistance in this population. Factors that predicted a lack of response to the initial IVIG dose were identified. We found that 18% did not respond to the first IVIG dose. The three scoring methods were unable to reliably predict IVIG resistance, with sensitivities of 23-32% and specificities of 67-87%. Calculating a predictive score that was specific for this population was also unsuccessful. The factors that predicted a lacked of response to the first IVIG dose included low albumin, elevated total bilirubin and ethnicity. The established risk scoring methods created for Japanese populations with Kawasaki disease were not suitable for predicting IVIG resistance in Caucasian Israeli children and we were unable to create a specific scoring method that was able to do this. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Vasomotor and physical menopausal symptoms are associated with sleep quality.

PubMed

Kim, Min-Ju; Yim, Gyeyoon; Park, Hyun-Young

2018-01-01

Sleep disturbance is one of the common complaints in menopause. This study investigated the relationship between menopausal symptoms and sleep quality in middle-aged women. This cross-sectional observational study involved 634 women aged 44-56 years attending a healthcare center at Kangbuk Samsung Hospitals. Sleep quality was measured using the Pittsburgh Sleep Quality Index (PSQI).Multiple linear regression analysis was performed to assess the associations between Menopause-specific Quality of Life (MENQOL) scores and PSQI scores and Menopause-specific Quality of Life (MENQOL)scores. The mean PSQI score was 3.6±2.3, and the rates of poor sleep quality(PSQI score > 5) in premenopausal, perimenopausal, and postmenopausal women were 14.4%, 18.2%, and 30.2%, respectively. Total PSQI score, specifically the sleep latency, habitual sleep efficiency and sleep disturbances scores, were significantly increased in postmenopausal women. Multiple linear regression analysis adjusted for age, BMI, hypertension, diabetes, smoking, marital status, family income, education, employment status, parity, physical activity, depression symptoms, perceived stress and menopausal status showed that higher PSQI score was positively correlated with higher vasomotor(ß = 0.240, P = 0.020)and physical(ß = 0.572, P<0.001) scores. Vasomotor and physical menopause symptoms was related to poor sleep quality. Effective management strategies aimed at reducing menopausal symptoms may improve sleep quality among women around the time of menopause.

Matrix directed adipogenesis and neurogenesis of mesenchymal stem cells derived from adipose tissue and bone marrow.

PubMed

Lee, Junmin; Abdeen, Amr A; Tang, Xin; Saif, Taher A; Kilian, Kristopher A

2016-09-15

Mesenchymal stem cells (MSCs) can differentiate into multiple lineages through guidance from the biophysical and biochemical properties of the extracellular matrix. In this work we conduct a combinatorial study of matrix properties that influence adipogenesis and neurogenesis including: adhesion proteins, stiffness, and cell geometry, for mesenchymal stem cells derived from adipose tissue (AT-MSCs) and bone marrow (BM-MSCs). We uncover distinct differences in integrin expression, the magnitude of traction stress, and lineage specification to adipocytes and neuron-like cells between cell sources. In the absence of media supplements, adipogenesis in AT-MSCs is not significantly influenced by matrix properties, while the converse is true in BM-MSCs. Both cell types show changes in the expression of neurogenesis markers as matrix cues are varied. When cultured on laminin conjugated microislands of the same adhesive area, BM-MSCs display elevated adipogenesis markers, while AT-MSCs display elevated neurogenesis markers; integrin analysis suggests neurogenesis in AT-MSCs is guided by adhesion through integrin αvβ3. Overall, the properties of the extracellular matrix guides MSC adhesion and lineage specification to different degrees and outcomes, in spite of their similarities in general characteristics. This work will help guide the selection of MSCs and matrix components for applications where high fidelity of differentiation outcome is desired. Mesenchymal stem cells (MSCs) are an attractive cell type for stem cell therapies; however, in order for these cells to be useful in medicine, we need to understand how they respond to the physical and chemical environments of tissue. Here, we explore how two promising sources of MSCs-those derived from bone marrow and from adipose tissue-respond to the compliance and composition of tissue using model extracellular matrices. Our results demonstrate a source-specific propensity to undergo adipogenesis and neurogenesis, and uncover a role for adhesion, and the degree of traction force exerted on the substrate in guiding these lineage outcomes. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Effects of dynamic matrix remodelling on en masse migration of fibroblasts on collagen matrices.

PubMed

Ozcelikkale, Altug; Dutton, J Craig; Grinnell, Frederick; Han, Bumsoo

2017-10-01

Fibroblast migration plays a key role during various physiological and pathological processes. Although migration of individual fibroblasts has been well studied, migration in vivo often involves simultaneous locomotion of fibroblasts sited in close proximity, so-called ' en masse migration', during which intensive cell-cell interactions occur. This study aims to understand the effects of matrix mechanical environments on the cell-matrix and cell-cell interactions during en masse migration of fibroblasts on collagen matrices. Specifically, we hypothesized that a group of migrating cells can significantly deform the matrix, whose mechanical microenvironment dramatically changes compared with the undeformed state, and the alteration of the matrix microenvironment reciprocally affects cell migration. This hypothesis was tested by time-resolved measurements of cell and extracellular matrix movement during en masse migration on collagen hydrogels with varying concentrations. The results illustrated that a group of cells generates significant spatio-temporal deformation of the matrix before and during the migration. Cells on soft collagen hydrogels migrate along tortuous paths, but, as the matrix stiffness increases, cell migration patterns become aligned with each other and show coordinated migration paths. As cells migrate, the matrix is locally compressed, resulting in a locally stiffened and dense matrix across the collagen concentration range studied. © 2017 The Author(s).

Correcting the MoCA for education: effect on sensitivity.

PubMed

Gagnon, Genevieve; Hansen, Kevin T; Woolmore-Goodwin, Sarah; Gutmanis, Iris; Wells, Jennie; Borrie, Michael; Fogarty, Jennifer

2013-09-01

The goal of this study was to quantify the impact of the suggested education correction on the sensitivity and specificity of the Montreal Cognitive Assessment (MoCA). Twenty-five outpatients with dementia and 39 with amnestic mild cognitive impairment (aMCI) underwent a diagnostic evaluation, which included the MoCA. Thirty-seven healthy controls also completed the MoCA and psychiatric, medical, neurological, functional, and cognitive difficulties were ruled out. For the total MoCA score, unadjusted for education, a cut-off score of 26 yielded the best balance between sensitivity and specificity (80% and 89% respectively) in identifying cognitive impairment (people with either dementia or aMCI, versus controls). When applying the education correction, sensitivity decreased from 80% to 69% for a small specificity increase (89% to 92%). The cut-off score yielding the best balance between sensitivity and specificity for the education adjusted MoCA score fell to 25 (61% and 97%, respectively). Adjusting the MoCA total score for education had a detrimental effect on sensitivity with only a slight increase in specificity. Clinically, this loss in sensitivity can lead to an increased number of false negatives, as education level does not always correlate to premorbid intellectual function. Clinical judgment about premorbid status should guide interpretation. However, as this effect may be cohort specific, age and education corrected norms and cut-offs should be developed to help guide MoCA interpretation.

Stochastic theory of photon flow in homogeneous and heterogeneous anisotropic biological and artificial material

NASA Astrophysics Data System (ADS)

Miller, Steven D.

1995-05-01

Standard Monte Carlo methods used in photon diffusion score absorbed photons or statistical weight deposited within voxels comprising a mesh. An alternative approach to a stochastic description is considered for rapid surface flux calculations and finite medias. Matrix elements are assigned to a spatial lattice whose function is to score vector intersections of scattered photons making transitions into either the forward or back solid angle half spaces. These complete matrix elements can be related to the directional fluxes within the lattice space. This model differentiates between ballistic, quasi-ballistic, and highly diffuse photon contributions, and effectively models the subsurface generation of a scattered light flux from a ballistic source. The connection between a path integral and diffusion is illustrated. Flux perturbations can be effectively illustrated for tissue-tumor-tissue and for 3 layer systems with strong absorption in one or more layers. For conditions where the diffusion theory has difficulties such as strong absorption, highly collimated sources, small finite volumes, and subsurface regions, the computation time of the algorithm is rapid with good accuracy and compliments other description of photon diffusion. The model has the potential to do computations relevant to photodynamic therapy (PDT) and analysis of laser beam interaction with tissues.

Structural brain connectivity and cognitive ability differences: A multivariate distance matrix regression analysis.

PubMed

Ponsoda, Vicente; Martínez, Kenia; Pineda-Pardo, José A; Abad, Francisco J; Olea, Julio; Román, Francisco J; Barbey, Aron K; Colom, Roberto

2017-02-01

Neuroimaging research involves analyses of huge amounts of biological data that might or might not be related with cognition. This relationship is usually approached using univariate methods, and, therefore, correction methods are mandatory for reducing false positives. Nevertheless, the probability of false negatives is also increased. Multivariate frameworks have been proposed for helping to alleviate this balance. Here we apply multivariate distance matrix regression for the simultaneous analysis of biological and cognitive data, namely, structural connections among 82 brain regions and several latent factors estimating cognitive performance. We tested whether cognitive differences predict distances among individuals regarding their connectivity pattern. Beginning with 3,321 connections among regions, the 36 edges better predicted by the individuals' cognitive scores were selected. Cognitive scores were related to connectivity distances in both the full (3,321) and reduced (36) connectivity patterns. The selected edges connect regions distributed across the entire brain and the network defined by these edges supports high-order cognitive processes such as (a) (fluid) executive control, (b) (crystallized) recognition, learning, and language processing, and (c) visuospatial processing. This multivariate study suggests that one widespread, but limited number, of regions in the human brain, supports high-level cognitive ability differences. Hum Brain Mapp 38:803-816, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Curcumin attenuates blood-brain barrier disruption after subarachnoid hemorrhage in mice.

PubMed

Yuan, Jichao; Liu, Wei; Zhu, Haitao; Zhang, Xuan; Feng, Yang; Chen, Yaxing; Feng, Hua; Lin, Jiangkai

2017-01-01

Early brain injury, one of the most important mechanisms underlying subarachnoid hemorrhage (SAH), comprises edema formation and blood-brain barrier (BBB) disruption. Curcumin, an active extract from the rhizomes of Curcuma longa, alleviates neuroinflammation by as yet unknown neuroprotective mechanisms. In this study, we examined whether curcumin treatment ameliorates SAH-induced brain edema and BBB permeability changes, as well as the mechanisms underlying this phenomenon. We induced SAH in mice via endovascular perforation, administered curcumin 15 min after surgery and evaluated neurologic scores, brain water content, Evans blue extravasation, Western blot assay results, and immunohistochemical analysis results 24 h after surgery. Curcumin significantly improved neurologic scores and reduced brain water content in treated mice compared with SAH mice. Furthermore, curcumin decreased Evans blue extravasation, matrix metallopeptidase-9 expression, and the number of Iba-1-positive microglia in treated mice compared with SAH mice. At last, curcumin treatment increased the expression of the tight junction proteins zonula occludens-1 and occludin in treated mice compared with vehicle-treated and sample SAH mice. We demonstrated that curcumin inhibits microglial activation and matrix metallopeptidase-9 expression, thereby reducing brain edema and attenuating post-SAH BBB disruption in mice. Copyright © 2016 Elsevier Inc. All rights reserved.

Expression of extracellular matrix metalloproteinase inducer (EMMPRIN) in the endometrium of patients with repeated implantation failure after in vitro fertilization.

PubMed

Turgut, A; Goruk, N Y; Tunc, S Y; Agaçayak, E; Alabalik, U; Yalinkaya, A; Gül, T

2014-01-01

To compare the immunohistochemical expression of extracellular matrix metalloproteinase inducer (EMMPRIN) in repeated implantation failure (RIF) patients with normal fertile controls. The study group consisted of primary infertile patients with RIF and normal fertile controls between January 2011 and February 2013. Endometrial samples received at the luteal phase were exposed to immunohistochemical staining for EMMPRIN antibodies. EMMPRIN expression of endometrial glandular epithelial cells, stromal cells and vascular endothelial cells were evaluated. The main outcome measure was defined as immunohistochemical score with regard to the severity and extent of staining. The study group consisted of 26 primary infertile patients, whereas the control group consisted of 40 normal fertile controls. The fertile group was found to have stronger expression of EMMPRIN than the study group when endometrial glandular epithelial cells, stromal cells and vascular endothelial cells were evaluated with regards to the severity of staining (p < 0.001), the extent of staining (p < 0.001) and total staining score (p < 0.001). This is the first study showing low expression of EMMPRIN in the endometrial cells of the patients with RIF compared with fertile healthy controls. We suggest that reduced EMMPRIN expression in the human endometrium may lead to poor endometrial receptivity.

Identification of Medically Relevant Species of Arthroconidial Yeasts by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Kolecka, Anna; Khayhan, Kantarawee; Groenewald, Marizeth; Theelen, Bart; Arabatzis, Michael; Velegraki, Aristea; Kostrzewa, Markus; Mares, Mihai; Taj-Aldeen, Saad J.

2013-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) was used for an extensive identification study of arthroconidial yeasts, using 85 reference strains from the CBS-KNAW yeast collection and 134 clinical isolates collected from medical centers in Qatar, Greece, and Romania. The test set included 72 strains of ascomycetous yeasts (Galactomyces, Geotrichum, Saprochaete, and Magnusiomyces spp.) and 147 strains of basidiomycetous yeasts (Trichosporon and Guehomyces spp.). With minimal preparation time, MALDI-TOF MS proved to be an excellent diagnostic tool that provided reliable identification of most (98%) of the tested strains to the species level, with good discriminatory power. The majority of strains were correctly identified at the species level with good scores (>2.0) and seven of the tested strains with log score values between 1.7 and 2.0. The MALDI-TOF MS results obtained were consistent with validated internal transcribed spacer (ITS) and/or large subunit (LSU) ribosomal DNA sequencing results. Expanding the mass spectrum database by increasing the number of reference strains for closely related species, including those of nonclinical origin, should enhance the usefulness of MALDI-TOF MS-based diagnostic analysis of these arthroconidial fungi in medical and other laboratories. PMID:23678074

A Practical Guide to Assessing Adult Firesetters' Fire-Specific Treatment Needs Using the Four Factor Fire Scales.

PubMed

Ó Ciardha, Caoilte; Tyler, Nichola; Gannon, Theresa A

2015-01-01

Practitioners working with offenders who have set fires have access to very few measures examining fire-specific treatment needs (e.g., fire interest, fire attitudes). In this article we examine the new Four Factor Fire Scales (Ó Ciardha et al., 2015), which may be used by practitioners to examine fire-specific treatment needs for offenders who have set deliberate fires. We present a standardized scoring procedure when using these scales, as well as an associated scoring template for practitioner use. Norm data are based on male and female firesetters (n = 378) and nonfiresetters (n = 187) recruited from 19 prison establishments (including six female establishments, one young offender institution) and 12 secure mixed-gender mental health settings. We present a full overview of all data we have collected to date relating to the Four Factor Fire Scales across prison, mental health, and young offending participants. For each population, we present mean scores as well as associated cutoff scores and reliable change indices to aid practitioners in their interpretation of scores. The Four Factor Fire Scales provide professionals working in the area with a robust template for administering, scoring, and interpreting the fire-specific factors currently identified as playing a role in deliberate firesetting behavior. Strengths and limitations of the measure are discussed.

Residency program trainee-satisfaction correlate with results of the European board examination in neurosurgery.

PubMed

Stienen, Martin N; Netuka, David; Demetriades, Andreas K; Ringel, Florian; Gautschi, Oliver P; Gempt, Jens; Kuhlen, Dominique; Schaller, Karl

2016-10-01

Substantial country differences in neurosurgical training throughout Europe have recently been described, ranging from subjective rating of training quality to objective working hours per week. The aim of this study was to analyse whether these differences translate into the results of the written and oral part of the European Board Examination in Neurological Surgery (EBE-NS). Country-specific composite scores for satisfaction with quality of theoretical and practical training, as well as working hours per week, were obtained from an electronic survey distributed among European neurosurgical residents between June 2014 and March 2015. These were related to anonymous country-specific results of the EBE-NS between 2009 and 2016, using uni- and multivariate linear regression analysis. A total of n = 1025 written and n = 63 oral examination results were included. There was a significant linear relationship between the country-specific EBE-NS result in the written part and the country-specific composite score for satisfaction with quality of theoretical training [adjusted regression coefficient (RC) -3.80, 95 % confidence interval (CI) -5.43-7 -2.17, p < 0.001], but not with practical training or working time. For the oral part, there was a linear relationship between the country-specific EBE-NS result and the country-specific composite score for satisfaction with quality of practical training (RC 9.47, 95 % CI 1.47-17.47, p = 0.021), however neither with satisfaction with quality of theoretical training nor with working time. With every one-step improvement on the country-specific satisfaction score for theoretical training, the score in the EBE-NS Part 1 increased by 3.8 %. With every one-step improvement on the country-specific satisfaction score for practical training, the score in the EBE-NS Part 2 increased by 9.47 %. Improving training conditions is likely to have a direct positive influence on the knowledge level of trainees, as measured by the EBE-NS. The effect of the actual working time on the theoretical and practical knowledge of neurosurgical trainees appears to be insignificant.

Automatic histologically-closer classification of skin lesions.

PubMed

Rebouças Filho, Pedro Pedrosa; Peixoto, Solon Alves; Medeiros da Nóbrega, Raul Victor; Hemanth, D Jude; Medeiros, Aldisio Gonçalves; Sangaiah, Arun Kumar; de Albuquerque, Victor Hugo C

2018-06-04

According to the American Cancer Society, melanoma is one of the most common types of cancer in the world. In 2017, approximately 87,110 new cases of skin cancer were diagnosed in the United States alone. A dermatoscope is a tool that captures lesion images with high resolution and is one of the main clinical tools to diagnose, evaluate and monitor this disease. This paper presents a new approach to classify melanoma automatically using structural co-occurrence matrix (SCM) of main frequencies extracted from dermoscopy images. The main advantage of this approach consists in transform the SCM in an adaptive feature extractor improving his power of discrimination using only the image as parameter. The images were collected from the International Skin Imaging Collaboration (ISIC) 2016, 2017 and Pedro Hispano Hospital (PH2) datasets. Specificity (Spe), sensitivity (Sen), positive predictive value, F Score, Harmonic Mean, accuracy (Acc) and area under the curve (AUC) were used to verify the efficiency of the SCM. The results show that the SCM in the frequency domain work automatically, where it obtained better results in comparison with local binary patterns, gray-level co-occurrence matrix and invariant moments of Hu as well as compared with recent works with the same datasets. The results of the proposed approach were: Spe 95.23%, 92.15% and 99.4%, Sen 94.57%, 89.9% and 99.2%, Acc 94.5%, 89.93% and 99%, and AUC 92%, 90% and 99% in ISIC 2016, 2017 and PH2 datasets, respectively. Copyright © 2018 Elsevier Ltd. All rights reserved.

General and disease-specific use of outcomes scores for the shoulder: a survey of AOSSM, AANA, and ISAKOS members.

PubMed

Provencher, Matthew T; Frank, Rachel M; Scuderi, Matthew G; Solomon, Daniel J; Ghodadra, Neil S; Bach, Bernard R; McCarty, Eric; Romeo, Anthony A

2014-09-01

To report on the knowledge and use of both general and disease-specific shoulder outcomes scores among orthopedic surgeons. A 22-question Internet survey was administered to members of the American Orthopaedic Society for Sports Medicine, the Arthroscopy Association of North American, and the International Society of Arthroscopy, Knee Surgery, and Orthopedic Sports Medicine via voluntary e-mail participation. Questions targeted demographic information, preferred surgical management of shoulder conditions, and the preferred use of shoulder outcomes instruments in clinical practice. Excluding defunct and duplicate e-mails among membership societies, a total of 3892 unique e-mails were sent, from which 1129 surveys were returned and were fully completed (29%). The largest number of respondents were in private practice (52%); 21% were in academia; and 26% were in a mix of settings. As for location, 74% practiced in the United States, 10% in Europe, 8% in Mexico/South America, and 6% in Asia. A total of 31% total respondents used scores all or most of the time, and 30% used scores at least some of the time. Respondents felt that the 3 most commonly utilized shoulder scores were the American Shoulder and Elbow Surgeons (ASES) score, the University of California at Los Angeles (UCLA) score, and the Constant score. The majority of respondents (76%) performed all-arthroscopic instability repairs. The ASES and Western Ontario Shoulder Instability Index (WOSI) scores were the most preferred measures to monitor instability patients, whether or not the scores were actually implemented in their practice. Most perform between 10 and 25 superior labrum anterior-posterior repairs per year and preferred the ASES, UCLA, and Constant scores for these repairs; rotator cuff repair preferred outcomes instruments were similar. When asked to choose 1 score for all shoulder conditions, the ASES was the clear favorite. This study reports the knowledge and utilization of shoulder scores for both general and disease-specific conditions. Most respondents preferred the ASES score for most shoulder conditions; however, other scores, such as the WOSI, the Constant, and the Short-Form (SF)-36/12, were popular. This information offers insight into the current and future use of shoulder outcomes both for general and disease-specific use.

Exploration of Analysis Methods for Diagnostic Imaging Tests: Problems with ROC AUC and Confidence Scores in CT Colonography

PubMed Central

Mallett, Susan; Halligan, Steve; Collins, Gary S.; Altman, Doug G.

2014-01-01

Background Different methods of evaluating diagnostic performance when comparing diagnostic tests may lead to different results. We compared two such approaches, sensitivity and specificity with area under the Receiver Operating Characteristic Curve (ROC AUC) for the evaluation of CT colonography for the detection of polyps, either with or without computer assisted detection. Methods In a multireader multicase study of 10 readers and 107 cases we compared sensitivity and specificity, using radiological reporting of the presence or absence of polyps, to ROC AUC calculated from confidence scores concerning the presence of polyps. Both methods were assessed against a reference standard. Here we focus on five readers, selected to illustrate issues in design and analysis. We compared diagnostic measures within readers, showing that differences in results are due to statistical methods. Results Reader performance varied widely depending on whether sensitivity and specificity or ROC AUC was used. There were problems using confidence scores; in assigning scores to all cases; in use of zero scores when no polyps were identified; the bimodal non-normal distribution of scores; fitting ROC curves due to extrapolation beyond the study data; and the undue influence of a few false positive results. Variation due to use of different ROC methods exceeded differences between test results for ROC AUC. Conclusions The confidence scores recorded in our study violated many assumptions of ROC AUC methods, rendering these methods inappropriate. The problems we identified will apply to other detection studies using confidence scores. We found sensitivity and specificity were a more reliable and clinically appropriate method to compare diagnostic tests. PMID:25353643

Exploration of analysis methods for diagnostic imaging tests: problems with ROC AUC and confidence scores in CT colonography.

PubMed

Mallett, Susan; Halligan, Steve; Collins, Gary S; Altman, Doug G

2014-01-01

Different methods of evaluating diagnostic performance when comparing diagnostic tests may lead to different results. We compared two such approaches, sensitivity and specificity with area under the Receiver Operating Characteristic Curve (ROC AUC) for the evaluation of CT colonography for the detection of polyps, either with or without computer assisted detection. In a multireader multicase study of 10 readers and 107 cases we compared sensitivity and specificity, using radiological reporting of the presence or absence of polyps, to ROC AUC calculated from confidence scores concerning the presence of polyps. Both methods were assessed against a reference standard. Here we focus on five readers, selected to illustrate issues in design and analysis. We compared diagnostic measures within readers, showing that differences in results are due to statistical methods. Reader performance varied widely depending on whether sensitivity and specificity or ROC AUC was used. There were problems using confidence scores; in assigning scores to all cases; in use of zero scores when no polyps were identified; the bimodal non-normal distribution of scores; fitting ROC curves due to extrapolation beyond the study data; and the undue influence of a few false positive results. Variation due to use of different ROC methods exceeded differences between test results for ROC AUC. The confidence scores recorded in our study violated many assumptions of ROC AUC methods, rendering these methods inappropriate. The problems we identified will apply to other detection studies using confidence scores. We found sensitivity and specificity were a more reliable and clinically appropriate method to compare diagnostic tests.

Estimation of mean response via effective balancing score

PubMed Central

Hu, Zonghui; Follmann, Dean A.; Wang, Naisyin

2015-01-01

Summary We introduce effective balancing scores for estimation of the mean response under a missing at random mechanism. Unlike conventional balancing scores, the effective balancing scores are constructed via dimension reduction free of model specification. Three types of effective balancing scores are introduced: those that carry the covariate information about the missingness, the response, or both. They lead to consistent estimation with little or no loss in efficiency. Compared to existing estimators, the effective balancing score based estimator relieves the burden of model specification and is the most robust. It is a near-automatic procedure which is most appealing when high dimensional covariates are involved. We investigate both the asymptotic and the numerical properties, and demonstrate the proposed method in a study on Human Immunodeficiency Virus disease. PMID:25797955

Advances in biomimetic regeneration of elastic matrix structures

PubMed Central

Sivaraman, Balakrishnan; Bashur, Chris A.

2012-01-01

Elastin is a vital component of the extracellular matrix, providing soft connective tissues with the property of elastic recoil following deformation and regulating the cellular response via biomechanical transduction to maintain tissue homeostasis. The limited ability of most adult cells to synthesize elastin precursors and assemble them into mature crosslinked structures has hindered the development of functional tissue-engineered constructs that exhibit the structure and biomechanics of normal native elastic tissues in the body. In diseased tissues, the chronic overexpression of proteolytic enzymes can cause significant matrix degradation, to further limit the accumulation and quality (e.g., fiber formation) of newly deposited elastic matrix. This review provides an overview of the role and importance of elastin and elastic matrix in soft tissues, the challenges to elastic matrix generation in vitro and to regenerative elastic matrix repair in vivo, current biomolecular strategies to enhance elastin deposition and matrix assembly, and the need to concurrently inhibit proteolytic matrix disruption for improving the quantity and quality of elastogenesis. The review further presents biomaterial-based options using scaffolds and nanocarriers for spatio-temporal control over the presentation and release of these biomolecules, to enable biomimetic assembly of clinically relevant native elastic matrix-like superstructures. Finally, this review provides an overview of recent advances and prospects for the application of these strategies to regenerating tissue-type specific elastic matrix structures and superstructures. PMID:23355960

Phenotype of hepatocyte spheroids in Arg-GLY-Asp (RGD) containing a thermo-reversible extracellular matrix.

PubMed

Park, Keun-Hong; Bae, You Han

2002-07-01

The spheroid of specific cells is often regarded as the better form in artificial organs and mammalian cell bioreactors for improved cell-specific functions. In this study, freshly harvested primary rat hepatocytes, which had been cultivated as spheroids and entrapped in a synthetic thermo-reversible extracellular matrix, were examined for differentiated morphology and enhanced liver-specific functions as compared to a control set (hepatocytes in single-cell form). A copolymer of N-isopropylacrylamide (98 mole % in the feed) and acrylic acid (poly(NiPAAm-co-AAc)), and the adhesion molecule, an Arg-Gly-Asp (RGD)-incorporated thermo-reversible matrix, were used to entrap hepatocytes in the form of either spheroids or single cells. In a 28-day culture period, the spheroids in the RGD-incorporated gel maintained higher viability and produced albumin and urea at constant rates, while there was lower cell viability and less albumin secretion by the spheroids in p(NiPAAm-co-AAc). Hepatocytes cultured as spheroids in the RGD-incorporated gel would constitute a potentially useful three-dimensional cell system for application in a bio-artificial liver device.

Accuracy of whole-genome prediction using a genetic architecture-enhanced variance-covariance matrix.

PubMed

Zhang, Zhe; Erbe, Malena; He, Jinlong; Ober, Ulrike; Gao, Ning; Zhang, Hao; Simianer, Henner; Li, Jiaqi

2015-02-09

Obtaining accurate predictions of unobserved genetic or phenotypic values for complex traits in animal, plant, and human populations is possible through whole-genome prediction (WGP), a combined analysis of genotypic and phenotypic data. Because the underlying genetic architecture of the trait of interest is an important factor affecting model selection, we propose a new strategy, termed BLUP|GA (BLUP-given genetic architecture), which can use genetic architecture information within the dataset at hand rather than from public sources. This is achieved by using a trait-specific covariance matrix ( T: ), which is a weighted sum of a genetic architecture part ( S: matrix) and the realized relationship matrix ( G: ). The algorithm of BLUP|GA (BLUP-given genetic architecture) is provided and illustrated with real and simulated datasets. Predictive ability of BLUP|GA was validated with three model traits in a dairy cattle dataset and 11 traits in three public datasets with a variety of genetic architectures and compared with GBLUP and other approaches. Results show that BLUP|GA outperformed GBLUP in 20 of 21 scenarios in the dairy cattle dataset and outperformed GBLUP, BayesA, and BayesB in 12 of 13 traits in the analyzed public datasets. Further analyses showed that the difference of accuracies for BLUP|GA and GBLUP significantly correlate with the distance between the T: and G: matrices. The new strategy applied in BLUP|GA is a favorable and flexible alternative to the standard GBLUP model, allowing to account for the genetic architecture of the quantitative trait under consideration when necessary. This feature is mainly due to the increased similarity between the trait-specific relationship matrix ( T: matrix) and the genetic relationship matrix at unobserved causal loci. Applying BLUP|GA in WGP would ease the burden of model selection. Copyright © 2015 Zhang et al.

The amino-terminal matrix assembly domain of fibronectin stabilizes cell shape and prevents cell cycle progression.

PubMed

Christopher, R A; Judge, S R; Vincent, P A; Higgins, P J; McKeown-Longo, P J

1999-10-01

Adhesion to the extracellular matrix modulates the cellular response to growth factors and is critical for cell cycle progression. The present study was designed to address the relationship between fibronectin matrix assembly and cell shape or shape dependent cellular processes. The binding of fibronectin's amino-terminal matrix assembly domain to adherent cells represents the initial step in the assembly of exogenous fibronectin into the extracellular matrix. When added to monolayers of pulmonary artery endothelial cells, the 70 kDa fragment of fibronectin (which contains the matrix assembly domain) stabilized both the extracellular fibronectin matrix as well as the actin cytoskeleton against cytochalasin D-mediated structural reorganization. This activity appeared to require specific fibronectin sequences as fibronectin fragments containing the cell adhesion domain as well as purified vitronectin were ineffective inhibitors of cytochalasin D-induced cytoarchitectural restructuring. Such pronounced morphologic consequences associated with exposure to the 70 kDa fragment suggested that this region of the fibronectin molecule may affect specific growth traits known to be influenced by cell shape. To assess this possibility, the 70 kDa fragment was added to scrape-wounded monolayers of bovine microvessel endothelium and the effects on two shape-dependent processes (i.e. migration and proliferation) were measured as a function of time after injury and location from the wound. The addition of amino-terminal fragments of fibronectin to the monolayer significantly inhibited (by >50%) wound closure. Staining of wounded monolayers with BrdU, moreover, indicated that either the 70 kDa or 25 kDa amino-terminal fragments of fibronectin, but not the 40 kDa collagen binding fragment, also inhibited cell cycle progression. These results suggest that the binding of fibronectin's amino-terminal region to endothelial cell layers inhibits cell cycle progression by stabilizing cell shape.

Research on evaluation of third-party governance operation services for environmental pollution

NASA Astrophysics Data System (ADS)

Xu, Bingsheng; Ling, Lin; Jin, Huang

2017-11-01

This paper focuses on the evaluation of third-party governance operation services for environmental pollution, and determines the evaluation indicator system composed of 5 primary indicators as the basic competence of enterprise, operation of equipment, technique economics, environmental benefit and management level, and 26 secondary indicators via policies and regulations, standards, literature research and expert consultation in combination with the composition elements, service value judgment factors and full-life cycle of the work, providing theoretical support for the effect evaluation of third-governance over the environmental pollution in China. Then, the hierarchical analytic matrix is formed by analyzing the environmental pollution governance evaluation indicator system via analytic hierarchy process and scoring the importance of various indicators by experts by applying the Delphi method. The feature vector of the matrix is then calculated to obtain the weight of each indicator and verify the effectiveness of the Delphi method and obtain the comprehensive weight by judging the consistency of the matrix, so as to finally determine the overall ordering level of the importance of secondary indicators.

A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms.

PubMed

Li, Bin; Comi, Troy J; Si, Tong; Dunham, Sage J B; Sweedler, Jonathan V

2016-11-01

Matrix-assisted laser desorption/ionization imaging of biofilms cultured on agar plates is challenging because of problems related to matrix deposition onto agar. We describe a one-step, spray-based application of a 2,5-dihydroxybenzoic acid solution for direct matrix-assisted laser desorption/ionization imaging of hydrated Bacillus subtilis biofilms on agar. Using both an optimized airbrush and a home-built automatic sprayer, region-specific distributions of signaling metabolites and cannibalistic factors were visualized from B. subtilis cells cultivated on biofilm-promoting medium. The approach provides a homogeneous, relatively dry coating on hydrated samples, improving spot to spot signal repeatability compared with sieved matrix application, and is easily adapted for imaging a range of agar-based biofilms. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Analysis of medical screening and surveillance in 21 Occupational Safety and Health Administration standards: support for a generic medical surveillance standard.

PubMed

Silverstein, M

1994-09-01

Twenty-one Occupational Safety and Health Act (OSHA) standards were identified which contain medical service provisions intended to help in the identification and control of harmful health effects of workplace exposures. The utility and effectiveness of these provisions have not previously been evaluated. All 21 standards were reviewed and assigned numerical scores for each of 24 potential medical program elements. Several of these elements were combined to calculate Quality Control, Screening Utility, and Surveillance Utility scores for each standard. Total scores varied greatly, suggesting a lack of consistency and uniformity which was even more obvious when the actual regulatory language was examined. The mean Quality score was only 26% of potential points. Seventeen of 21 standards received less than half the total possible Quality score. When arrayed on a two by two matrix only two standards scored above 50% for both Screening and Surveillance Utility. It was concluded that the medical service provisions in OSHA standards are lacking in consistency and coherence. Two major shortcomings are the lack of quality control elements and the absence of surveillance features which would permit medical program results to be utilized for prevention activities including the identification and control of workplace hazards. A generic occupational medical surveillance standard could address these current weaknesses. Elements of such a generic standard are proposed.

Diet Quality and Colorectal Cancer Risk in the Women's Health Initiative Observational Study

PubMed Central

Vargas, Ashley J.; Neuhouser, Marian L.; George, Stephanie M.; Thomson, Cynthia A.; Ho, Gloria Y. F.; Rohan, Thomas E.; Kato, Ikuko; Nassir, Rami; Hou, Lifang; Manson, JoAnn E.

2016-01-01

Abstract Diet quality index scores on Healthy Eating Index 2010 (HEI-2010), Alternative HEI-2010, alternative Mediterranean Diet Index, and the Dietary Approaches to Stop Hypertension (DASH) index have been inversely associated with all-cause and cancer-specific death. This study assessed the association between these scores and colorectal cancer (CRC) incidence as well as CRC-specific mortality in the Women's Health Initiative Observational Study (1993–2012), a US study of postmenopausal women. During an average of 12.4 years of follow-up, there were 938 cases of CRC and 238 CRC-specific deaths. We estimated multivariate hazard ratios and 95% confidence intervals for relationships between quintiles of diet scores (from baseline food frequency questionnaires) and outcomes. HEI-2010 score (hazard ratios were 0.81, 0.77, and 0.73 with P values of 0.04, 0.01, and <0.01 for quintiles 3–5 vs. quintile 1, respectively) and DASH score (hazard ratios were 0.72, 0.74, and 0.78 with P values of <0.01, <0.01, and 0.03 for quintiles 3–5 vs. quintile 1, respectively), but not other diet scores, were associated with a lower risk of CRC in adjusted models. No diet scores were significantly associated with CRC-specific mortality. Closer adherence to HEI-2010 and DASH dietary recommendations was inversely associated with risk of CRC in this large cohort of postmenopausal women. PMID:27267948

Jones matrix polarization-correlation mapping of biological crystals networks

NASA Astrophysics Data System (ADS)

Ushenko, O. G.; Ushenko, Yu. O.; Pidkamin, L. Y.; Sidor, M. I.; Vanchuliak, O.; Motrich, A. V.; Gorsky, M. P.; Meglinskiy, I.; Marchuk, Yu. F.

2017-08-01

It has been proposed the optical model of Jones-matrix description of mechanisms of optical anisotropy of polycrystalline films of human bile, namely optical activity and birefringence. The algorithm of reconstruction of distributions of parameters - optical rotation angles and phase shifts of the indicated anisotropy types has been elaborated. The objective criteria of differentiation of bile films taken from healthy donors and patients with cholelithiasis by means of statistic analysis of such distributions have been determined. The operational characteristics (sensitivity, specificity and accuracy) of Jones-matrix reconstruction method of optical anisotropy parameters were defined.

Supermacroporous cryogel matrix for integrated protein isolation. Immobilized metal affinity chromatographic purification of urokinase from cell culture broth of a human kidney cell line.

PubMed

Kumar, Ashok; Bansal, Vibha; Andersson, Jonatan; Roychoudhury, Pradip K; Mattiasson, Bo

2006-01-20

A new type of supermacroporous, monolithic, cryogel affinity adsorbent was developed, allowing the specific capture of urokinase from conditioned media of human fibrosarcoma cell line HT1080. The affinity adsorbent was designed with the objective of using it as a capture column in an integrated perfusion/protein separation bioreactor setup. A comparative study between the utility of this novel cryogel based matrix and the conventional Sepharose based affinity matrix for the continuous capture of urokinase in an integrated bioreactor system was performed. Cu(II)-ion was coupled to epoxy activated polyacrylamide cryogel and Sepharose using iminodiacetic acid (IDA) as the chelating ligand. About 27-fold purification of urokinase from the conditioned culture media was achieved with Cu(II)-IDA-polyacrylamide cryogel column giving specific activity of about 814 Plough units (PU)/mg protein and enzyme yields of about 80%. High yields (95%) were obtained with Cu(II)-IDA-Sepharose column by virtue of its high binding capacity. However, the adsorbent showed lower selectivity as compared to cryogel matrix giving specific activity of 161 PU/mg protein and purification factor of 5.3. The high porosity, selectivity and reasonably good binding capacity of Cu(II)-IDA-polyacrylamide cryogel column make it a promising option for use as a protein capture column in integrated perfusion/separation processes. The urokinase peak pool from Cu(II)-IDA-polyacrylamide cryogel column could be further resolved into separate fractions for high and low molecular weight forms of urokinase by gel filtration chromatography on Sephacryl S-200. The selectivity of the cryogel based IMAC matrix for urokinase was found to be higher as compared to that of Cu(II)-IDA-Sepharose column.

The effect of rater training on scoring performance and scale-specific expertise amongst occupational therapists participating in a multicentre study: a single-group pre-post-test study.

PubMed

Hansen, Tina; Elholm Madsen, Esben; Sørensen, Annette

2016-01-01

In order to enhance the quality of the data collected in a multicentre validation study of a revised Danish version of the McGill Ingestive Skills Assessment (MISA), the authors developed a rater training programme. The purpose of the present study was to evaluate the effect of the training on scoring performance and scale-specific expertise amongst raters. During 2 days of rater training, 81 occupational therapists (OTs) were qualified to observe and score dysphagic clients' mealtime performance according to the criteria of 36 MISA-items. The training effects were evaluated pre- to post-training using percentage exact agreement (PA) of scored MISA items of a case-vignette and a Likert scale self-report of scale-specific expertise. PA increased significantly from pre- to post-training (Z = -4.404, p < 0.001), although items for which the case-vignette reflected deficient mealtime performance appeared most difficult to score. The OTs scale-specific expertise improved significantly (knowledge: Z = -7.857, p < 0.001 and confidence: Z = -7.838, p < 0.001). Rater training improved OTs scoring performance when using the Danish MISA as well as their perceived scale-specific expertise. Future rater training should emphasis the items identified as those most difficult to score. Additionally, further studies addressing different training approaches and durations are warranted. When occupational therapists (OTs) use the McGill Ingestive Skills Assessment (MISA) they observe, interpret and record occupational performance of dysphagic clients participating in a meal. This is a highly complex task, which might introduce unwanted variability in measurement scores. A 2-day rater training programme was developed and this builds on the findings of several studies. These suggest that combinations of different training methods tend to yield the most effective results. Participation in the newly developed training programme on how to administer the MISA significantly reduces unwanted variability in measurement scores and improves OTs' competency. The training programme could be used in undergraduate and postgraduate dysphagia education initiatives to help OTs understanding of the content and the scoring criteria for each aspect of occupational performance during a meal, thus developing observation skills as well as recognizing and avoiding the most common errors in measurement scores.

A single-arm trial indirect comparison investigation: a proof-of-concept method to predict venous leg ulcer healing time for a new acellular synthetic matrix matched to standard care control.

PubMed

Shannon, Ronald; Nelson, Andrea

2017-08-01

To compare data on time to healing from two separate cohorts: one treated with a new acellular synthetic matrix plus standard care (SC) and one matched from four large UK pragmatic, randomised controlled trials [venous leg ulcer (VLU) evidence network]. We introduce a new proof-of-concept strategy to a VLU clinical evidence network, propensity score matching and sensitivity analysis to predict the feasibility of the new acellular synthetic matrix plus SC for success in future randomised, controlled clinical trials. Prospective data on chronic VLUs from a safety and effectiveness study on an acellular synthetic matrix conducted in one wound centre in the UK (17 patients) and three wound centres in Australia (36 patients) were compared retrospectively to propensity score-matched data from patients with comparable leg ulcer disease aetiology, age, baseline ulcer area, ulcer duration, multi-layer compression bandaging and majority of care completed in specialist wound centres (average of 1 visit per week), with the outcome measures at comparable follow-up periods from patients enrolled in four prospective, multicentre, pragmatic, randomised studies of venous ulcers in the UK (the comparison group; VLU evidence network). Analysis using Kaplan-Meier survival curves showed a mean healing time of 73·1 days for ASM plus SC (ASM) treated ulcers in comparison with 83·5 days for comparison group ulcers treated with SC alone (Log rank test, χ 2 5·779, P = 0·016) within 12 weeks. Sensitivity analysis indicates that an unobserved covariate would have to change the odds of healing for SC by a factor of 1·1 to impact the baseline results. Results from this study predict a significant effect on healing time when using a new ASM as an adjunct to SC in the treatment of non-healing venous ulcers in the UK, but results are sensitive to unobserved covariates that may be important in healing time comparison. © 2016 Medicalhelplines.com Inc and John Wiley & Sons Ltd.

Improved Identification of Membrane Proteins by MALDI-TOF MS/MS Using Vacuum Sublimated Matrix Spots on an Ultraphobic Chip Surface

PubMed Central

Poetsch, Ansgar; Schlüsener, Daniela; Florizone, Christine; Eltis, Lindsay; Menzel, Christoph; Rögner, Matthias; Steinert, Kerstin; Roth, Udo

2008-01-01

Integral membrane proteins are notoriously difficult to identify and analyze by mass spectrometry because of their low abundance and limited number of trypsin cleavage sites. Our strategy to address this problem is based on a novel technology for MALDI-MS peptide sample preparation that increases the success rate of membrane protein identification by increasing the sensitivity of the MALDI-TOF system. For this, we used sample plates with predeposited matrix spots of CHCA crystals prepared by vacuum sublimation onto an extremely low wettable (ultraphobic) surface. In experiments using standard peptides, an up to 10-fold gain of sensitivity was found for on-chip preparations compared with classical dried-droplet preparations on a steel target. In order to assess the performance of the chips with membrane proteins, three model proteins (bacteriorhodopsin, subunit IV(a) of ATP synthase, and the cp47 subunit from photosystem II) were analyzed. To mimic realistic analysis conditions, purified proteins were separated by SDS-PAGE and digested with trypsin. The digest MALDI samples were prepared either by dried-droplet technique on steel plates using CHCA as matrix, or applied directly onto the matrix spots of the chip surface. Significantly higher signal-to-noise ratios were observed for all of the spectra resulting from on-chip preparations of different peptides. In a second series of experiments, the membrane proteome of Rhodococcus jostii RHA1 was investigated by AIEC/SDS-PAGE in combination with MALDI-TOF MS/MS. As in the first experiments, Coomassie-stained SDS-PAGE bands were digested and the two different preparation methods were compared. For preparations on the Mass·Spec·Turbo Chip, 43 of 60 proteins were identified, whereas only 30 proteins were reliably identified after classical sample preparation. Comparison of the obtained Mascot scores, which reflect the confidence level of the protein identifications, revealed that for 70% of the identified proteins, higher scores were obtained by on-chip sample preparation. Typically, this gain was a consequence of higher sequence coverage due to increased sensitivity. PMID:19137096

Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences.

PubMed

An, Ji-Yong; Meng, Fan-Rong; You, Zhu-Hong; Fang, Yu-Hong; Zhao, Yu-Jun; Zhang, Ming

2016-01-01

We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM) model and Local Phase Quantization (LPQ) to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the LPQ feature representation on a Position Specific Scoring Matrix (PSSM), reducing the influence of noise using a Principal Component Analysis (PCA), and using a Relevance Vector Machine (RVM) based classifier. We perform 5-fold cross-validation experiments on Yeast and Human datasets, and we achieve very high accuracies of 92.65% and 97.62%, respectively, which is significantly better than previous works. To further evaluate the proposed method, we compare it with the state-of-the-art support vector machine (SVM) classifier on the Yeast dataset. The experimental results demonstrate that our RVM-LPQ method is obviously better than the SVM-based method. The promising experimental results show the efficiency and simplicity of the proposed method, which can be an automatic decision support tool for future proteomics research.

The Use of Task-based Cognitive Tests for Defining Vocational Aptness of Individuals with Disabilities.

PubMed

Kwon, Jae-Sung; Oh, Duck-Won

2015-06-01

The purpose of this study was to demonstrate the use of task-based cognitive tests to detect potential problems in the assessment of work training for vocational rehabilitation. Eleven participants with a normal range of cognitive functioning scores were recruited for this study. Participants were all trainees who participated in a vocational training program. The Rey Complex Figure Test and the Allen Cognitive Level Screen were randomly administered to all participants. Responses to the tests were qualitatively analyzed with matrix and scatter charts. Observational outcomes derived from the tests indicated that response errors, distortions, and behavioral problems occurred in most participants. These factors may impede occupational performance despite normal cognitive function. These findings suggest that the use of task-based tests may be beneficial for detecting potential problems associated with the work performance of people with disabilities. Specific analysis using the task-based tests may be necessary to complete the decision-making process for vocational aptness. Furthermore, testing should be led by professionals with a higher specialization in this field.

MOWGLI: prediction of protein-MannOse interacting residues With ensemble classifiers usinG evoLutionary Information.

PubMed

Pai, Priyadarshini P; Mondal, Sukanta

2016-10-01

Proteins interact with carbohydrates to perform various cellular interactions. Of the many carbohydrate ligands that proteins bind with, mannose constitute an important class, playing important roles in host defense mechanisms. Accurate identification of mannose-interacting residues (MIR) may provide important clues to decipher the underlying mechanisms of protein-mannose interactions during infections. This study proposes an approach using an ensemble of base classifiers for prediction of MIR using their evolutionary information in the form of position-specific scoring matrix. The base classifiers are random forests trained by different subsets of training data set Dset128 using 10-fold cross-validation. The optimized ensemble of base classifiers, MOWGLI, is then used to predict MIR on protein chains of the test data set Dtestset29 which showed a promising performance with 92.0% accurate prediction. An overall improvement of 26.6% in precision was observed upon comparison with the state-of-art. It is hoped that this approach, yielding enhanced predictions, could be eventually used for applications in drug design and vaccine development.

The relationship between intelligence and training gains is moderated by training strategy.

PubMed

Lee, Hyunkyu; Boot, Walter R; Baniqued, Pauline L; Voss, Michelle W; Prakash, Ruchika Shaurya; Basak, Chandramallika; Kramer, Arthur F

2015-01-01

We examined the relationship between training regimen and fluid intelligence in the learning of a complex video game. Fifty non-game-playing young adults were trained on a game called Space Fortress for 30 hours with one of two training regimens: (1) Hybrid Variable-Priority Training (HVT), with part-task training and a focus on improving specific skills and managing task priorities, and (2) Full Emphasis Training (FET) in which participants practiced the whole game to obtain the highest overall score. Fluid intelligence was measured with the Raven's Progressive Matrix task before training. With FET, fluid intelligence was positively associated with learning, suggesting that intellectual ability played a substantial role in determining individual differences in training success. In contrast, with HVT, fluid intelligence was not associated with learning, suggesting that individual differences in fluid intelligence do not factor into training success in a regimen that emphasizes component tasks and flexible task coordination. By analyzing training effects in terms of individual differences and training regimens, the current study offers a training approach that minimizes the potentially limiting effect of individual differences.

A Partial Least Squares Based Procedure for Upstream Sequence Classification in Prokaryotes.

PubMed

Mehmood, Tahir; Bohlin, Jon; Snipen, Lars

2015-01-01

The upstream region of coding genes is important for several reasons, for instance locating transcription factor, binding sites, and start site initiation in genomic DNA. Motivated by a recently conducted study, where multivariate approach was successfully applied to coding sequence modeling, we have introduced a partial least squares (PLS) based procedure for the classification of true upstream prokaryotic sequence from background upstream sequence. The upstream sequences of conserved coding genes over genomes were considered in analysis, where conserved coding genes were found by using pan-genomics concept for each considered prokaryotic species. PLS uses position specific scoring matrix (PSSM) to study the characteristics of upstream region. Results obtained by PLS based method were compared with Gini importance of random forest (RF) and support vector machine (SVM), which is much used method for sequence classification. The upstream sequence classification performance was evaluated by using cross validation, and suggested approach identifies prokaryotic upstream region significantly better to RF (p-value < 0.01) and SVM (p-value < 0.01). Further, the proposed method also produced results that concurred with known biological characteristics of the upstream region.

An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.

PubMed

Delorenzi, Mauro; Speed, Terry

2002-04-01

Large-scale sequence data require methods for the automated annotation of protein domains. Many of the predictive methods are based either on a Position Specific Scoring Matrix (PSSM) of fixed length or on a window-less Hidden Markov Model (HMM). The performance of the two approaches is tested for Coiled-Coil Domains (CCDs). The prediction of CCDs is used frequently, and its optimization seems worthwhile. We have conceived MARCOIL, an HMM for the recognition of proteins with a CCD on a genomic scale. A cross-validated study suggests that MARCOIL improves predictions compared to the traditional PSSM algorithm, especially for some protein families and for short CCDs. The study was designed to reveal differences inherent in the two methods. Potential confounding factors such as differences in the dimension of parameter space and in the parameter values were avoided by using the same amino acid propensities and by keeping the transition probabilities of the HMM constant during cross-validation. The prediction program and the databases are available at http://www.wehi.edu.au/bioweb/Mauro/Marcoil

A Transfer Learning Approach for Applying Matrix Factorization to Small ITS Datasets

ERIC Educational Resources Information Center

Voß, Lydia; Schatten, Carlotta; Mazziotti, Claudia; Schmidt-Thieme, Lars

2015-01-01

Machine Learning methods for Performance Prediction in Intelligent Tutoring Systems (ITS) have proven their efficacy; specific methods, e.g. Matrix Factorization (MF), however suffer from the lack of available information about new tasks or new students. In this paper we show how this problem could be solved by applying Transfer Learning (TL),…

78 FR 76067 - Defense Federal Acquisition Regulation Supplement: Item Unique Identifier Update (DFARS Case 2011...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-16

... with the Air Transport Association Common Support Data Dictionary; and (ii) The encoded data elements... 211.274-2(a)(2) and (3) are revised to consolidate requirements. The definition of ``data matrix... Registry'' is added at 252.211-7003(c)(2). The phrase ``ECC200 data matrix specification'' is added at 252...

Diagnostic efficiency of Mueller-matrix polarization reconstruction system of the phase structure of liver tissue

NASA Astrophysics Data System (ADS)

Zabolotna, Natalia I.; Pavlov, Sergii V.; Radchenko, Kostiantyn O.; Stasenko, Vladyslav A.; Wójcik, Waldemar; Kussambayeva, Nazym

2015-12-01

The application field of using the Mueller-matrix polarizing reconstruction system of phase structure of biological layer for optical-anisotropic parameters differentiation of histological sections of healthy and rat's liver with hepatitis were investigated. Comparison of system informativity with known systems on indexes of sensitivity, specificity and balanced accuracy were performed.

MALDI (matrix assisted laser desorption ionization) Imaging Mass Spectrometry (IMS) of skin: Aspects of sample preparation.

PubMed

de Macedo, Cristiana Santos; Anderson, David M; Schey, Kevin L

2017-11-01

MALDI (matrix assisted laser desorption ionization) Imaging Mass Spectrometry (IMS) allows molecular analysis of biological materials making possible the identification and localization of molecules in tissues, and has been applied to address many questions on skin pathophysiology, as well as on studies about drug absorption and metabolism. Sample preparation for MALDI IMS is the most important part of the workflow, comprising specimen collection and preservation, tissue embedding, cryosectioning, washing, and matrix application. These steps must be carefully optimized for specific analytes of interest (lipids, proteins, drugs, etc.), representing a challenge for skin analysis. In this review, critical parameters for MALDI IMS sample preparation of skin samples will be described. In addition, specific applications of MALDI IMS of skin samples will be presented including wound healing, neoplasia, and infection. Copyright © 2017 Elsevier B.V. All rights reserved.

Fully Ceramic Microencapsulated Fuel Development for LWR Applications

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

Snead, Lance Lewis; Besmann, Theodore M; Terrani, Kurt A

2012-01-01

The concept, fabrication, and key feasibility issues of a new fuel form based on the microencapsulated (TRISO-type) fuel which has been specifically engineered for LWR application and compacted within a SiC matrix will be presented. This fuel, the so-called fully ceramic microencapsulated fuel is currently undergoing development as an accident tolerant fuel for potential UO2 replacement in commercial LWRs. While the ability of this fuel to facilitate normal LWR cycle performance is an ongoing effort within the program, this will not be a focus of this paper. Rather, key feasibility and performance aspects of the fuel will be presented includingmore » the ability to fabricate a LWR-specific TRISO, the need for and route to a high thermal conductivity and fully dense matrix that contains neutron poisons, and the performance of that matrix under irradiation and the interaction of the fuel with commercial zircaloy clad.« less

Metal Matrix Composite Materials for Aerospace Applications

NASA Technical Reports Server (NTRS)

Bhat, Biliyar N.; Jones, C. S. (Technical Monitor)

2001-01-01

Metal matrix composites (MMC) are attractive materials for aerospace applications because of their high specific strength, high specific stiffness, and lower thermal expansion coefficient. They are affordable since complex parts can be produced by low cost casting process. As a result there are many commercial and Department of Defense applications of MMCs today. This seminar will give an overview of MMCs and their state-of-the-art technology assessment. Topics to be covered are types of MMCs, fabrication methods, product forms, applications, and material selection issues for design and manufacture. Some examples of current and future aerospace applications will also be presented and discussed.

A modified tensionless gingival grafting technique using acellular dermal matrix.

PubMed

Taylor, John B; Gerlach, Robert C; Herold, Robert W; Bisch, Frederick C; Dixon, Douglas R

2010-10-01

Conventional surgical procedures designed for autogenous tissue material may not be appropriate when using acellular dermal matrix (ADM) for the treatment of gingival recessions. This article describes a new surgical technique that addresses the unique and sensitive aspects of ADM specifically to improve esthetic outcomes and gain increased clinical predictability when treating Miller Class I and II gingival recession defects. In this paper, a root coverage case is described and the specific steps and rationale for this new technique are explained. This technique has been predictable clinically, with results comparable to those achieved using autogenous tissue.

3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution.

PubMed

Körsgen, Martin; Pelster, Andreas; Dreisewerd, Klaus; Arlinghaus, Heinrich F

2016-02-01

The analytical sensitivity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is largely affected by the specific analyte-matrix interaction, in particular by the possible incorporation of the analytes into crystalline MALDI matrices. Here we used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the incorporation of three peptides with different hydrophobicities, bradykinin, Substance P, and vasopressin, into two classic MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA). For depth profiling, an Ar cluster ion beam was used to gradually sputter through the matrix crystals without causing significant degradation of matrix or biomolecules. A pulsed Bi3 ion cluster beam was used to image the lateral analyte distribution in the center of the sputter crater. Using this dual beam technique, the 3D distribution of the analytes and spatial segregation effects within the matrix crystals were imaged with sub-μm resolution. The technique could in the future enable matrix-enhanced (ME)-ToF-SIMS imaging of peptides in tissue slices at ultra-high resolution. Graphical Abstract ᅟ.

3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution

NASA Astrophysics Data System (ADS)

Körsgen, Martin; Pelster, Andreas; Dreisewerd, Klaus; Arlinghaus, Heinrich F.

2016-02-01

The analytical sensitivity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is largely affected by the specific analyte-matrix interaction, in particular by the possible incorporation of the analytes into crystalline MALDI matrices. Here we used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the incorporation of three peptides with different hydrophobicities, bradykinin, Substance P, and vasopressin, into two classic MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA). For depth profiling, an Ar cluster ion beam was used to gradually sputter through the matrix crystals without causing significant degradation of matrix or biomolecules. A pulsed Bi3 ion cluster beam was used to image the lateral analyte distribution in the center of the sputter crater. Using this dual beam technique, the 3D distribution of the analytes and spatial segregation effects within the matrix crystals were imaged with sub-μm resolution. The technique could in the future enable matrix-enhanced (ME)-ToF-SIMS imaging of peptides in tissue slices at ultra-high resolution.

Attention Problems and Stability of WISC-IV Scores Among Clinically Referred Children.

PubMed

Green Bartoi, Marla; Issner, Jaclyn Beth; Hetterscheidt, Lesley; January, Alicia M; Kuentzel, Jeffrey Garth; Barnett, Douglas

2015-01-01

We examined the stability of Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) scores among 51 diverse, clinically referred 8- to 16-year-olds (M(age) = 11.24 years, SD = 2.36). Children were referred to and tested at an urban, university-based training clinic; 70% of eligible children completed follow-up testing 12 months to 40 months later (M = 22.05, SD = 5.94). Stability for index scores ranged from .58 (Processing Speed) to .81 (Verbal Comprehension), with a stability of .86 for Full-Scale IQ. Subtest score stability ranged from .35 (Letter-Number Sequencing) to .81 (Vocabulary). Indexes believed to be more susceptible to concentration (Processing Speed and Working Memory) had lower stability. We also examined attention problems as a potential moderating factor of WISC-IV index and subtest score stability. Children with attention problems had significantly lower stability for Digit Span and Matrix Reasoning subtests compared with children without attention problems. These results provide support for the temporal stability of the WISC-IV and also provide some support for the idea that attention problems contribute to children producing less stable IQ estimates when completing the WISC-IV. We hope our report encourages further examination of this hypothesis and its implications.

BioSAVE: display of scored annotation within a sequence context.

PubMed

Pollock, Richard F; Adryan, Boris

2008-03-20

Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation) within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains) from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage.

BioSAVE: Display of scored annotation within a sequence context

PubMed Central

Pollock, Richard F; Adryan, Boris

2008-01-01

Background Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. Results We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation) within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains) from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. Conclusion Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage. PMID:18366701

Deletion of Dual Specificity Phosphatase 1 Does Not Predispose Mice to Increased Spontaneous Osteoarthritis

PubMed Central

Pest, Michael Andrew; Pest, Courtney Alice; Bellini, Melina Rodrigues; Feng, Qingping; Beier, Frank

2015-01-01

Background Osteoarthritis (OA) is a degenerative joint disease with poorly understood etiology and pathobiology. Mitogen activated protein kinases (MAPKs) including ERK and p38 play important roles in the mediation of downstream pathways involved in cartilage degenerative processes. Dual specificity phosphatase 1 (DUSP1) dephosphorylates the threonine/serine and tyrosine sites on ERK and p38, causing deactivation of downstream signalling. In this study we examined the role of DUSP1 in spontaneous OA development at 21 months of age using a genetically modified mouse model deficient in Dusp1 (DUSP1 knockout mouse). Results Utilizing histochemical stains of paraffin embedded knee joint sections in DUSP1 knockout and wild type female and male mice, we showed similar structural progression of cartilage degeneration associated with OA at 21 months of age. A semi-quantitative cartilage degeneration scoring system also demonstrated similar scores in the various aspects of the knee joint articular cartilage in DUSP1 knockout and control mice. Examination of overall articular cartilage thickness in the knee joint demonstrated similar results between DUSP1 knockout and wild type mice. Immunostaining for cartilage neoepitopes DIPEN, TEGE and C1,2C was similar in the cartilage lesion sites and chondrocyte pericellular matrix of both experimental groups. Likewise, immunostaining for phosphoERK and MMP13 showed similar intensity and localization between groups. SOX9 immunostaining demonstrated a decreased number of positive cells in DUSP1 knockout mice, with correspondingly decreased staining intensity. Analysis of animal walking patterns (gait) did not show a discernable difference between groups. Conclusion Loss of DUSP1 does not cause changes in cartilage degeneration and gait in a mouse model of spontaneous OA at 21 months of age. Altered staining was observed in SOX9 immunostaining which may prove promising for future studies examining the role of DUSPs in cartilage and OA, as well as models of post-traumatic OA. PMID:26562438

Beneficial effects of ursodeoxycholic acid via inhibition of airway remodelling, apoptosis of airway epithelial cells, and Th2 immune response in murine model of chronic asthma.

PubMed

Işık, S; Karaman, M; Çilaker Micili, S; Çağlayan-Sözmen, Ş; Bağrıyanık, H Alper; Arıkan-Ayyıldız, Z; Uzuner, N; Karaman, Ö

In previous studies, anti-inflammatory, anti-apoptotic and immunomodulatory effects of ursodeoxycholic acid (UDCA) on liver diseases have been shown. In this study, we aimed to investigate the effects of UDCA on airway remodelling, epithelial apoptosis, and T Helper (Th)-2 derived cytokine levels in a murine model of chronic asthma. Twenty-seven BALB/c mice were divided into five groups; PBS-Control, OVA-Placebo, OVA-50mg/kg UDCA, OVA-150mg/kg UDCA, OVA-Dexamethasone. Mice in groups OVA-50mg/kg UDCA, OVA-150mg/kg UDCA, OVA-Dexamethasone received the UDCA (50mg/kg), UDCA (150mg/kg), and dexamethasone, respectively. Epithelium thickness, sub-epithelial smooth muscle thickness, number of mast and goblet cells of samples isolated from the lung were measured. Immunohistochemical scorings of the lung tissue for matrix metalloproteinase-9 (MMP-9), vascular endothelial growth factor (VEG-F), transforming growth factor-beta (TGF-β), terminal deoxynucleotidyl transferase-mediated dUTP nick endlabeling (TUNEL) and cysteine-dependent aspartate-specific proteases (caspase)-3 were determined. IL-4, IL-5, IL-13, Nitric oxide, ovalbumin-specific immunoglobulin (Ig) E levels were quantified. The dose of 150mg/kg UDCA treatment led to lower epithelial thickness, sub-epithelial smooth muscle thickness, goblet and mast cell numbers compared to placebo. Except for MMP-9 and TUNEL all immunohistochemical scores were similar in both UDCA treated groups and the placebo. All cytokine levels were significantly lower in group IV compared to the placebo. These findings suggested that the dose of 150mg/kg UDCA improved all histopathological changes of airway remodelling and its beneficial effects might be related to modulating Th-2 derived cytokines and the inhibition of apoptosis of airway epithelial cells. Copyright © 2017 SEICAP. Published by Elsevier España, S.L.U. All rights reserved.

Unusual Mesoporous Carbonaceous Matrix Loading with Sulfur as the Cathode of Lithium Sulfur Battery with Exceptionally Stable High Rate Performance.

PubMed

Qian, Weiwei; Gao, Qiuming; Li, Zeyu; Tian, Weiqian; Zhang, Hang; Zhang, Qiang

2017-08-30

Unusual three-dimensional mesoporous carbon/reduced graphene oxide (MP-C/rGO) matrix possessing graphene nanolayer pore walls built up by three to five graphene monosheets and some carbon particles with the sizes of about 5 nm located between the graphene nanolayers was prepared by facile freeze-drying and then carbonization of the poly(vinyl alcohol) and graphene oxide mixture. The mesoporous carbonaceous MP-C/rGO sample has a high specific surface area of 661.6 m 2 g -1 , large specific pore volume of 1.54 m 3 g -1 , and focused pore size distribution of 2-10 nm. About 64 wt % sulfur could be held in the pores of the MP-C/rGO matrix. As the cathode of a Li-S battery, the MP-C/rGO/S composite showed excellent electrochemical property including a high initial specific capacity of 919 mA h g -1 at 1 C with the capacity retention ratio of 63.3% and the Coulombic efficiency above 90% after 500 cycles. Meanwhile, the initial specific capacity of 602 mA h g -1 at 5 C and remaining capacity of 391 mA h g -1 after 500 cycles with an outstanding Coulombic efficiency of 97% indicate its exceptionally stable rate performance.

Comparison of polypropylene mesh and porcine-derived, cross-linked urinary bladder matrix materials implanted in the rabbit vagina and abdomen.

PubMed

Fan, Xuemei; Wang, Yanzhou; Wang, Yu; Xu, Huicheng

2014-05-01

Our aim was to compare histological and biomechanical effects of polypropylene (PP) mesh and porcine-derived, cross-linked urinary bladder matrix (cUBM) graft materials using a rabbit vaginal and abdominal model. Forty rabbits were implanted with PP mesh (n = 20) or cUBM (n = 20) in the vagina and abdomen. Two grafts (PP or cUBM) of the same type were placed into each site, so each rabbit had four grafts. Grafts were harvested 12 weeks later and processed for histologic analysis and biomechanical testing. There were high rates of two types of grafts missing in the vagina. Vaginal PP was associated with erosion reaction (67%), whereas abdominal PP and cUBM showed no sign of erosion. All patches adhered to rectus abdominis or vaginal mucosa and shrank to varying degrees, especially for PP grafts. Compared with vaginal PP, vaginal cUBM induced milder chronic inflammation response, had lower scores (P = 0.000) for inflammation response, and showed higher scores for neovascularization (P = 0.000) and fibroblastic proliferation (P = 0.002). In the abdomen, both histopathological parameters were insignificantly different (P > 0.05) between cUBM and PP. The mechanical properties of UBM did not deteriorate following implantation, whereas the ultimate tensile strength and elastic modulus of vaginal PP increased. PP had higher scores for tensile and break strength than did cUBM (P < 0.05). The cUBM has good biocompatibility, high ability to integrate with the vagina, and maintains mechanical properties in vivo. It may be a promising material for pelvic floor reconstruction.

Clock Drawing Test and the diagnosis of amnestic mild cognitive impairment: can more detailed scoring systems do the work?

PubMed

Rubínová, Eva; Nikolai, Tomáš; Marková, Hana; Siffelová, Kamila; Laczó, Jan; Hort, Jakub; Vyhnálek, Martin

2014-01-01

The Clock Drawing Test is a frequently used cognitive screening test with several scoring systems in elderly populations. We compare simple and complex scoring systems and evaluate the usefulness of the combination of the Clock Drawing Test with the Mini-Mental State Examination to detect patients with mild cognitive impairment. Patients with amnestic mild cognitive impairment (n = 48) and age- and education-matched controls (n = 48) underwent neuropsychological examinations, including the Clock Drawing Test and the Mini-Mental State Examination. Clock drawings were scored by three blinded raters using one simple (6-point scale) and two complex (17- and 18-point scales) systems. The sensitivity and specificity of these scoring systems used alone and in combination with the Mini-Mental State Examination were determined. Complex scoring systems, but not the simple scoring system, were significant predictors of the amnestic mild cognitive impairment diagnosis in logistic regression analysis. At equal levels of sensitivity (87.5%), the Mini-Mental State Examination showed higher specificity (31.3%, compared with 12.5% for the 17-point Clock Drawing Test scoring scale). The combination of Clock Drawing Test and Mini-Mental State Examination scores increased the area under the curve (0.72; p < .001) and increased specificity (43.8%), but did not increase sensitivity, which remained high (85.4%). A simple 6-point scoring system for the Clock Drawing Test did not differentiate between healthy elderly and patients with amnestic mild cognitive impairment in our sample. Complex scoring systems were slightly more efficient, yet still were characterized by high rates of false-positive results. We found psychometric improvement using combined scores from the Mini-Mental State Examination and the Clock Drawing Test when complex scoring systems were used. The results of this study support the benefit of using combined scores from simple methods.

Pulmonary immunity and extracellular matrix interactions.

PubMed

O'Dwyer, David N; Gurczynski, Stephen J; Moore, Bethany B

2018-04-09

The lung harbors a complex immune system composed of both innate and adaptive immune cells. Recognition of infection and injury by receptors on lung innate immune cells is crucial for generation of antigen-specific responses by adaptive immune cells. The extracellular matrix of the lung, comprising the interstitium and basement membrane, plays a key role in the regulation of these immune systems. The matrix consists of several hundred assembled proteins that interact to form a bioactive scaffold. This template, modified by enzymes, acts to facilitate cell function and differentiation and changes dynamically with age and lung disease. Herein, we explore relationships between innate and adaptive immunity and the lung extracellular matrix. We discuss the interactions between extracellular matrix proteins, including glycosaminoglycans, with prominent effects on innate immune signaling effectors such as toll-like receptors. We describe the relationship of extracellular matrix proteins with adaptive immunity and leukocyte migration to sites of injury within the lung. Further study of these interactions will lead to greater knowledge of the role of matrix biology in lung immunity. The development of novel therapies for acute and chronic lung disease is dependent on a comprehensive understanding of these complex matrix-immunity interactions. Copyright © 2017 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Cell–material interactions on biphasic polyurethane matrix

PubMed Central

Dicesare, Patrick; Fox, Wade M.; Hill, Michael J.; Krishnan, G. Rajesh; Yang, Shuying; Sarkar, Debanjan

2013-01-01

Cell–matrix interaction is a key regulator for controlling stem cell fate in regenerative tissue engineering. These interactions are induced and controlled by the nanoscale features of extracellular matrix and are mimicked on synthetic matrices to control cell structure and functions. Recent studies have shown that nanostructured matrices can modulate stem cell behavior and exert specific role in tissue regeneration. In this study, we have demonstrated that nanostructured phase morphology of synthetic matrix can control adhesion, proliferation, organization and migration of human mesenchymal stem cells (MSCs). Nanostructured biodegradable polyurethanes (PU) with segmental composition exhibit biphasic morphology at nanoscale dimensions and can control cellular features of MSCs. Biodegradable PU with polyester soft segment and hard segment composed of aliphatic diisocyanates and dipeptide chain extender were designed to examine the effect polyurethane phase morphology. By altering the polyurethane composition, morphological architecture of PU was modulated and its effect was examined on MSC. Results show that MSCs can sense the nanoscale morphology of biphasic polyurethane matrix to exhibit distinct cellular features and, thus, signifies the relevance of matrix phase morphology. The role of nanostructured phases of a synthetic matrix in controlling cell–matrix interaction provides important insights for regulation of cell behavior on synthetic matrix and, therefore, is an important tool for engineering tissue regeneration. PMID:23255285

Structured Matrix Completion with Applications to Genomic Data Integration.

PubMed

Cai, Tianxi; Cai, T Tony; Zhang, Anru

2016-01-01

Matrix completion has attracted significant recent attention in many fields including statistics, applied mathematics and electrical engineering. Current literature on matrix completion focuses primarily on independent sampling models under which the individual observed entries are sampled independently. Motivated by applications in genomic data integration, we propose a new framework of structured matrix completion (SMC) to treat structured missingness by design. Specifically, our proposed method aims at efficient matrix recovery when a subset of the rows and columns of an approximately low-rank matrix are observed. We provide theoretical justification for the proposed SMC method and derive lower bound for the estimation errors, which together establish the optimal rate of recovery over certain classes of approximately low-rank matrices. Simulation studies show that the method performs well in finite sample under a variety of configurations. The method is applied to integrate several ovarian cancer genomic studies with different extent of genomic measurements, which enables us to construct more accurate prediction rules for ovarian cancer survival.

Modeling the Mechanical Behavior of Ceramic Matrix Composite Materials

NASA Technical Reports Server (NTRS)

Jordan, William

1998-01-01

Ceramic matrix composites are ceramic materials, such as SiC, that have been reinforced by high strength fibers, such as carbon. Designers are interested in using ceramic matrix composites because they have the capability of withstanding significant loads while at relatively high temperatures (in excess of 1,000 C). Ceramic matrix composites retain the ceramic materials ability to withstand high temperatures, but also possess a much greater ductility and toughness. Their high strength and medium toughness is what makes them of so much interest to the aerospace community. This work concentrated on two different tasks. The first task was to do an extensive literature search into the mechanical behavior of ceramic matrix composite materials. This report contains the results of this task. The second task was to use this understanding to help interpret the ceramic matrix composite mechanical test results that had already been obtained by NASA. Since the specific details of these test results are subject to the International Traffic in Arms Regulations (ITAR), they are reported in a separate document (Jordan, 1997).

Use of the Sequential Organ Failure Assessment score for evaluating outcome among obstetric patients admitted to the intensive care unit.

PubMed

Jain, Shruti; Guleria, Kiran; Suneja, Amita; Vaid, Neelam B; Ahuja, Sharmila

2016-03-01

To evaluate the prognostic value of the Sequential Organ Failure Assessment (SOFA) score among obstetric patients admitted to the intensive care unit (ICU). A prospective study was conducted among 90 consecutive obstetric patients who were admitted to the ICU of Guru Teg Bahadur Hospital, Delhi, India, between October 6, 2010, and December 25, 2011. Maximum SOFA score was calculated for each of the six organ systems. Receiver operating characteristic curves were used to determine critical cutoff values for total, maximum total, and mean total SOFA scores at various time points. Total SOFA score at admission displayed an area under the curve (AUC) of 0.949, a cutoff value of at least 8.5, sensitivity of 86.7%, and specificity of 90.0%. Maximum total SOFA score had an AUC of 0.980, a cutoff value of at least 10.0, sensitivity of 96.7%, and specificity of 90.0%. Mean total SOFA score had an AUC of 0.997, a cutoff value of at least 9.0, sensitivity of 96.7%, and specificity of 96.7%. In terms of discriminatory power for predicting mortality among obstetric patients admitted to the ICU, total SOFA score at admission was the most relevant, simple, and accurate measure. Copyright © 2015 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

Interest in sports and belief in sports superstitions.

PubMed

McClearn, Duane G

2004-06-01

51 nonathletes, students (45 women) at a medium-sized southern university, were administered a survey containing three scales: an Interest in Sports Scale, a Belief in Sports Superstitions Scale, and Tobacyk and Milford's Paranormal Belief Scale (1983). Scores on the Interest in Sports Scale were significantly correlated with scores on the Belief in Sports Superstitions Scale, which measured adherence specifically to sports superstitions, but not with scores on the Paranormal Belief Scale, which measured a wide variety of irrational beliefs. Thus, participants with high interest in sports showed a tendency to subscribe to the type of irrational belief associated specifically with sports. Scores on the Belief in Sports Superstitions Scale were positively correlated with scores on the Paranormal Belief Scale.