Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases

PubMed Central

Romero Navarro, J. Alberto; Phillips-Mora, Wilbert; Arciniegas-Leal, Adriana; Mata-Quirós, Allan; Haiminen, Niina; Mustiga, Guiliana; Livingstone III, Donald; van Bakel, Harm; Kuhn, David N.; Parida, Laxmi; Kasarskis, Andrew; Motamayor, Juan C.

2017-01-01

Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years. Using high-density markers, the diversity of clones was expressed relative to 10 known ancestral cacao populations, and significant effects of ancestry were observed in productivity and disease resistance. Genome-wide association (GWA) was performed, and six markers were significantly associated with frosty pod disease resistance. In addition, genomic selection was performed, and consistent with the observed extensive linkage disequilibrium, high predictive ability was observed at low marker densities for all traits. Finally, quantitative trait locus mapping and differential expression analysis of two cultivars with contrasting disease phenotypes were performed to identify genes underlying frosty pod disease resistance, identifying a significant quantitative trait locus and 35 differentially expressed genes using two independent differential expression analyses. These results indicate that in breeding populations of heterozygous and recently admixed individuals, mapping approaches can be used for low complexity traits like pod color cacao, or in other species single gene disease resistance, however genomic selection for quantitative traits remains highly effective relative to mapping. Our results can help guide the breeding process for sustainable improved cacao productivity. PMID:29184558

Quantitative computed tomography measurements of emphysema for diagnosing asthma-chronic obstructive pulmonary disease overlap syndrome

PubMed Central

Xie, Mengshuang; Wang, Wei; Dou, Shuang; Cui, Liwei; Xiao, Wei

2016-01-01

Background The diagnostic criteria of asthma–COPD overlap syndrome (ACOS) are controversial. Emphysema is characteristic of COPD and usually does not exist in typical asthma patients. Emphysema in patients with asthma suggests the coexistence of COPD. Quantitative computed tomography (CT) allows repeated evaluation of emphysema noninvasively. We investigated the value of quantitative CT measurements of emphysema in the diagnosis of ACOS. Methods This study included 404 participants; 151 asthma patients, 125 COPD patients, and 128 normal control subjects. All the participants underwent pulmonary function tests and a high-resolution CT scan. Emphysema measurements were taken with an Airway Inspector software. The asthma patients were divided into high and low emphysema index (EI) groups based on the percentage of low attenuation areas less than −950 Hounsfield units. The characteristics of asthma patients with high EI were compared with those having low EI or COPD. Results The normal value of percentage of low attenuation areas less than −950 Hounsfield units in Chinese aged >40 years was 2.79%±2.37%. COPD patients indicated more severe emphysema and more upper-zone-predominant distribution of emphysema than asthma patients or controls. Thirty-two (21.2%) of the 151 asthma patients had high EI. Compared with asthma patients with low EI, those with high EI were significantly older, more likely to be male, had more pack-years of smoking, had more upper-zone-predominant distribution of emphysema, and had greater airflow limitation. There were no significant differences in sex ratios, pack-years of smoking, airflow limitation, or emphysema distribution between asthma patients with high EI and COPD patients. A greater number of acute exacerbations were seen in asthma patients with high EI compared with those with low EI or COPD. Conclusion Asthma patients with high EI fulfill the features of ACOS, as described in the Global Initiative for Asthma and Global Initiative for Chronic Obstructive Lung Disease guidelines. Quantitative CT measurements of emphysema may help in diagnosing ACOS. PMID:27226711

Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase

PubMed Central

Lucas, James E; Siegel, Justin B

2015-01-01

Enzyme active site residues are often highly conserved, indicating a significant role in function. In this study we quantitate the functional contribution for all conserved molecular interactions occurring within a Michaelis complex for mannitol 2-dehydrogenase derived from Pseudomonas fluorescens (pfMDH). Through systematic mutagenesis of active site residues, we reveal that the molecular interactions in pfMDH mediated by highly conserved residues not directly involved in reaction chemistry can be as important to catalysis as those directly involved in the reaction chemistry. This quantitative analysis of the molecular interactions within the pfMDH active site provides direct insight into the functional role of each molecular interaction, several of which were unexpected based on canonical sequence conservation and structural analyses. PMID:25752240

A Computer-Aided Analysis Method of SPECT Brain Images for Quantitative Treatment Monitoring: Performance Evaluations and Clinical Applications.

PubMed

Zheng, Xiujuan; Wei, Wentao; Huang, Qiu; Song, Shaoli; Wan, Jieqing; Huang, Gang

2017-01-01

The objective and quantitative analysis of longitudinal single photon emission computed tomography (SPECT) images are significant for the treatment monitoring of brain disorders. Therefore, a computer aided analysis (CAA) method is introduced to extract a change-rate map (CRM) as a parametric image for quantifying the changes of regional cerebral blood flow (rCBF) in longitudinal SPECT brain images. The performances of the CAA-CRM approach in treatment monitoring are evaluated by the computer simulations and clinical applications. The results of computer simulations show that the derived CRMs have high similarities with their ground truths when the lesion size is larger than system spatial resolution and the change rate is higher than 20%. In clinical applications, the CAA-CRM approach is used to assess the treatment of 50 patients with brain ischemia. The results demonstrate that CAA-CRM approach has a 93.4% accuracy of recovered region's localization. Moreover, the quantitative indexes of recovered regions derived from CRM are all significantly different among the groups and highly correlated with the experienced clinical diagnosis. In conclusion, the proposed CAA-CRM approach provides a convenient solution to generate a parametric image and derive the quantitative indexes from the longitudinal SPECT brain images for treatment monitoring.

Using PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics

PubMed Central

Lavallée-Adam, Mathieu

2017-01-01

PSEA-Quant analyzes quantitative mass spectrometry-based proteomics datasets to identify enrichments of annotations contained in repositories such as the Gene Ontology and Molecular Signature databases. It allows users to identify the annotations that are significantly enriched for reproducibly quantified high abundance proteins. PSEA-Quant is available on the web and as a command-line tool. It is compatible with all label-free and isotopic labeling-based quantitative proteomics methods. This protocol describes how to use PSEA-Quant and interpret its output. The importance of each parameter as well as troubleshooting approaches are also discussed. PMID:27010334

Prediction of high-stage liver fibrosis using ADC value on diffusion-weighted imaging and quantitative enhancement ratio at the hepatobiliary phase of Gd-EOB-DTPA-enhanced MRI at 1.5 T.

PubMed

Harada, Taiyo L; Saito, Kazuhiro; Araki, Yoichi; Matsubayashi, Jun; Nagao, Toshitaka; Sugimoto, Katsutoshi; Tokuuye, Koichi

2018-05-01

Background Recently, diffusion-weighted imaging (DWI) and quantitative enhancement ratio measured at the hepatobiliary phase (HBP) of Gd-EOB-DTPA-enhanced magnetic resonance imaging (MRI) has been established as an effective method for evaluating liver fibrosis. Purpose To evaluate which is a more favorable surrogate marker in predicting high-stage liver fibrosis, apparently diffusion coefficient (ADC) value or quantitative enhancement ratio measured on HBP. Material and Methods Eighty-three patients with 99 surgically resected hepatic lesions were enrolled in this study. DWI was performed with b-values of 100 and 800 s/mm 2 . Regions of interest were set on ADC map, and the HBP of Gd-EOB-DTPA-enhanced MRI, to calculate ADC value, liver-to-muscle ratio (LMR), liver-to-spleen ratio (LSR), and contrast enhancement index (CEI) of liver. We compared these parameters between low-stage fibrosis (F0, F1, and F2) and high-stage fibrosis (F3 and F4). Receiver operating characteristic analysis was performed to compare the diagnostic performance when distinguishing low-stage fibrosis from high-stage fibrosis. Results LMR and CEI were significantly lower at high-stage fibrosis than at the low stage ( P < 0.01 and P = 0.04, respectively), whereas LSR did not show a significant difference ( P = 0.053). No significant difference was observed in diagnostic performance between LMR and CEI ( P = 0.185). The best sensitivity and specificity, when an LMR of 2.80 or higher was considered to be low-stage fibrosis, were 82.4% and 75.6%, respectively. ADC value showed no significant differences among fibrosis grades ( P = 0.320). Conclusion LMR and CEI were both adequate surrogate parameters to distinguish high-stage fibrosis from low-stage fibrosis.

Light sheet theta microscopy for rapid high-resolution imaging of large biological samples.

PubMed

Migliori, Bianca; Datta, Malika S; Dupre, Christophe; Apak, Mehmet C; Asano, Shoh; Gao, Ruixuan; Boyden, Edward S; Hermanson, Ola; Yuste, Rafael; Tomer, Raju

2018-05-29

Advances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy approaches to image large samples quantitatively and at high resolution. While light sheet microscopy (LSM), with its high planar imaging speed and low photo-bleaching, can be effective, scaling up to larger imaging volumes has been hindered by the use of orthogonal light sheet illumination. To address this fundamental limitation, we have developed light sheet theta microscopy (LSTM), which uniformly illuminates samples from the same side as the detection objective, thereby eliminating limits on lateral dimensions without sacrificing the imaging resolution, depth, and speed. We present a detailed characterization of LSTM, and demonstrate its complementary advantages over LSM for rapid high-resolution quantitative imaging of large intact samples with high uniform quality. The reported LSTM approach is a significant step for the rapid high-resolution quantitative mapping of the structure and function of very large biological systems, such as a clarified thick coronal slab of human brain and uniformly expanded tissues, and also for rapid volumetric calcium imaging of highly motile animals, such as Hydra, undergoing non-isomorphic body shape changes.

Qualitative and quantitative evaluation of some vocal function parameters following fitting of a prosthesis.

PubMed

Cavalot, A L; Palonta, F; Preti, G; Nazionale, G; Ricci, E; Vione, N; Albera, R; Cortesina, G

2001-12-01

The insertion of a prosthesis and restoration with pectoralis major myocutaneous flaps for patients subjected to total pharyngolaryngectomy is a technique now universally accepted; however the literature on the subject is lacking. Our study considers 10 patients subjected to total pharyngolaryngectomy and restoration with pectoralis major myocutaneous flaps who were fitted with vocal function prostheses and a control group of 50 subjects treated with a total laryngectomy without pectoralis major myocutaneous flaps and who were fitted with vocal function prostheses. Specific qualitative and quantitative parameters were compared. The quantitative measurement of the levels of voice intensity and the evaluation of the harmonics-to-noise ratio were not statistically significant (p > 0.05) between the two study groups at either high- or low-volume speech. On the contrary, statistically significant differences were found (p < 0.05) for the basic frequency of both the low and the high volume voice. For the qualitative analysis seven parameters were established for evaluation by trained and untrained listeners: on the basis of these parameters the control group had statistically better voices.

Quantitative evaluation of retinal degeneration in royal college of surgeons rats by contrast enhanced ultrahigh resolution optical coherence tomography

NASA Astrophysics Data System (ADS)

Syu, Jia-Pu; Su, Min-Jyun; Chen, Po-Wei; Ke, Chang-Chih; Chiou, Shih-Hwa; Kuo, Wen-Chuan

2018-02-01

This study presents a spectral domain optical coherence tomography (SD-OCT) using supercontinuum laser combined with a fundus photography for in vivo high-resolution imaging of retinal degeneration in Royal College of Surgeons (RCS-/- rat). These findings were compared with the Sprague-Dawley (SD) rats and the corresponding histology. Quantitative measurements show that changes in thickness were not significantly different between SD control and young RCS retinas (4 weeks). However, in old RCS rats (55 weeks), the thickness of photoreceptor layer decreased significantly as compared to young RCS rats (both 4 weeks and 5 weeks). After contrast enhancement method, this platform will be useful for the quantitative evaluation of the degree of retinal degeneration, treatment outcome after therapy, and drug screening development in the future.

Quantitative fluorescence in intracranial tumor: implications for ALA-induced PpIX as an intraoperative biomarker

PubMed Central

Valdés, Pablo A.; Leblond, Frederic; Kim, Anthony; Harris, Brent T.; Wilson, Brian C.; Fan, Xiaoyao; Tosteson, Tor D.; Hartov, Alex; Ji, Songbai; Erkmen, Kadir; Simmons, Nathan E.; Paulsen, Keith D.; Roberts, David W.

2011-01-01

Object Accurate discrimination between tumor and normal tissue is crucial for optimal tumor resection. Qualitative fluorescence of protoporphyrin IX (PpIX), synthesized endogenously following δ-aminolevulinic acid (ALA) administration, has been used for this purpose in high-grade glioma (HGG). The authors show that diagnostically significant but visually imperceptible concentrations of PpIX can be quantitatively measured in vivo and used to discriminate normal from neoplastic brain tissue across a range of tumor histologies. Methods The authors studied 14 patients with diagnoses of low-grade glioma (LGG), HGG, meningioma, and metastasis under an institutional review board–approved protocol for fluorescence-guided resection. The primary aim of the study was to compare the diagnostic capabilities of a highly sensitive, spectrally resolved quantitative fluorescence approach to conventional fluorescence imaging for detection of neoplastic tissue in vivo. Results A significant difference in the quantitative measurements of PpIX concentration occurred in all tumor groups compared with normal brain tissue. Receiver operating characteristic (ROC) curve analysis of PpIX concentration as a diagnostic variable for detection of neoplastic tissue yielded a classification efficiency of 87% (AUC = 0.95, specificity = 92%, sensitivity = 84%) compared with 66% (AUC = 0.73, specificity = 100%, sensitivity = 47%) for conventional fluorescence imaging (p < 0.0001). More than 81% (57 of 70) of the quantitative fluorescence measurements that were below the threshold of the surgeon's visual perception were classified correctly in an analysis of all tumors. Conclusions These findings are clinically profound because they demonstrate that ALA-induced PpIX is a targeting biomarker for a variety of intracranial tumors beyond HGGs. This study is the first to measure quantitative ALA-induced PpIX concentrations in vivo, and the results have broad implications for guidance during resection of intracranial tumors. PMID:21438658

Explaining worker strain and learning: how important are emotional job demands?

PubMed

Taris, Toon W; Schreurs, Paul J G

2009-05-01

This study examined the added value of emotional job demands in explaining worker well-being, relative to the effects of task characteristics, such as quantitative job demands, job control, and coworker support. Emotional job demands were expected to account for an additional proportion of the variance in well-being. Cross-sectional data were obtained from 11,361 female Dutch home care employees. Hierarchical stepwise regression analysis demonstrated that low control, low support and high quantitative demands were generally associated with lower well-being (as measured in terms of emotional exhaustion, dedication, professional accomplishment and learning). Moreover, high emotional demands were in three out of four cases significantly associated with adverse well-being, in these cases accounting for an additional 1-6% of the variance in the outcome variables. In three out of eight cases the main effects of emotional demands on well-being were qualified by support and control, such that high control and high support either buffered the adverse effects of high emotional demands on well-being or increased the positive effects thereof. All in all, high emotional demands are as important a risk factor for worker well-being as well-established concepts like low job control and high quantitative job demands.

Characterization of enzymatically induced degradation of articular cartilage using high frequency ultrasound

NASA Astrophysics Data System (ADS)

Töyräs, J.; Rieppo, J.; Nieminen, M. T.; Helminen, H. J.; Jurvelin, J. S.

1999-11-01

Ultrasound may provide a quantitative technique for the characterization of cartilage changes typical of early osteoarthrosis. In this study, specific changes in bovine articular cartilage were induced using collagenase and chondroitinase ABC, enzymes that selectively degrade collagen fibril network and digest proteoglycans, respectively. Changes in cartilage structure and properties were quantified using high frequency ultrasound, microscopic analyses and mechanical indentation tests. The ultrasound reflection coefficient of the physiological saline-cartilage interface (R1) decreased significantly (-96.4%, p<0.01) in the collagenase digested cartilage compared to controls. Also a significantly lower ultrasound velocity (-6.2%, p<0.01) was revealed after collagenase digestion. After chondroitinase ABC digestion, a new acoustic interface at the depth of the enzyme penetration front was detected. Cartilage thickness, as determined with ultrasound, showed a high, linear correlation (R = 0.943, n = 60, average difference 0.073 mm (4.0%)) with the thickness measured by the needle-probe method. Both enzymes induced a significant decrease in the Young's modulus of cartilage (p<0.01). Our results indicate that high frequency ultrasound provides a sensitive technique for the analysis of cartilage structure and properties. Possibly ultrasound may be utilized in vivo as a quantitative probe during arthroscopy.

Quantitative Myocardial Perfusion Imaging Versus Visual Analysis in Diagnosing Myocardial Ischemia: A CE-MARC Substudy.

PubMed

Biglands, John D; Ibraheem, Montasir; Magee, Derek R; Radjenovic, Aleksandra; Plein, Sven; Greenwood, John P

2018-05-01

This study sought to compare the diagnostic accuracy of visual and quantitative analyses of myocardial perfusion cardiovascular magnetic resonance against a reference standard of quantitative coronary angiography. Visual analysis of perfusion cardiovascular magnetic resonance studies for assessing myocardial perfusion has been shown to have high diagnostic accuracy for coronary artery disease. However, only a few small studies have assessed the diagnostic accuracy of quantitative myocardial perfusion. This retrospective study included 128 patients randomly selected from the CE-MARC (Clinical Evaluation of Magnetic Resonance Imaging in Coronary Heart Disease) study population such that the distribution of risk factors and disease status was proportionate to the full population. Visual analysis results of cardiovascular magnetic resonance perfusion images, by consensus of 2 expert readers, were taken from the original study reports. Quantitative myocardial blood flow estimates were obtained using Fermi-constrained deconvolution. The reference standard for myocardial ischemia was a quantitative coronary x-ray angiogram stenosis severity of ≥70% diameter in any coronary artery of >2 mm diameter, or ≥50% in the left main stem. Diagnostic performance was calculated using receiver-operating characteristic curve analysis. The area under the curve for visual analysis was 0.88 (95% confidence interval: 0.81 to 0.95) with a sensitivity of 81.0% (95% confidence interval: 69.1% to 92.8%) and specificity of 86.0% (95% confidence interval: 78.7% to 93.4%). For quantitative stress myocardial blood flow the area under the curve was 0.89 (95% confidence interval: 0.83 to 0.96) with a sensitivity of 87.5% (95% confidence interval: 77.3% to 97.7%) and specificity of 84.5% (95% confidence interval: 76.8% to 92.3%). There was no statistically significant difference between the diagnostic performance of quantitative and visual analyses (p = 0.72). Incorporating rest myocardial blood flow values to generate a myocardial perfusion reserve did not significantly increase the quantitative analysis area under the curve (p = 0.79). Quantitative perfusion has a high diagnostic accuracy for detecting coronary artery disease but is not superior to visual analysis. The incorporation of rest perfusion imaging does not improve diagnostic accuracy in quantitative perfusion analysis. Copyright © 2018 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Clinical value of protein expression of kallikrein-related peptidase 7 (KLK7) in ovarian cancer.

PubMed

Dorn, Julia; Gkazepis, Apostolos; Kotzsch, Matthias; Kremer, Marcus; Propping, Corinna; Mayer, Katharina; Mengele, Karin; Diamandis, Eleftherios P; Kiechle, Marion; Magdolen, Viktor; Schmitt, Manfred

2014-01-01

Expression of the kallikrein-related peptidase 7 (KLK7) is dysregulated in ovarian cancer. We assessed KLK7 expression by ELISA and quantitative immunohistochemistry and analyzed its association with clinicopathological parameters and patients' outcome. KLK7 antigen concentrations were determined in tumor tissue extracts of 98 ovarian cancer patients by ELISA. For analysis of KLK7 immunoexpression in ovarian cancer tissue microarrays, a manual quantitative scoring system as well as a software tool for quantitative high-throughput automated image analysis was used. In immunohistochemical analyses, expression levels of KLK7 were not associated with patients' outcome. However, in multivariate analyses, KLK7 antigen levels in tumor tissue extracts were significantly associated with both overall and progression-free survival: ovarian cancer patients with high KLK7 levels had a significantly, 2-fold lower risk of death [hazard ratio (HR)=0.51, 95% confidence interval (CI)=0.29-0.90, p=0.019] or relapse [HR=0.47, 95% CI=0.25-0.91, p=0.024), as compared with patients who displayed low KLK7 levels. Our results indicate that - in contrast to earlier findings - high KLK7 antigen levels in tumor tissue extracts may be associated with a better prognosis of ovarian cancer patients.

The Influence of Self-Efficacy Beliefs and Metacognitive Prompting on Genetics Problem Solving Ability among High School Students in Kenya

NASA Astrophysics Data System (ADS)

Aurah, Catherine Muhonja

Within the framework of social cognitive theory, the influence of self-efficacy beliefs and metacognitive prompting on genetics problem solving ability among high school students in Kenya was examined through a mixed methods research design. A quasi-experimental study, supplemented by focus group interviews, was conducted to investigate both the outcomes and the processes of students' genetics problem-solving ability. Focus group interviews substantiated and supported findings from the quantitative instruments. The study was conducted in 17 high schools in Western Province, Kenya. A total of 2,138 high school students were purposively sampled. A sub-sample of 48 students participated in focus group interviews to understand their perspectives and experiences during the study so as to corroborate the quantitative data. Quantitative data were analyzed through descriptive statistics, zero-order correlations, 2 x 2 factorial ANOVA,, and sequential hierarchical multiple regressions. Qualitative data were transcribed, coded, and reported thematically. Results revealed metacognitive prompts had significant positive effects on student problem-solving ability independent of gender. Self-efficacy and metacognitive prompting significantly predicted genetics problem-solving ability. Gender differences were revealed, with girls outperforming boys on the genetics problem-solving test. Furthermore, self-efficacy moderated the relationship between metacognitive prompting and genetics problem-solving ability. This study established a foundation for instructional methods for biology teachers and recommendations are made for implementing metacognitive prompting in a problem-based learning environment in high schools and science teacher education programs in Kenya.

A Correlational Study of Graphic Organizers and Science Achievement of English Language Learners

NASA Astrophysics Data System (ADS)

Clarke, William Gordon

English language learners (ELLs) demonstrate lower academic performance and have lower graduation and higher dropout rates than their non-ELL peers. The primary purpose of this correlational quantitative study was to investigate the relationship between the use of graphic organizer-infused science instruction and science learning of high school ELLs. Another objective was to determine if the method of instruction, socioeconomic status (SES), gender, and English language proficiency (ELP) were predictors of academic achievement of high school ELLs. Data were gathered from a New York City (NYC) high school fall 2012-2013 archival records of 145 ninth-grade ELLs who had received biology instruction in freestanding English as a second language (ESL) classes, followed by a test of their learning of the material. Fifty-four (37.2%) of these records were of students who had learned science by the conventional textbook method, and 91 (62.8%) by using graphic organizers. Data analysis employed the Statistical Package for the Social Sciences (SPSS) software for multiple regression analysis, which found graphic organizer use to be a significant predictor of New York State Regents Living Environment (NYSRLE) test scores (p < .01). One significant regression model was returned whereby, when combined, the four predictor variables (method of instruction, SES, gender, and ELP) explained 36% of the variance of the NYSRLE score. Implications of the study findings noted graphic organizer use as advantageous for ELL science achievement. Recommendations made for practice were for (a) the adoption of graphic organizer infused-instruction, (b) establishment of a protocol for the implementation of graphic organizer-infused instruction, and (c) increased length of graphic organizer instructional time. Recommendations made for future research were (a) a replication quantitative correlational study in two or more high schools, (b) a quantitative quasi-experimental quantitative study to determine the influence of graphic organizer instructional intervention and ELL science achievement, (c) a quantitative quasi-experimental study to determine the effect of teacher-based factors on graphic organizer-infused instruction, and (c) a causal comparative study to determine the efficacy of graphic organizer use in testing modifications for high school ELL science.

High-coverage quantitative proteomics using amine-specific isotopic labeling.

PubMed

Melanson, Jeremy E; Avery, Steven L; Pinto, Devanand M

2006-08-01

Peptide dimethylation with isotopically coded formaldehydes was evaluated as a potential alternative to techniques such as the iTRAQ method for comparative proteomics. The isotopic labeling strategy and custom-designed protein quantitation software were tested using protein standards and then applied to measure proteins levels associated with Alzheimer's disease (AD). The method provided high accuracy (10% error), precision (14% RSD) and coverage (70%) when applied to the analysis of a standard solution of BSA by LC-MS/MS. The technique was then applied to measure protein abundance levels in brain tissue afflicted with AD relative to normal brain tissue. 2-D LC-MS analysis identified 548 unique proteins (p<0.05). Of these, 349 were quantified with two or more peptides that met the statistical criteria used in this study. Several classes of proteins exhibited significant changes in abundance. For example, elevated levels of antioxidant proteins and decreased levels of mitochondrial electron transport proteins were observed. The results demonstrate the utility of the labeling method for high-throughput quantitative analysis.

Distress in significant others of patients with chronic fatigue syndrome: A systematic review of the literature.

PubMed

Harris, Kamelia; Band, Rebecca J; Cooper, Hazel; Macintyre, Vanessa G; Mejia, Anilena; Wearden, Alison J

2016-11-01

The objective of this study was to systematically review existing empirical research assessing levels and correlates of distress in significant others of patients with chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME). Systematic searches in CINAHL, Web of Science and PsycINFO were conducted in August 2014. The search was repeated in January 2015 to check for newly published articles. Studies published in English with quantitative, qualitative, or mixed designs exploring distress, poor subjective health, poor mental health, reduced quality of life and well-being, and symptoms of depression and anxiety in significant others (>18 years) of children and adults with CFS/ME were included. Quality appraisal of included studies was carried out. Quantitative and qualitative studies were summarized separately. Six articles met eligibility criteria. Two quantitative studies with significant others of adult patients, and one quantitative and two mixed-methods studies with significant others of child patients showed moderate to high levels of distress. One qualitative study (adult patients) found minimal evidence of distress and that acceptance of CFS/ME was related to better adjustment. In the quantitative and mixed-methods studies, significant others who attributed some level of responsibility for symptoms to the patient, or who were female, or whose partners had poorer mental health, had higher levels of distress. The small number of studies to date, the contrary evidence from a qualitative study, and the limited data available on levels of distress in significant others of patients with CFS/ME mean that our conclusion that distress levels are elevated is provisional. We recommend that future qualitative studies focus on this particular topic. Further longitudinal studies exploring correlates of distress within the context of a predictive theoretical model would be helpful. Statement of contribution What is already known on this subject? Chronic fatigue syndrome (CFS/ME) entails considerable economic, social, and personal costs. Uncertainties exist around diagnosis and management. This may lead to particular difficulties for significant others trying to support patients. What does this study add? Few studies have examined distress and its correlates in significant others of people with CFS/ME. Significant others report elevated levels of distress on quantitative measures. © 2016 The British Psychological Society.

Evaluation of a solid-phase extraction method for benzoylecgonine urine analysis in a high-throughput forensic urine drug-testing laboratory.

PubMed

Stout, Peter R; Gehlhausen, Jay M; Horn, Carl K; Klette, Kevin L

2002-10-01

A novel extraction and derivatization procedure for the cocaine metabolite benzoylecgonine (BZE) was developed and evaluated for use in a high-volume forensic urine analysis laboratory. Extractions utilized a Speedisk 48 positive pressure extraction manifold and polymer-based cation-exchange extraction columns. Samples were derivatized by the addition of pentafluoropropionic anhydride and pentafluoropropanol. All analyses were performed in selected ion monitoring mode; ions included m/z 421, 300, 272, 429, and 303 with m/z 421 to 429 ratio used for quantitation. The average extraction efficiency was 80%. Seventy-five common over-the-counter products, including prescription drugs, drug metabolites, and other drugs of abuse, demonstrated no significant interference with respect to chromatography or quantitation. The limit of detection and limit of quantitation were calculated at 12.5 ng/mL, and the assay was linear from 12.5 to 20,000 ng/mL with an r2 of 0.99932. A series of 20 precision samples (100 ng/mL) produced an average response of 97.8 ng/mL and a percent coefficient of variation of 4.1%. A set of 79 archived human urine samples that had previously been found to contain BZE were analyzed by 3 separate laboratories. The results did not differ significantly from prior quantitation or between laboratories. The Speedisk has proven viable for a high-volume production facility reducing overall cost of analysis by decreasing analysis time and minimizing waste production while meeting strict forensic requirements.

Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders

PubMed Central

Marquet, Pierre; Depeursinge, Christian; Magistretti, Pierre J.

2014-01-01

Abstract. Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed. PMID:26157976

Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders.

PubMed

Marquet, Pierre; Depeursinge, Christian; Magistretti, Pierre J

2014-10-01

Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed.

Validation of Greyscale-Based Quantitative Ultrasound in Manual Wheelchair Users

PubMed Central

Collinger, Jennifer L.; Fullerton, Bradley; Impink, Bradley G.; Koontz, Alicia M.; Boninger, Michael L.

2010-01-01

Objective The primary aim of this study is to establish the validity of greyscale-based quantitative ultrasound (QUS) measures of the biceps and supraspinatus tendons. Design Nine QUS measures of the biceps and supraspinatus tendons were computed from ultrasound images collected from sixty-seven manual wheelchair users. Shoulder pathology was measured using questionnaires, physical examination maneuvers, and a clinical ultrasound grading scale. Results Increased age, duration of wheelchair use, and body mass correlated with a darker, more homogenous tendon appearance. Subjects with pain during physical examination tests for biceps tenderness and acromioclavicular joint tenderness exhibited significantly different supraspinatus QUS values. Even when controlling for tendon depth, QUS measures of the biceps tendon differed significantly between subjects with healthy tendons, mild tendinosis, and severe tendinosis. Clinical grading of supraspinatus tendon health was correlated with QUS measures of the supraspinatus tendon. Conclusions Quantitative ultrasound is valid method to quantify tendinopathy and may allow for early detection of tendinosis. Manual wheelchair users are at a high risk for developing shoulder tendon pathology and may benefit from quantitative ultrasound-based research that focuses on identifying interventions designed to reduce this risk. PMID:20407304

Academic Rigor and Economic Value: GED[R] and High School Students' Perceptions and Misperceptions of the GED[R] vs. the High School Diploma

ERIC Educational Resources Information Center

Horne, Lela M.; Rachal, John R.; Shelley, Kyna

2012-01-01

A mixed methods framework utilized quantitative and qualitative data to determine whether statistically significant differences existed between high school and GED[R] student perceptions of credential value. An exploratory factor analysis (n=326) extracted four factors and then a MANOVA procedure was performed with a stratified quota sample…

Improving Climate and Achievement in a Troubled Urban High School through the Talent Development Model.

ERIC Educational Resources Information Center

McPartland, James; Balfanz, Robert; Jordan, Will; Legters, Nettie

1998-01-01

A case study of a large nonselective urban high school in Baltimore (Maryland) describes the design and implementation of a comprehensive package of school reforms, the Talent Development Model with Career Academies. Qualitative and quantitative evidence is provided on significant improvements in school climate, student attendance, promotion…

Teacher Attitudes on Including Students with Behavior Intervention Plans in a High-School Inclusive Classroom

ERIC Educational Resources Information Center

Tucker, Thurman D.

2017-01-01

This research examined attitudes to determine factors influencing teachers' attitudes toward including students with behavior intervention plans in inclusive high-school classrooms. For Research Question 1 one-way ANOVAs analyzed quantitative data with no significant differences found and qualitative data discovered common patterns that BIPs are…

Mass Spectral Characterization and UPLC Quantitation of 3-Deoxyanthocyanidins in Sorghum bicolor Varietals.

PubMed

Stern, Nathan P; Rana, Jatinder; Chandra, Amitabh; Balles, John

2018-01-01

A quantitative ultra-performance LC (UPLC) method was developed and validated to successfully separate, identify, and quantitate the major polyphenolic compounds present in different varieties of sorghum (Sorghum bicolor) feedstock. The method was linear from 3.2 to 320 ppm, with an r2 of 0.99999 when using luteolinidin chloride as the external standard. Method accuracy was determined to be 99.5%, and precision of replicate preparations was less than 1% RSD. Characterization by UPLC-MS determined that the predominant polyphenolic components of the sorghum varietals were 3-deoxyanthocyanidins (3-DXAs). High-throughput screening for 3-DXA identified four unique classes within the sorghum varieties. Certain feedstock varieties have been found to have a high potential to not only be plant-based colorants, but also provide significant amounts of bioactive 3-DXAs, making them of unique interest to the dietary supplement industry.

Quantitative analysis of professionally trained versus untrained voices.

PubMed

Siupsinskiene, Nora

2003-01-01

The aim of this study was to compare healthy trained and untrained voices as well as healthy and dysphonic trained voices in adults using combined voice range profile and aerodynamic tests, to define the normal range limiting values of quantitative voice parameters and to select the most informative quantitative voice parameters for separation between healthy and dysphonic trained voices. Three groups of persons were evaluated. One hundred eighty six healthy volunteers were divided into two groups according to voice training: non-professional speakers group consisted of 106 untrained voices persons (36 males and 70 females) and professional speakers group--of 80 trained voices persons (21 males and 59 females). Clinical group consisted of 103 dysphonic professional speakers (23 males and 80 females) with various voice disorders. Eighteen quantitative voice parameters from combined voice range profile (VRP) test were analyzed: 8 of voice range profile, 8 of speaking voice, overall vocal dysfunction degree and coefficient of sound, and aerodynamic maximum phonation time. Analysis showed that healthy professional speakers demonstrated expanded vocal abilities in comparison to healthy non-professional speakers. Quantitative voice range profile parameters- pitch range, high frequency limit, area of high frequencies and coefficient of sound differed significantly between healthy professional and non-professional voices, and were more informative than speaking voice or aerodynamic parameters in showing the voice training. Logistic stepwise regression revealed that VRP area in high frequencies was sufficient to discriminate between healthy and dysphonic professional speakers for male subjects (overall discrimination accuracy--81.8%) and combination of three quantitative parameters (VRP high frequency limit, maximum voice intensity and slope of speaking curve) for female subjects (overall model discrimination accuracy--75.4%). We concluded that quantitative voice assessment with selected parameters might be useful for evaluation of voice education for healthy professional speakers as well as for detection of vocal dysfunction and evaluation of rehabilitation effect in dysphonic professionals.

HAADF-STEM atom counting in atom probe tomography specimens: Towards quantitative correlative microscopy.

PubMed

Lefebvre, W; Hernandez-Maldonado, D; Moyon, F; Cuvilly, F; Vaudolon, C; Shinde, D; Vurpillot, F

2015-12-01

The geometry of atom probe tomography tips strongly differs from standard scanning transmission electron microscopy foils. Whereas the later are rather flat and thin (<20 nm), tips display a curved surface and a significantly larger thickness. As far as a correlative approach aims at analysing the same specimen by both techniques, it is mandatory to explore the limits and advantages imposed by the particular geometry of atom probe tomography specimens. Based on simulations (electron probe propagation and image simulations), the possibility to apply quantitative high angle annular dark field scanning transmission electron microscopy to of atom probe tomography specimens has been tested. The influence of electron probe convergence and the benefice of deconvolution of electron probe point spread function electron have been established. Atom counting in atom probe tomography specimens is for the first time reported in this present work. It is demonstrated that, based on single projections of high angle annular dark field imaging, significant quantitative information can be used as additional input for refining the data obtained by correlative analysis of the specimen in APT, therefore opening new perspectives in the field of atomic scale tomography. Copyright © 2015 Elsevier B.V. All rights reserved.

Environmental and Microbial Features Affecting Denitrification and Anammox Hotspots in an Estuarine Ecosystem

NASA Astrophysics Data System (ADS)

Lisa, J.; Song, B.; Lefcheck, J. S.; Tobias, C. R.

2016-02-01

Biogeochemical hotspots are characterized as a few sites that exhibit extremely high reaction rates relative to surrounding area, and often account for a high percentage of the overall reaction rates in an ecosystem. Criteria for quantitatively identifying these sites have not been well established. Further, the underlying mechanisms of hotspots have been described in terms of environmental conditions, with little attention paid to the microbial community. The objectives of this study were to establish quantitative criteria to identify denitrification and anammox hotspots, and determine the underlying microbial and environmental factors responsible for elevated N2 production. We used 15N isotope pairing incubation experiments to measure denitrification and anammox rates in the New River Estuary, NC. Quantitative PCR assays of nitrous oxide reductase (nosZ Clades I and II) and hydrazine oxidoreductase (hzo) genes were conducted to estimate denitrifier and anammox abundance. Structural Equation Modeling (SEM) was used to elucidate complex causal relationships between environmental and biological variables. Denitrification hotspots, quantitatively defined as statistical outliers, accounted for 35.6% total denitrification while comprising only 7.3% of the sites. Anammox hotspots,10.6% of the sites, accounted for 60.9% of total anammox. SEM revealed increased sediment organics at lower salinities supported higher functional gene abundance, which in turn resulted in higher N2 production. Surprisingly, denitrification rates were significantly and positively correlated with nosZ Clade II gene abundance, after accounting for the non-significant contributions of the naturally more abundant nosZ Clade I, and other environmental covariates. This is the first time that a quantitative definition of biogeochemical hotspots was put forth and used to determine the importance of anammox and denitrification hotspots in estuarine nitrogen removal capacity. Despite the low area coverage, denitrification and anammox hotspots are major nitrogen removal components and may play a significant role in mitigating eutrophication.

Selected Reaction Monitoring to Differentiate and Relatively Quantitate Isomers of Sulfated and Unsulfated Core 1 O-Glycans from Salivary MUC7 Protein in Rheumatoid Arthritis*

PubMed Central

Flowers, Sarah A.; Ali, Liaqat; Lane, Catherine S.; Olin, Magnus; Karlsson, Niclas G.

2013-01-01

Rheumatoid arthritis is a common and debilitating systemic inflammatory condition affecting up to 1% of the world's population. This study aimed to investigate the immunological significance of O-glycans in chronic arthritis at a local and systemic level. O-Glycans released from synovial glycoproteins during acute and chronic arthritic conditions were compared and immune-reactive glycans identified. The sulfated core 1 O-glycan (Galβ1–3GalNAcol) was immune reactive, showing a different isomeric profile in the two conditions. From acute reactive arthritis, three isomers could be sequenced, but in patients with chronic rheumatoid arthritis, only a single 3-Gal sulfate-linked isomer could be identified. The systemic significance of this glycan epitope was investigated using the salivary mucin MUC7 in patients with rheumatoid arthritis and normal controls. To analyze this low abundance glycan, a selected reaction monitoring (SRM) method was developed to differentiate and relatively quantitate the core 1 O-glycan and the sulfated core 1 O-glycan Gal- and GalNAc-linked isomers. The acquisition of highly sensitive full scan linear ion trap MS/MS spectra in addition to quantitative SRM data allowed the 3- and 6-linked Gal isomers to be differentiated. The method was used to relatively quantitate the core 1 glycans from MUC7 to identify any systemic changes in this carbohydrate epitope. A statistically significant increase in sulfation was identified in salivary MUC7 from rheumatoid arthritis patients. This suggests a potential role for this epitope in chronic inflammation. This study was able to develop an SRM approach to specifically identify and relatively quantitate sulfated core 1 isomers and the unsulfated structure. The expansion of this method may afford an avenue for the high throughput investigation of O-glycans. PMID:23457413

Apparatus and method for quantitative determination of materials contained in fluids

DOEpatents

Radziemski, Leon J.; Cremers, David A.

1985-01-01

Apparatus and method for near real-time in-situ monitoring of particulates and vapors contained in fluids. Initial filtration of a known volume of the fluid sample is combined with laser-induced dielectric breakdown spectroscopy of the filter employed to obtain qualitative and quantitative information with high sensitivity. Application of the invention to monitoring of beryllium, beryllium oxide, or other beryllium-alloy dusts is demonstrated. Significant shortening of analysis time is achieved from those of the usual chemical techniques of analysis.

Apparatus and method for quantitative determination of materials contained in fluids

DOEpatents

Radziemski, L.J.; Cremers, D.A.

1982-09-07

Apparatus and method for near real-time in-situ monitoring of particulates and vapors contained in fluids are described. Initial filtration of a known volume of the fluid sample is combined with laser-induced dielectric breakdown spectroscopy of the filter employed to obtain qualitative and quantitative information with high sensitivity. Application of the invention to monitoring of beryllium, beryllium oxide, or other beryllium-alloy dusts is shown. Significant shortening of analysis time is achieved from the usual chemical techniques of analysis.

Printing 2-dimentional droplet array for single-cell reverse transcription quantitative PCR assay with a microfluidic robot.

PubMed

Zhu, Ying; Zhang, Yun-Xia; Liu, Wen-Wen; Ma, Yan; Fang, Qun; Yao, Bo

2015-04-01

This paper describes a nanoliter droplet array-based single-cell reverse transcription quantitative PCR (RT-qPCR) assay method for quantifying gene expression in individual cells. By sequentially printing nanoliter-scale droplets on microchip using a microfluidic robot, all liquid-handling operations including cell encapsulation, lysis, reverse transcription, and quantitative PCR with real-time fluorescence detection, can be automatically achieved. The inhibition effect of cell suspension buffer on RT-PCR assay was comprehensively studied to achieve high-sensitivity gene quantification. The present system was applied in the quantitative measurement of expression level of mir-122 in single Huh-7 cells. A wide distribution of mir-122 expression in single cells from 3061 copies/cell to 79998 copies/cell was observed, showing a high level of cell heterogeneity. With the advantages of full-automation in liquid-handling, simple system structure, and flexibility in achieving multi-step operations, the present method provides a novel liquid-handling mode for single cell gene expression analysis, and has significant potentials in transcriptional identification and rare cell analysis.

Printing 2-Dimentional Droplet Array for Single-Cell Reverse Transcription Quantitative PCR Assay with a Microfluidic Robot

PubMed Central

Zhu, Ying; Zhang, Yun-Xia; Liu, Wen-Wen; Ma, Yan; Fang, Qun; Yao, Bo

2015-01-01

This paper describes a nanoliter droplet array-based single-cell reverse transcription quantitative PCR (RT-qPCR) assay method for quantifying gene expression in individual cells. By sequentially printing nanoliter-scale droplets on microchip using a microfluidic robot, all liquid-handling operations including cell encapsulation, lysis, reverse transcription, and quantitative PCR with real-time fluorescence detection, can be automatically achieved. The inhibition effect of cell suspension buffer on RT-PCR assay was comprehensively studied to achieve high-sensitivity gene quantification. The present system was applied in the quantitative measurement of expression level of mir-122 in single Huh-7 cells. A wide distribution of mir-122 expression in single cells from 3061 copies/cell to 79998 copies/cell was observed, showing a high level of cell heterogeneity. With the advantages of full-automation in liquid-handling, simple system structure, and flexibility in achieving multi-step operations, the present method provides a novel liquid-handling mode for single cell gene expression analysis, and has significant potentials in transcriptional identification and rare cell analysis. PMID:25828383

High-definition optical coherence tomography intrinsic skin ageing assessment in women: a pilot study.

PubMed

Boone, M A L M; Suppa, M; Marneffe, A; Miyamoto, M; Jemec, G B E; Del Marmol, V

2015-10-01

Several non-invasive two-dimensional techniques with different lateral resolution and measurable depth range have proved to be useful in assessing and quantifying morphological changes in skin ageing. Among these, only in vivo microscopy techniques permit histometric measurements in vivo. Qualitative and quantitative assessment of chronological (intrinsic) age-related (IAR) morphological changes of epidermis, dermo-epidermal junction (DEJ), papillary dermis (PD), papillary-reticular dermis junction and reticular dermis (RD) have been performed by high-definition optical coherence tomography in real time 3-D. HD-OCT images were taken at the internal site of the right upper arm. Qualitative HD-OCT IAR descriptors were reported at skin surface, at epidermal layer, DEJ, PD and upper RD. Quantitative evaluation of age-related compaction and backscattered intensity or brightness of different skin layers was performed by using the plugin plot z-axis profile of ImageJ(®) software permitting intensity assessment of HD-OCT (DICOM) images (3-D images). Analysis was in blind from all clinical information. Sixty, fair-skinned (Fitzpatrick types I-III) healthy females were analysed retrospectively in this study. The subjects belonged to three age groups: twenty in group I aged 20-39, twenty in group II aged 40-59 and twenty in group III aged 60-79. Only intrinsic ageing in women has been studied. Significant age-related qualitative and quantitative differences could be noticed. IAR changes in dermal matrix fibers morphology/organisation and in microvasculature were observed. The brightness and compaction of the different skin layers increased significantly with intrinsic skin ageing. The depth of visibility of fibers in RD increased significantly in the older age group. In conclusion, HD-OCT allows 3-D in vivo and real time qualitative and quantitative assessment of chronological (intrinsic) age-related morphological skin changes at high resolution from skin surface to a depth of the superficial reticular dermis.

Analysis of metalaxyl racemate using high performance liquid chromatography coupled with four kinds of detectors.

PubMed

Chen, Tao; Fan, Jun; Gao, Ruiqi; Wang, Tai; Yu, Ying; Zhang, Weiguang

2016-10-07

Chiral stationary phase-high performance liquid chromatography coupled with various detectors has been one of most commonly used methods for analysis and separation of chiral compounds over the past decades. Various detectors exhibit different characteristics in qualitative and quantitative studies under different chromatographic conditions. Herein, a comparative evaluation of HPLC coupled with ultraviolet, optical rotation, refractive index, and evaporative light scattering detectors has been conducted for qualitative and quantitative analyses of metalaxyl racemate. Effects of separation conditions on the peak area ratio between two enantiomers, including sample concentration, column temperature, mobile phase composition, as well as flow rate, have been investigated in detail. In addition, the limits of detection, the limits of quantitation, quantitative range and precision for these two enantiomers by using four detectors have been also studied. As indicated, the chromatographic separation conditions have been slight effects on ultraviolet and refractive index detections and the peak area ratio between two enantiomers remains almost unchanged, but the evaporative light scattering detection has been significantly affected by the above-mentioned chromatographic conditions and the corresponding peak area ratios varied greatly. Moreover, the limits of detection, the limits of quantitation, and the quantitative ranges of two enantiomers with UV detection were remarkably lower by 1-2 magnitudes than the others. Copyright © 2016 Elsevier B.V. All rights reserved.

Using PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics.

PubMed

Lavallée-Adam, Mathieu; Yates, John R

2016-03-24

PSEA-Quant analyzes quantitative mass spectrometry-based proteomics datasets to identify enrichments of annotations contained in repositories such as the Gene Ontology and Molecular Signature databases. It allows users to identify the annotations that are significantly enriched for reproducibly quantified high abundance proteins. PSEA-Quant is available on the Web and as a command-line tool. It is compatible with all label-free and isotopic labeling-based quantitative proteomics methods. This protocol describes how to use PSEA-Quant and interpret its output. The importance of each parameter as well as troubleshooting approaches are also discussed. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

High resolution OCT quantitative analysis of the space between the IOL and the posterior capsule during the early cataract postoperative period.

PubMed

Tao, Aizhu; Lu, Ping; Li, Jin; Shao, Yilei; Wang, Jianhua; Shen, Meixiao; Zhao, Yinying; Lu, Fan

2013-10-25

We quantitatively characterized the space between the IOL and the posterior capsule (IOL-PC space) during the early postphacoemulsification period, using high resolution optical coherence tomography (OCT). We recruited 30 eyes of 30 patients who underwent phacoemulsification and randomly divided them into two groups. Acrysof Natural IQ IOLs were implanted in one group (n = 15), and Adapt-AO IOLs were implanted into the other (n = 15). A custom-built OCT instrument was used to image the IOL-PC space at 1 day, 1 week, and 1 month after surgery. Slit-lamp examination and auto refraction were performed at each visit. The IOL-PC spaces in the IQ group were 0.72 ± 0.35, 0.40 ± 0.24, and 0.23 ± 0.16 mm(2) at 1 day, 1 week, and 1 month after surgery, respectively. At each of these times, the values for the AO group were significantly smaller (P < 0.001). Compared to 1 day after surgery, significant changes in the ACDs and refractive errors occurred up to 1 month postoperatively in the IQ group; however, changes in the ACD and refractive error were significant only at 1 week in the AO group. The decreases in IOL-PC space and in ACD during the early postoperative period were associated with a myopic shift. It appeared that the different IOL designs had a role in closure of the IOL-PC space. High resolution OCT was suitable for quantitative analysis of IOL-PC space. (ClinicalTrials.gov number, NCT01605812.).

Quantitative breast MRI radiomics for cancer risk assessment and the monitoring of high-risk populations

NASA Astrophysics Data System (ADS)

Mendel, Kayla R.; Li, Hui; Giger, Maryellen L.

2016-03-01

Breast density is routinely assessed qualitatively in screening mammography. However, it is challenging to quantitatively determine a 3D density from a 2D image such as a mammogram. Furthermore, dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is used more frequently in the screening of high-risk populations. The purpose of our study is to segment parenchyma and to quantitatively determine volumetric breast density on pre-contrast axial DCE-MRI images (i.e., non-contrast) using a semi-automated quantitative approach. In this study, we retroactively examined 3D DCE-MRI images taken for breast cancer screening of a high-risk population. We analyzed 66 cases with ages between 28 and 76 (mean 48.8, standard deviation 10.8). DCE-MRIs were obtained on a Philips 3.0 T scanner. Our semi-automated DCE-MRI algorithm includes: (a) segmentation of breast tissue from non-breast tissue using fuzzy cmeans clustering (b) separation of dense and fatty tissues using Otsu's method, and (c) calculation of volumetric density as the ratio of dense voxels to total breast voxels. We examined the relationship between pre-contrast DCE-MRI density and clinical BI-RADS density obtained from radiology reports, and obtained a statistically significant correlation [Spearman ρ-value of 0.66 (p < 0.0001)]. Our method within precision medicine may be useful for monitoring high-risk populations.

Quantitative estimation of the high-intensity zone in the lumbar spine: comparison between the symptomatic and asymptomatic population.

PubMed

Liu, Chao; Cai, Hong-Xin; Zhang, Jian-Feng; Ma, Jian-Jun; Lu, Yin-Jiang; Fan, Shun-Wu

2014-03-01

The high-intensity zone (HIZ) on magnetic resonance imaging (MRI) has been studied for more than 20 years, but its diagnostic value in low back pain (LBP) is limited by the high incidence in asymptomatic subjects. Little effort has been made to improve the objective assessment of HIZ. To develop quantitative measurements for HIZ and estimate intra- and interobserver reliability and to clarify different signal intensity of HIZ in patients with or without LBP. A measurement reliability and prospective comparative study. A consecutive series of patients with LBP between June 2010 and May 2011 (group A) and a successive series of asymptomatic controls during the same period (group B). Incidence of HIZ; quantitative measures, including area of disc, area and signal intensity of HIZ, and magnetic resonance imaging index; and intraclass correlation coefficients (ICCs) for intra- and interobserver reliability. On the basis of HIZ criteria, a series of quantitative dimension and signal intensity measures was developed for assessing HIZ. Two experienced spine surgeons traced the region of interest twice within 4 weeks for assessment of the intra- and interobserver reliability. The quantitative variables were compared between groups A and B. There were 72 patients with LBP and 79 asymptomatic controls enrolling in this study. The prevalence of HIZ in group A and group B was 45.8% and 20.2%, respectively. The intraobserver agreement was excellent for the quantitative measures (ICC=0.838-0.977) as well as interobserver reliability (ICC=0.809-0.935). The mean signal of HIZ in group A was significantly brighter than in group B (57.55±14.04% vs. 45.61±7.22%, p=.000). There was no statistical difference of area of disc and HIZ between the two groups. The magnetic resonance imaging index was found to be higher in group A when compared with group B (3.94±1.71 vs. 3.06±1.50), but with a p value of .050. A series of quantitative measurements for HIZ was established and demonstrated excellent intra- and interobserver reliability. The signal intensity of HIZ was different in patients with or without LBP, and significant brighter signal was observed in symptomatic subjects. Copyright © 2014 Elsevier Inc. All rights reserved.

Racial Differences in Quantitative Measures of Area and Volumetric Breast Density

PubMed Central

McCarthy, Anne Marie; Keller, Brad M.; Pantalone, Lauren M.; Hsieh, Meng-Kang; Synnestvedt, Marie; Conant, Emily F.; Armstrong, Katrina; Kontos, Despina

2016-01-01

Abstract Background: Increased breast density is a strong risk factor for breast cancer and also decreases the sensitivity of mammographic screening. The purpose of our study was to compare breast density for black and white women using quantitative measures. Methods: Breast density was assessed among 5282 black and 4216 white women screened using digital mammography. Breast Imaging-Reporting and Data System (BI-RADS) density was obtained from radiologists’ reports. Quantitative measures for dense area, area percent density (PD), dense volume, and volume percent density were estimated using validated, automated software. Breast density was categorized as dense or nondense based on BI-RADS categories or based on values above and below the median for quantitative measures. Logistic regression was used to estimate the odds of having dense breasts by race, adjusted for age, body mass index (BMI), age at menarche, menopause status, family history of breast or ovarian cancer, parity and age at first birth, and current hormone replacement therapy (HRT) use. All statistical tests were two-sided. Results: There was a statistically significant interaction of race and BMI on breast density. After accounting for age, BMI, and breast cancer risk factors, black women had statistically significantly greater odds of high breast density across all quantitative measures (eg, PD nonobese odds ratio [OR] = 1.18, 95% confidence interval [CI] = 1.02 to 1.37, P = .03, PD obese OR = 1.26, 95% CI = 1.04 to 1.53, P = .02). There was no statistically significant difference in BI-RADS density by race. Conclusions: After accounting for age, BMI, and other risk factors, black women had higher breast density than white women across all quantitative measures previously associated with breast cancer risk. These results may have implications for risk assessment and screening. PMID:27130893

Ketamine as a novel treatment for major depressive disorder and bipolar depression: a systematic review and quantitative meta-analysis.

PubMed

Lee, Ellen E; Della Selva, Megan P; Liu, Anson; Himelhoch, Seth

2015-01-01

Given the significant disability, morbidity and mortality associated with depression, the promising recent trials of ketamine highlight a novel intervention. A meta-analysis was conducted to assess the efficacy of ketamine in comparison with placebo for the reduction of depressive symptoms in patients who meet criteria for a major depressive episode. Two electronic databases were searched in September 2013 for English-language studies that were randomized placebo-controlled trials of ketamine treatment for patients with major depressive disorder or bipolar depression and utilized a standardized rating scale. Studies including participants receiving electroconvulsive therapy and adolescent/child participants were excluded. Five studies were included in the quantitative meta-analysis. The quantitative meta-analysis showed that ketamine significantly reduced depressive symptoms. The overall effect size at day 1 was large and statistically significant with an overall standardized mean difference of 1.01 (95% confidence interval 0.69-1.34) (P<.001), with the effects sustained at 7 days postinfusion. The heterogeneity of the studies was low and not statistically significant, and the funnel plot showed no publication bias. The large and statistically significant effect of ketamine on depressive symptoms supports a promising, new and effective pharmacotherapy with rapid onset, high efficacy and good tolerability. Copyright © 2015. Published by Elsevier Inc.

Assessment of renal perfusion with contrast-enhanced ultrasound: Preliminary results in early diabetic nephropathies.

PubMed

Dong, Yi; Wang, Wen-Ping; Lin, Pan; Fan, Peili; Mao, Feng

2016-01-01

We performed a prospective study to evaluate the value of contrast-enhanced ultrasound (CEUS) in quantitative evaluation of renal cortex perfusion in patients suspected of early diabetic nephropathies (DN), with the estimated GFR (MDRD equation) as the gold standard. The study protocol was approved by the hospital review board; each patient gave written informed consent. Our study included 46 cases (21 males and 25 females, mean age 55.6 ± 4.14 years) of clinical confirmed early DN patients. After intravenous bolus injection of 1 ml sulfur hexafluoride microbubbles of ultrasound contrast agent, real time CEUS of renal cortex was performed successively using a 2-5 MHz convex probe. Time-intensity curves (TICs) and quantitative indexes were created with Qlab software. Receiver operating characteristic (ROC) curves were used to predict the diagnostic criteria of CEUS quantitative indexes, and their diagnostic efficiencies were compared with resistance index (RI) and peak systolic velocity (PSV) of renal segmental arteries by chi square test. Our control group included forty-five healthy volunteers. Difference was considered statistically significant with P <  0.05. Changes of area under curve (AUC), derived peak intensity (DPI) were statistically significant (P <  0.05). DPI less than 12 and AUC greater than 1400 had high utility in DN, with 71.7% and 67.3% sensitivity, 77.8% and 80.0% specificity. These results were significantly better than those obtained with RI and PSV which had no significant difference in early stage of DN (P > 0.05). CEUS might be helpful to improve early diagnosis of DN by quantitative analyses. AUC and DPI might be valuable quantitative indexes.

Three-phase bone scintigraphy for diagnosis of Charcot neuropathic osteoarthropathy in the diabetic foot - does quantitative data improve diagnostic value?

PubMed

Fosbøl, M; Reving, S; Petersen, E H; Rossing, P; Lajer, M; Zerahn, B

2017-01-01

To investigate whether inclusion of quantitative data on blood flow distribution compared with visual qualitative evaluation improve the reliability and diagnostic performance of 99 m Tc-hydroxymethylene diphosphate three-phase bone scintigraphy (TPBS) in patients suspected for charcot neuropathic osteoarthropathy (CNO) of the foot. A retrospective cohort study of TPBS performed on 148 patients with suspected acute CNO referred from a single specialized diabetes care centre. The quantitative blood flow distribution was calculated based on the method described by Deutsch et al. All scintigraphies were re-evaluated by independent, blinded observers twice with and without quantitative data on blood flow distribution at ankle and focus level, respectively. The diagnostic validity of TPBS was determined by subsequent review of clinical data and radiological examinations. A total of 90 patients (61%) had confirmed diagnosis of CNO. The sensitivity, specificity and accuracy of three-phase bone scintigraphy without/with quantitative data were 89%/88%, 58%/62% and 77%/78%, respectively. The intra-observer agreement improved significantly by adding quantitative data in the evaluation (Kappa value 0·79/0·94). The interobserver agreement was not significantly improved. Adding quantitative data on blood flow distribution in the interpretation of TBPS improves intra-observer variation, whereas no difference in interobserver variation was observed. The sensitivity of TPBS in the diagnosis of CNO is high, but holds limited specificity. Diagnostic performance does not improve using quantitative data in the evaluation. This may be due to the reference intervals applied in the study or the absence of a proper gold standard diagnostic procedure for comparison. © 2015 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.

PubMed

Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie

2016-06-01

The Kuruma prawn, Marsupenaeus japonicus, is one of the most promising marine invertebrates in the industry in Asia, Europe and Australia. However, the increasing global temperatures result in considerable economic losses in M. japonicus farming. In the present study, to select genetically improved animals for the sustainable development of the Kuruma prawn industry, a high-resolution genetic linkage map and quantitative trait locus (QTL) identification were performed using the RAD technology. The maternal map contained 5849 SNP markers and spanned 3127.23 cM, with an average marker interval of 0.535 cM. Instead, the paternal map contained 3927 SNP markers and spanned 3326.19 cM, with an average marker interval of 0.847 cM. The consensus map contained 9289 SNP markers and spanned 3610.90 cM, with an average marker interval of 0.388 cM and coverage of 99.06 % of the genome. The markers were grouped into 41 linkage groups in the maps. Significantly, negative correlation was detected between high-temperature tolerance (UTT) and body weight (BW). The QTL mapping revealed 129 significant QTL loci for UTT and four significant QTL loci for BW at the genome-wide significance threshold. Among these QTLs, 129 overlapped with linked SNPs, and the remaining four were located in regions between contiguous SNPs. They explained the total phenotypic variance ranging from 8.9 to 12.4 %. Because of a significantly negative correlation between growth and high-temperature tolerance, we demonstrate that this high-resolution linkage map and QTLs would be useful for further marker-assisted selection in the genetic improvement of M. japonicus.

The Correlation between Self-Determination and ACT Scores for High School Students with Disabilities

ERIC Educational Resources Information Center

Brown, Deitra Learchelle

2017-01-01

A significant gap exists between the graduation rate of students with disabilities and their nondisabled. The purpose of this quantitative correlation study was to determine the relationship self-determination had on college and career readiness using ACT scores of students with high incident disabilities. This study was guided by the following…

High School Success: An Effective Intervention for Achievement and Dropout Prevention

ERIC Educational Resources Information Center

Lowder, Christopher Michael

2012-01-01

The purpose of this mixed-design study was to use quantitative and qualitative research to explore the effects of High School Success (a course for at-risk ninth graders) and its effectiveness on student achievement, attendance, and dropout prevention. The research questions address whether there is a significant difference between at-risk ninth…

Exploration of conformational spaces of high-mannose-type oligosaccharides by an NMR-validated simulation.

PubMed

Yamaguchi, Takumi; Sakae, Yoshitake; Zhang, Ying; Yamamoto, Sayoko; Okamoto, Yuko; Kato, Koichi

2014-10-06

Exploration of the conformational spaces of flexible biomacromolecules is essential for quantitatively understanding the energetics of their molecular recognition processes. We employed stable isotope- and lanthanide-assisted NMR approaches in conjunction with replica-exchange molecular dynamics (REMD) simulations to obtain atomic descriptions of the conformational dynamics of high-mannose-type oligosaccharides, which harbor intracellular glycoprotein-fate determinants in their triantennary structures. The experimentally validated REMD simulation provided quantitative views of the dynamic conformational ensembles of the complicated, branched oligosaccharides, and indicated significant expansion of the conformational space upon removal of a terminal mannose residue during the functional glycan-processing pathway. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The increase in the expression and hypomethylation of MUC4 gene with the progression of pancreatic ductal adenocarcinoma.

PubMed

Zhu, Yi; Zhang, Jing-jing; Zhu, Rong; Zhu, Yan; Liang, Wen-biao; Gao, Wen-tao; Yu, Jun-bo; Xu, Ze-kuan; Miao, Yi

2011-12-01

The MUC4 gene could have a key role in the progression of pancreatic cancer, but the quantitative measurement of its expression in clinical tissue samples remains a challenge. The correlations between MUC4 promoter methylation status in vivo and either pancreatic cancer progression or MUC4 mRNA expression need to be demonstrated. We used the techniques of quantitative real-time PCR and DNA methylation-specific PCR combined microdissection to precisely detect MUC4 expression and promoter methylation status in 116 microdissected foci from 57 patients with pancreatic ductal adenocarcinoma. Both mRNA expression and hypomethylation frequency increased from normal to precancerous lesions to pancreatic cancer. Multivariate Cox regression analysis showed that high-level MUC4 expression (P = 0.008) and tumor-node-metastasis staging (P = 0.038) were significant independent risk factors for predicting the prognosis of 57 patients. The MUC4 mRNA expression was not significantly correlated with promoter methylation status in 30 foci of pancreatic ductal adenocarcinoma. These results suggest that high mRNA expression and hypomethylation of the MUC4 gene could be involved in carcinogenesis and in the malignant development of pancreatic ductal adenocarcinoma. The MUC4 mRNA expression may become a new prognostic marker for pancreatic cancer. Microdissection-based quantitative real-time PCR and methylation-specific PCR contribute to the quantitative detection of MUC4 expression in clinical samples and reflect the epigenetic regulatory mechanisms of MUC4 in vivo.

Comparison of the COBAS TAQMAN HIV-1 HPS with VERSANT HIV-1 RNA 3.0 assay (bDNA) for plasma RNA quantitation in different HIV-1 subtypes.

PubMed

Gomes, Perpétua; Palma, Ana Carolina; Cabanas, Joaquim; Abecasis, Ana; Carvalho, Ana Patrícia; Ziermann, Rainer; Diogo, Isabel; Gonçalves, Fátima; Lobo, Céu Sousa; Camacho, Ricardo

2006-08-01

Quantitation of HIV-1 RNA levels in plasma has an undisputed prognostic value and is extremely important for evaluating response to antiretroviral therapy. The purpose of this study was to evaluate the performance of the real-time PCR COBAS TaqMan 48 analyser, comparing it to the existing VERSANT 3.0 (bDNA) for HIV-1 RNA quantitation in plasma of individuals infected with different HIV-1 subtypes (104 blood samples). A positive linear correlation between the two tests (r2 = 0.88) was found. Quantitation by the COBAS TaqMan assay was approximately 0.32log10 higher than by bDNA. The relationship between the two assays was similar within all subtypes with a Deming regression of <1 and <0 for the Bland-Altman plots. Overall, no significant differences were found in plasma viral load quantitation in different HIV-1 subtypes between both assays; therefore these assays are suitable for viral load quantitation of highly genetically diverse HIV-1 plasma samples.

Quantitative determination and validation of octreotide acetate using 1 H-NMR spectroscopy with internal standard method.

PubMed

Yu, Chen; Zhang, Qian; Xu, Peng-Yao; Bai, Yin; Shen, Wen-Bin; Di, Bin; Su, Meng-Xiang

2018-01-01

Quantitative nuclear magnetic resonance (qNMR) is a well-established technique in quantitative analysis. We presented a validated 1 H-qNMR method for assay of octreotide acetate, a kind of cyclic octopeptide. Deuterium oxide was used to remove the undesired exchangeable peaks, which was referred to as proton exchange, in order to make the quantitative signals isolated in the crowded spectrum of the peptide and ensure precise quantitative analysis. Gemcitabine hydrochloride was chosen as the suitable internal standard. Experimental conditions, including relaxation delay time, the numbers of scans, and pulse angle, were optimized first. Then method validation was carried out in terms of selectivity, stability, linearity, precision, and robustness. The assay result was compared with that by means of high performance liquid chromatography, which is provided by Chinese Pharmacopoeia. The statistical F test, Student's t test, and nonparametric test at 95% confidence level indicate that there was no significant difference between these two methods. qNMR is a simple and accurate quantitative tool with no need for specific corresponding reference standards. It has the potential of the quantitative analysis of other peptide drugs and standardization of the corresponding reference standards. Copyright © 2017 John Wiley & Sons, Ltd.

Validation of HPLC and UV spectrophotometric methods for the determination of meropenem in pharmaceutical dosage form.

PubMed

Mendez, Andreas S L; Steppe, Martin; Schapoval, Elfrides E S

2003-12-04

A high-performance liquid chromatographic method and a UV spectrophotometric method for the quantitative determination of meropenem, a highly active carbapenem antibiotic, in powder for injection were developed in present work. The parameters linearity, precision, accuracy, specificity, robustness, limit of detection and limit of quantitation were studied according to International Conference on Harmonization guidelines. Chromatography was carried out by reversed-phase technique on an RP-18 column with a mobile phase composed of 30 mM monobasic phosphate buffer and acetonitrile (90:10; v/v), adjusted to pH 3.0 with orthophosphoric acid. The UV spectrophotometric method was performed at 298 nm. The samples were prepared in water and the stability of meropenem in aqueous solution at 4 and 25 degrees C was studied. The results were satisfactory with good stability after 24 h at 4 degrees C. Statistical analysis by Student's t-test showed no significant difference between the results obtained by the two methods. The proposed methods are highly sensitive, precise and accurate and can be used for the reliable quantitation of meropenem in pharmaceutical dosage form.

Quantitative Proteomics of Sleep-Deprived Mouse Brains Reveals Global Changes in Mitochondrial Proteins

PubMed Central

Li, Tie-Mei; Zhang, Ju-en; Lin, Rui; Chen, She; Luo, Minmin; Dong, Meng-Qiu

2016-01-01

Sleep is a ubiquitous, tightly regulated, and evolutionarily conserved behavior observed in almost all animals. Prolonged sleep deprivation can be fatal, indicating that sleep is a physiological necessity. However, little is known about its core function. To gain insight into this mystery, we used advanced quantitative proteomics technology to survey the global changes in brain protein abundance. Aiming to gain a comprehensive profile, our proteomics workflow included filter-aided sample preparation (FASP), which increased the coverage of membrane proteins; tandem mass tag (TMT) labeling, for relative quantitation; and high resolution, high mass accuracy, high throughput mass spectrometry (MS). In total, we obtained the relative abundance ratios of 9888 proteins encoded by 6070 genes. Interestingly, we observed significant enrichment for mitochondrial proteins among the differentially expressed proteins. This finding suggests that sleep deprivation strongly affects signaling pathways that govern either energy metabolism or responses to mitochondrial stress. Additionally, the differentially-expressed proteins are enriched in pathways implicated in age-dependent neurodegenerative diseases, including Parkinson’s, Huntington’s, and Alzheimer’s, hinting at possible connections between sleep loss, mitochondrial stress, and neurodegeneration. PMID:27684481

Artificial stone dust-induced functional and inflammatory abnormalities in exposed workers monitored quantitatively by biometrics.

PubMed

Ophir, Noa; Shai, Amir Bar; Alkalay, Yifat; Israeli, Shani; Korenstein, Rafi; Kramer, Mordechai R; Fireman, Elizabeth

2016-01-01

The manufacture of kitchen and bath countertops in Israel is based mainly on artificial stone that contains 93% silica as natural quartz, and ∼3500 workers are involved in cutting and processing it. Artificial stone produces high concentrations of silica dust. Exposure to crystalline silica may cause silicosis, an irreversible lung disease. Our aim was to screen exposed workers by quantitative biometric monitoring of functional and inflammatory parameters. 68 exposed artificial stone workers were compared to 48 nonexposed individuals (controls). Exposed workers filled in questionnaires, and all participants underwent pulmonary function tests and induced sputum analyses. Silica was quantitated by a Niton XL3 X-ray fluorescence spectrometer. Pulmonary function test results of exposed workers were significantly lower and induced sputa showed significantly higher neutrophilic inflammation compared to controls; both processes were slowed down by the use of protective measures in the workplace. Particle size distribution in induced sputum samples of exposed workers was similar to that of artificial stone dust, which contained aluminium, zirconium and titanium in addition to silica. In conclusion, the quantitation of biometric parameters is useful for monitoring workers exposed to artificial stone in order to avoid deterioration over time.

Effectiveness of Myocardial Contrast Echocardiography Quantitative Analysis during Adenosine Stress versus Visual Analysis before Percutaneous Therapy in Acute Coronary Pain: A Coronary Artery TIMI Grading Comparing Study

PubMed Central

Yang, Lixia; Mu, Yuming; Quaglia, Luiz Augusto; Tang, Qi; Guan, Lina; Wang, Chunmei; Shih, Ming Chi

2012-01-01

The study aim was to compare two different stress echocardiography interpretation techniques based on the correlation with thrombosis in myocardial infarction (TIMI ) flow grading from acute coronary syndrome (ACS) patients. Forty-one patients with suspected ACS were studied before diagnostic coronary angiography with myocardial contrast echocardiography (MCE) at rest and at stress. The correlation of visual interpretation of MCE and TIMI flow grade was significant. The quantitative analysis (myocardial perfusion parameters: A, β, and A × β) and TIMI flow grade were significant. MCE visual interpretation and TIMI flow grade had a high degree of agreement, on diagnosing myocardial perfusion abnormality. If one considers TIMI flow grade <3 as abnormal, MCE visual interpretation at rest had 73.1% accuracy with 58.2% sensitivity and 84.2% specificity and at stress had 80.4% accuracy with 76.6% sensitivity and 83.3% specificity. The MCE quantitative analysis has better accuracy with 100% of agreement with different level of TIMI flow grading. MCE quantitative analysis at stress has showed a direct correlation with TIMI flow grade, more significant than the visual interpretation technique. Further studies could measure the clinical relevance of this more objective approach to managing acute coronary syndrome patient before percutaneous coronary intervention (PCI). PMID:22778555

Quantitative proteomics to study carbapenem resistance in Acinetobacter baumannii

PubMed Central

Tiwari, Vishvanath; Tiwari, Monalisa

2014-01-01

Acinetobacter baumannii is an opportunistic pathogen causing pneumonia, respiratory infections and urinary tract infections. The prevalence of this lethal pathogen increases gradually in the clinical setup where it can grow on artificial surfaces, utilize ethanol as a carbon source. Moreover it resists desiccation. Carbapenems, a β-lactam, are the most commonly prescribed drugs against A. baumannii. Resistance against carbapenem has emerged in Acinetobacter baumannii which can create significant health problems and is responsible for high morbidity and mortality. With the development of quantitative proteomics, a considerable progress has been made in the study of carbapenem resistance of Acinetobacter baumannii. Recent updates showed that quantitative proteomics has now emerged as an important tool to understand the carbapenem resistance mechanism in Acinetobacter baumannii. Present review also highlights the complementary nature of different quantitative proteomic methods used to study carbapenem resistance and suggests to combine multiple proteomic methods for understanding the response to antibiotics by Acinetobacter baumannii. PMID:25309531

Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

PubMed

Gunar, O V; Sakhno, N G

2015-12-30

The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Mezyk, Stephen P.; Mincher, Bruce J.; Nilsson, Mikael

This document is the final report for the Nuclear Energy Universities Program (NEUP) grant 10-910 (DE-AC07-05ID14517) “Alpha Radiolysis of Nuclear Solvent Extraction Ligands used for An(III) and Ln(III) Separations”. The goal of this work was to obtain a quantitative understanding of the impacts of both low Linear Energy Transfer (LET, gamma-rays) and high LET (alpha particles) radiation chemistry occurring in future large-scale separations processes. This quantitative understanding of the major radiation effects on diluents and ligands is essential for optimal process implementation, and could result in significant cost savings in the future.

A prioritization of generic safety issues. Supplement 19, Revision insertion instructions

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

None

1995-11-01

The report presents the safety priority ranking for generic safety issues related to nuclear power plants. The purpose of these rankings is to assist in the timely and efficient allocation of NRC resources for the resolution of those safety issues that have a significant potential for reducing risk. The safety priority rankings are HIGH, MEDIUM, LOW, and DROP, and have been assigned on the basis of risk significance estimates, the ratio of risk to costs and other impacts estimated to result if resolution of the safety issues were implemented, and the consideration of uncertainties and other quantitative or qualitative factors.more » To the extent practical, estimates are quantitative. This document provides revisions and amendments to the report.« less

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma*

PubMed Central

Abbatiello, Susan E.; Schilling, Birgit; Mani, D. R.; Zimmerman, Lisa J.; Hall, Steven C.; MacLean, Brendan; Albertolle, Matthew; Allen, Simon; Burgess, Michael; Cusack, Michael P.; Gosh, Mousumi; Hedrick, Victoria; Held, Jason M.; Inerowicz, H. Dorota; Jackson, Angela; Keshishian, Hasmik; Kinsinger, Christopher R.; Lyssand, John; Makowski, Lee; Mesri, Mehdi; Rodriguez, Henry; Rudnick, Paul; Sadowski, Pawel; Sedransk, Nell; Shaddox, Kent; Skates, Stephen J.; Kuhn, Eric; Smith, Derek; Whiteaker, Jeffery R.; Whitwell, Corbin; Zhang, Shucha; Borchers, Christoph H.; Fisher, Susan J.; Gibson, Bradford W.; Liebler, Daniel C.; MacCoss, Michael J.; Neubert, Thomas A.; Paulovich, Amanda G.; Regnier, Fred E.; Tempst, Paul; Carr, Steven A.

2015-01-01

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data, we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to subnanogram/ml sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and interlaboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy-isotope-labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an interlaboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality control measures, enables sensitive, specific, reproducible, and quantitative measurements of proteins and peptides in complex biological matrices such as plasma. PMID:25693799

20180312 - Mechanistic Modeling of Developmental Defects through Computational Embryology (SOT)

EPA Science Inventory

Significant advances in the genome sciences, in automated high-throughput screening (HTS), and in alternative methods for testing enable rapid profiling of chemical libraries for quantitative effects on diverse cellular activities. While a surfeit of HTS data and information is n...

Use of a capillary electrophoresis instrument with laser-induced fluorescence detection for DNA quantitation. Comparison of YO-PRO-1 and PicoGreen assays.

PubMed

Guillo, Christelle; Ferrance, Jerome P; Landers, James P

2006-04-28

Highly selective and sensitive assays are required for detection and quantitation of the small masses of DNA typically encountered in clinical and forensic settings. High detection sensitivity is achieved using fluorescent labeling dyes and detection techniques such as spectrofluorometers, microplate readers and cytometers. This work describes the use of a laser-induced fluorescence (LIF) detector in conjunction with a commercial capillary electrophoresis instrument for DNA quantitation. PicoGreen and YO-PRO-1, two fluorescent DNA labeling dyes, were used to assess the potential of the system for routine DNA analysis. Linearity, reproducibility, sensitivity, limits of detection and quantitation, and sample stability were examined for the two assays. The LIF detector response was found to be linear (R2 > 0.999) and reproducible (RSD < 9%) in both cases. The PicoGreen assay displayed lower limits of detection and quantitation (20 pg and 60 pg, respectively) than the YO-PRO-1 assay (60 pg and 260 pg, respectively). Although a small variation in fluorescence was observed for the DNA/dye complexes over time, quantitation was not significantly affected and the solutions were found to be relatively stable for 80 min. The advantages of the technique include a 4- to 40-fold reduction in the volume of sample required compared to traditional assays, a 2- to 20-fold reduction in the volume of reagents consumed, fast and automated analysis, and low cost (no specific instrumentation required).

Quantitative Protein Topography Analysis and High-Resolution Structure Prediction Using Hydroxyl Radical Labeling and Tandem-Ion Mass Spectrometry (MS)*

PubMed Central

Kaur, Parminder; Kiselar, Janna; Yang, Sichun; Chance, Mark R.

2015-01-01

Hydroxyl radical footprinting based MS for protein structure assessment has the goal of understanding ligand induced conformational changes and macromolecular interactions, for example, protein tertiary and quaternary structure, but the structural resolution provided by typical peptide-level quantification is limiting. In this work, we present experimental strategies using tandem-MS fragmentation to increase the spatial resolution of the technique to the single residue level to provide a high precision tool for molecular biophysics research. Overall, in this study we demonstrated an eightfold increase in structural resolution compared with peptide level assessments. In addition, to provide a quantitative analysis of residue based solvent accessibility and protein topography as a basis for high-resolution structure prediction; we illustrate strategies of data transformation using the relative reactivity of side chains as a normalization strategy and predict side-chain surface area from the footprinting data. We tested the methods by examination of Ca+2-calmodulin showing highly significant correlations between surface area and side-chain contact predictions for individual side chains and the crystal structure. Tandem ion based hydroxyl radical footprinting-MS provides quantitative high-resolution protein topology information in solution that can fill existing gaps in structure determination for large proteins and macromolecular complexes. PMID:25687570

School Factors Related to Reading Achievement in Rural Schools with and without High Poverty

ERIC Educational Resources Information Center

Miller, Seth W.

2013-01-01

This quantitative study identified how rural schools differ on five school-level factors related to student achievement according to their performance on Grade 3 reading. Through use of a MANOVA test, it was shown that principals of high-poverty rural schools that made AYP in Grade 3 reading reported significantly higher levels of guaranteed and…

A study of the relationships between "highly qualified" status, instructional practices, and students' science achievement in three high poverty Louisiana school systems

NASA Astrophysics Data System (ADS)

Clayton, Michelle

Using a mixed methods research design, the author examined the relationships between "highly qualified" status, instructional practices, and students' science achievement for six third grade teachers in three high poverty Louisiana school systems. The study analyzed qualitative and quantitative data for three science classes taught by "highly qualified" teachers and three science classes taught by "non-highly qualified" teachers. The qualitative portion of the study was conducted through classroom observations, teacher interviews, and lesson plan reviews. The qualitative data was coded and triangulated to determine whether the instructional practices of each teacher were more "teacher-centered" or "student-centered." The qualitative data analysis indicated various patterns and consistencies in the instructional practices used by the "highly qualified" and "non-highly qualified" teachers selected for this study. The quantitative portion of the study involved analysis of the students' science achievement data for the six third grade science teachers selected for the study. Science achievement was measured by the third grade Integrated Louisiana Education Assessment Program (iLEAP) scores. A two-way ANOVA indicated that there were statistically significant differences in the mean scores of the three high poverty Louisiana school systems as well as the students taught by "highly qualified" and "non-highly qualified" teachers and the interactions between the two: F(2, 123) = 46.99, p < 0.01; F(1, 123) = 4.54, p = 0.035; F(2, 123) = 3.73, p = 0.027. A separate one-way ANOVA indicated that statistically significant differences existed between the six participating teachers in the study: F (5, 123) = 20.386, p < 0.01). Tukey's HSD post-hoc tests and homogeneous subset analyses were conducted in order to determine which teachers' scores significantly differed from each other.

Highly sensitive fluorescence quantitative detection of specific DNA sequences with molecular beacons and nucleic acid dye SYBR Green I.

PubMed

Xiang, Dongshan; Zhai, Kun; Xiang, Wenjun; Wang, Lianzhi

2014-11-01

A highly sensitive fluorescence method of quantitative detection for specific DNA sequence is developed based on molecular beacon (MB) and nucleic acid dye SYBR Green I by synchronous fluorescence analysis. It is demonstrated by an oligonucleotide sequence of wild-type HBV (target DNA) as a model system. In this strategy, the fluorophore of MB is designed to be 6-carboxyfluorescein group (FAM), and the maximum excitation wavelength and maximum emission wavelength are both very close to that of SYBR Green I. In the presence of targets DNA, the MBs hybridize with the targets DNA and form double-strand DNA (dsDNA), the fluorophore FAM is separated from the quencher BHQ-1, thus the fluorophore emit fluorescence. At the same time, SYBR Green I binds to dsDNA, the fluorescence intensity of SYBR Green I is significantly enhanced. When targets DNA are detected by synchronous fluorescence analysis, the fluorescence peaks of FAM and SYBR Green I overlap completely, so the fluorescence signal of system will be significantly enhanced. Thus, highly sensitive fluorescence quantitative detection for DNA can be realized. Under the optimum conditions, the total fluorescence intensity of FAM and SYBR Green I exhibits good linear dependence on concentration of targets DNA in the range from 2×10(-11) to 2.5×10(-9)M. The detection limit of target DNA is estimated to be 9×10(-12)M (3σ). Compared with previously reported methods of detection DNA with MB, the proposed method can significantly enhance the detection sensitivity. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparative prognostic value of epidermal growth factor quantitative protein expression compared with FISH for head and neck squamous cell carcinoma.

PubMed

Pectasides, Eirini; Rampias, Theodore; Kountourakis, Panteleimon; Sasaki, Clarence; Kowalski, Diane; Fountzilas, George; Zaramboukas, Thomas; Rimm, David; Burtness, Barbara; Psyrri, Amanda

2011-05-01

Epidermal growth factor receptor (EGFR) overexpression correlates with recurrence and with treatment resistance in head and neck squamous cell carcinoma (HNSCC). The aim of this study was to evaluate the relationship of EGFR gene copy number utilizing FISH and protein expression with automated quantitative analysis (AQUA) and to correlate those with patient outcome. A tissue microarray composed of 102 HNSCC treated with (chemo)radiation was constructed and analyzed for EGFR copy number by FISH (Vysis; Abbott Laboratories) and EGFR protein expression using AQUA analysis of EGFR staining scored on a scale of 0 to 255. We evaluated associations of EGFR FISH status and AQUA score with clinicopathologic parameters and survival prognosis. Eleven (17.2%) of 64 tumors with FISH results showed EGFR high polysomy and/or gene amplification (FISH positive). Protein levels assessed by AQUA in FISH-positive cases were significantly higher (P = 0.04) than in FISH-negative cases. Using the continuous AQUA scores for EGFR expression, AQUA and FISH showed significant agreement (Pearson's ρ = 0.353, P = 0.04). Patients with high tumor EGFR protein expression had inferior 5-year overall survival (27.7%) compared with those with low tumor EGFR expression (54%; P = 0.029). There was no significant association between EGFR FISH status and overall survival (P = 0.201). In the multivariate model, high tumor EGFR protein expression status remained an independent prognostic factor for overall survival (P = 0.047). EGFR protein content correlates with gene copy number if protein content is quantitated and automatically analyzed, as with AQUA. EGFR protein levels assessed by AQUA strongly predict for patient outcome in HNSCC, whereas EGFR FISH status does not provide prognostic information. ©2011 AACR.

Effects of dynamic diffraction conditions on magnetic parameter determination in a double perovskite Sr2FeMoO6 using electron energy-loss magnetic chiral dichroism.

PubMed

Wang, Z C; Zhong, X Y; Jin, L; Chen, X F; Moritomo, Y; Mayer, J

2017-05-01

Electron energy-loss magnetic chiral dichroism (EMCD) spectroscopy, which is similar to the well-established X-ray magnetic circular dichroism spectroscopy (XMCD), can determine the quantitative magnetic parameters of materials with high spatial resolution. One of the major obstacles in quantitative analysis using the EMCD technique is the relatively poor signal-to-noise ratio (SNR), compared to XMCD. Here, in the example of a double perovskite Sr 2 FeMoO 6 , we predicted the optimal dynamical diffraction conditions such as sample thickness, crystallographic orientation and detection aperture position by theoretical simulations. By using the optimized conditions, we showed that the SNR of experimental EMCD spectra can be significantly improved and the error of quantitative magnetic parameter determined by EMCD technique can be remarkably lowered. Our results demonstrate that, with enhanced SNR, the EMCD technique can be a unique tool to understand the structure-property relationship of magnetic materials particularly in the high-density magnetic recording and spintronic devices by quantitatively determining magnetic structure and properties at the nanometer scale. Copyright © 2017 Elsevier B.V. All rights reserved.

A method for evaluating the murine pulmonary vasculature using micro-computed tomography.

PubMed

Phillips, Michael R; Moore, Scott M; Shah, Mansi; Lee, Clara; Lee, Yueh Z; Faber, James E; McLean, Sean E

2017-01-01

Significant mortality and morbidity are associated with alterations in the pulmonary vasculature. While techniques have been described for quantitative morphometry of whole-lung arterial trees in larger animals, no methods have been described in mice. We report a method for the quantitative assessment of murine pulmonary arterial vasculature using high-resolution computed tomography scanning. Mice were harvested at 2 weeks, 4 weeks, and 3 months of age. The pulmonary artery vascular tree was pressure perfused to maximal dilation with a radio-opaque casting material with viscosity and pressure set to prevent capillary transit and venous filling. The lungs were fixed and scanned on a specimen computed tomography scanner at 8-μm resolution, and the vessels were segmented. Vessels were grouped into categories based on lumen diameter and branch generation. Robust high-resolution segmentation was achieved, permitting detailed quantitation of pulmonary vascular morphometrics. As expected, postnatal lung development was associated with progressive increase in small-vessel number and arterial branching complexity. These methods for quantitative analysis of the pulmonary vasculature in postnatal and adult mice provide a useful tool for the evaluation of mouse models of disease that affect the pulmonary vasculature. Copyright © 2016 Elsevier Inc. All rights reserved.

Comprehensive quantitative analysis of Chinese patent drug YinHuang drop pill by ultra high-performance liquid chromatography quadrupole time of flight mass spectrometry.

PubMed

Wong, Tin-Long; An, Ya-Qi; Yan, Bing-Chao; Yue, Rui-Qi; Zhang, Tian-Bo; Ho, Hing-Man; Ren, Tian-Jing; Fung, Hau-Yee; Ma, Dik-Lung; Leung, Chung-Hang; Liu, Zhong-Liang; Pu, Jian-Xin; Han, Quan-Bin; Sun, Han-Dong

2016-06-05

YinHuang drop pill (YHDP) is a new preparation, derived from the traditional YinHuang (YH) decoction. Since drop pills are one of the newly developed forms of Chinese patent drugs, not much research has been done regarding the quality and efficacy. This study aims to establish a comprehensive quantitative analysis of the chemical profile of YHDP. ultra high-performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-Q-TOF-MS/MS) was used to identify 34 non-sugar small molecules including 15 flavonoids, 9 phenolic acids, 5 saponins, 1 iridoid, and 4 iridoid glycosides in YHDP samples, and 26 of them were quantitatively determined. Sugar composition of YHDP in terms of fructose, glucose and sucrose was examined via a high performance liquid chromatography-evaporative light scattering detector on an amide column (HPLC-NH2P-ELSD). Macromolecules were examined by high performance gel permeation chromatography coupled with ELSD (HPGPC-ELSD). The content of the drop pill's skeleton component PEG-4000 was also quantified via ultra-high performance liquid chromatography coupled with charged aerosol detector (UHPLC-CAD). The results showed that up to 73% (w/w) of YHDP could be quantitatively determined. Small molecules accounted for approximately 5%, PEG-4000 represented 68%, while no sugars or macromolecules were found. Furthermore, YHDP showed no significant differences in terms of daily dosage, compared to YinHuang granules and YinHuang oral liquid; however, it has a higher small molecules content compared to YinHuang lozenge. Copyright © 2016 Elsevier B.V. All rights reserved.

Investigation on Quantitative Structure Activity Relationships of a Series of Inducible Nitric Oxide.

PubMed

Sharma, Mukesh C; Sharma, S

2016-12-01

A series of 2-dihydro-4-quinazolin with potent highly selective inhibitors of inducible nitric oxide synthase activities was subjected to quantitative structure activity relationships (QSAR) analysis. Statistically significant equations with high correlation coefficient (r 2  = 0.8219) were developed. The k-nearest neighbor model has showed good cross-validated correlation coefficient and external validation values of 0.7866 and 0.7133, respectively. The selected electrostatic field descriptors the presence of blue ball around R1 and R4 in the quinazolinamine moiety showed electronegative groups favorable for nitric oxide synthase activity. The QSAR models may lead to the structural requirements of inducible nitric oxide compounds and help in the design of new compounds.

Development and validation of a generic high-performance liquid chromatography for the simultaneous separation and determination of six cough ingredients: Robustness study on core-shell particles.

PubMed

Yehia, Ali Mohamed; Essam, Hebatallah Mohamed

2016-09-01

A generally applicable high-performance liquid chromatographic method for the qualitative and quantitative determination of pharmaceutical preparations containing phenylephrine hydrochloride, paracetamol, ephedrine hydrochloride, guaifenesin, doxylamine succinate, and dextromethorphan hydrobromide is developed. Optimization of chromatographic conditions was performed for the gradient elution using different buffer pH values, flow rates and two C18 stationary phases. The method was developed using a Kinetex® C18 column as a core-shell stationary phase with a gradient profile using buffer pH 5.0 and acetonitrile at 2.0 mL/min flow rate. Detection was carried out at 220 nm and linear calibrations were obtained for all components within the studied ranges. The method was fully validated in agreement with ICH guidelines. The proposed method is specific, accurate and precise (RSD% < 3%). Limits of detection are lower than 2.0 μg/mL. Qualitative and quantitative responses were evaluated using experimental design to assist the method robustness. The method was proved to be highly robust against 10% change in buffer pH and flow rate (RSD% < 10%), however, the flow rate may significantly influence the quantitative responses of phenylephrine, paracetamol, and doxylamine (RSD% > 10%). Satisfactory results were obtained for commercial combinations analyses. Statistical comparison between the proposed chromatographic and official methods revealed no significant difference. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Estrogen receptor quantitation and staging as complementary prognostic indicators in breast cancer: a study of 583 patients.

PubMed

Godolphin, W; Elwood, J M; Spinelli, J J

1981-12-01

Estrogen receptor (ER) quantity was measured at the time of primary diagnosis on 583 patients with breast cancer seen at the major treatment centre in British Columbia between 1975 and 1979. Survival rates (overall, recurrence-free and post-recurrence) were assessed relative to ER concentration, staging, menopausal status, age, differentiation, and therapy. A linear trend in increased survival was demonstrable through variations in ER concentration from less than 1 to greater than 260 fmoles/mg cytosol protein. This trend was highly significant and remained after adjustment for stage, menopausal status, and age, and was seen for all groups of patients except those with metastatic disease. The association of high ER concentration with increased recurrence-free survival was not due to differing responses to adjuvant therapy, but the trend in post-recurrence survival was only significant in patients who had received hormonal therapy. Survival was as strongly associated with receptor concentration as with staging, and these two factors were almost completely independent. A proportional hazards model was fitted to produce predictions of survival, and showed that TNM stage III patients with high ER concentrations have a better survival than stage I or II patients with lower ER concentrations. This suggests that quantitative assessment of ER status is essential to definition of risk in breast cancer patients and that stratification in clinical trials and consideration for adjuvant therapy ought to be guided, in part, by a standardized ER-quantitative determination performed on the primary tumor.

A quantitative analysis of factors influencing the professional longevity of high school science teachers in Florida

NASA Astrophysics Data System (ADS)

Ridgley, James Alexander, Jr.

This dissertation is an exploratory quantitative analysis of various independent variables to determine their effect on the professional longevity (years of service) of high school science teachers in the state of Florida for the academic years 2011-2012 to 2013-2014. Data are collected from the Florida Department of Education, National Center for Education Statistics, and the National Assessment of Educational Progress databases. The following research hypotheses are examined: H1 - There are statistically significant differences in Level 1 (teacher variables) that influence the professional longevity of a high school science teacher in Florida. H2 - There are statistically significant differences in Level 2 (school variables) that influence the professional longevity of a high school science teacher in Florida. H3 - There are statistically significant differences in Level 3 (district variables) that influence the professional longevity of a high school science teacher in Florida. H4 - When tested in a hierarchical multiple regression, there are statistically significant differences in Level 1, Level 2, or Level 3 that influence the professional longevity of a high school science teacher in Florida. The professional longevity of a Floridian high school science teacher is the dependent variable. The independent variables are: (Level 1) a teacher's sex, age, ethnicity, earned degree, salary, number of schools taught in, migration count, and various years of service in different areas of education; (Level 2) a school's geographic location, residential population density, average class size, charter status, and SES; and (Level 3) a school district's average SES and average spending per pupil. Statistical analyses of exploratory MLRs and a HMR are used to support the research hypotheses. The final results of the HMR analysis show a teacher's age, salary, earned degree (unknown, associate, and doctorate), and ethnicity (Hispanic and Native Hawaiian/Pacific Islander); a school's charter status; and a school district's average SES are all significant predictors of a Florida high school science teacher's professional longevity. Although statistically significant in the initial exploratory MLR analyses, a teacher's ethnicity (Asian and Black), a school's geographic location (city and rural), and a school's SES are not statistically significant in the final HMR model.

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: II. Muscle weight and carcass composition.

PubMed

Nassar, M K; Goraga, Z S; Brockmann, G A

2012-12-01

In order to identify genetic factors influencing muscle weight and carcass composition in chicken, a linkage analysis was performed with 278 F(2) males of reciprocal crosses between the extremely different inbred lines New Hampshire (NHI) and White Leghorn (WL77). The NHI line had been selected for high meat yield and the WL77 for low egg weight before inbreeding. Highly significant quantitative trait loci (QTL) controlling body weight and the weights of carcass, breast muscle, drumsticks-thighs and wings were identified on GGA4 between 151.5 and 160.5 cM and on GGA27 between 4 and 52 cM. These genomic regions explained 13.7-40.2% and 5.3-13.8% of the phenotypic F(2) variances of the corresponding traits respectively. Additional genome-wide highly significant QTL for the weight of drumsticks-thighs were mapped on GGA1, 5 and 7. Moreover, significant QTL controlling body weight were found on GGA2 and 11. The data obtained in this study can be used for increasing the mapping resolution and subsequent gene targeting on GGA4 and 27 by combining data with other crosses where the same QTL were found. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Basal paravian functional anatomy illuminated by high-detail body outline

PubMed Central

Wang, Xiaoli; Pittman, Michael; Zheng, Xiaoting; Kaye, Thomas G.; Falk, Amanda R.; Hartman, Scott A.; Xu, Xing

2017-01-01

Body shape is a fundamental expression of organismal biology, but its quantitative reconstruction in fossil vertebrates is rare. Due to the absence of fossilized soft tissue evidence, the functional consequences of basal paravian body shape and its implications for the origins of avians and flight are not yet fully understood. Here we reconstruct the quantitative body outline of a fossil paravian Anchiornis based on high-definition images of soft tissues revealed by laser-stimulated fluorescence. This body outline confirms patagia-bearing arms, drumstick-shaped legs and a slender tail, features that were probably widespread among paravians. Finely preserved details also reveal similarities in propatagial and footpad form between basal paravians and modern birds, extending their record to the Late Jurassic. The body outline and soft tissue details suggest significant functional decoupling between the legs and tail in at least some basal paravians. The number of seemingly modern propatagial traits hint that feathering was a significant factor in how basal paravians utilized arm, leg and tail function for aerodynamic benefit. PMID:28248287

New Technology-Large-Area Three- Dimensional Surface Profiling Using Only Focused Air-Coupled Ultrasound-Given 1999 R&D 100 Award

NASA Technical Reports Server (NTRS)

Roth, Don J.; Kautz, Harold E.; Abel, Phillip B.; Whalen, Mike F.; Hendricks, J. Lynne; Bodis, James R.

2000-01-01

Surface topography, which significantly affects the performance of many industrial components, is normally measured with diamond-tip profilometry over small areas or with optical scattering methods over larger areas. To develop air-coupled surface profilometry, the NASA Glenn Research Center at Lewis Field initiated a Space Act Agreement with Sonix, Inc., through two Glenn programs, the Advanced High Temperature Engine Materials Program (HITEMP) and COMMTECH. The work resulted in quantitative surface topography profiles obtained using only high-frequency, focused ultrasonic pulses in air. The method is nondestructive, noninvasive, and noncontact, and it does not require light-reflective surfaces. Air surface profiling may be desirable when diamond-tip or laserbased methods are impractical, such as over large areas, when a significant depth range is required, or for curved surfaces. When the configuration is optimized, the method is reasonably rapid and all the quantitative analysis facilities are online, including two- and three-dimensional visualization, extreme value filtering (for faulty data), and leveling.

Quantitative analysis of glycerophospholipids by LC-MS: acquisition, data handling, and interpretation

PubMed Central

Myers, David S.; Ivanova, Pavlina T.; Milne, Stephen B.; Brown, H. Alex

2012-01-01

As technology expands what it is possible to accurately measure, so too the challenges faced by modern mass spectrometry applications expand. A high level of accuracy in lipid quantitation across thousands of chemical species simultaneously is demanded. While relative changes in lipid amounts with varying conditions may provide initial insights or point to novel targets, there are many questions that require determination of lipid analyte absolute quantitation. Glycerophospholipids present a significant challenge in this regard, given the headgroup diversity, large number of possible acyl chain combinations, and vast range of ionization efficiency of species. Lipidomic output is being used more often not just for profiling of the masses of species, but also for highly-targeted flux-based measurements which put additional burdens on the quantitation pipeline. These first two challenges bring into sharp focus the need for a robust lipidomics workflow including deisotoping, differentiation from background noise, use of multiple internal standards per lipid class, and the use of a scriptable environment in order to create maximum user flexibility and maintain metadata on the parameters of the data analysis as it occurs. As lipidomics technology develops and delivers more output on a larger number of analytes, so must the sophistication of statistical post-processing also continue to advance. High-dimensional data analysis methods involving clustering, lipid pathway analysis, and false discovery rate limitation are becoming standard practices in a maturing field. PMID:21683157

Quantitative characterization of nonstructural carbohydrates of mezcal Agave (Agave salmiana Otto ex Salm-Dick).

PubMed

Michel-Cuello, Christian; Juárez-Flores, Bertha Irene; Aguirre-Rivera, Juan Rogelio; Pinos-Rodríguez, Juan Manuel

2008-07-23

Fructans are the reserve carbohydrates in Agave spp. plants. In mezcal factories, fructans undergoes thermal hydrolysis to release fructose and glucose, which are the basis to produce this spirit. Carbohydrate content determines the yield of the final product, which depends on plant organ, ripeness stage, and thermal hydrolysis. Thus, a qualitative and quantitative characterization of nonstructural carbohydrates was conducted in raw and hydrolyzed juices extracted from Agave salmiana stems and leaves under three ripeness stages. By high-performance liquid chromatography (HPLC), fructose, glucose, sucrose, xylose, and maltose were identified in agave juice. Only the plant fraction with hydrolysis interaction was found to be significant in the glucose concentration plant. Interactions of the fraction with hydrolysis and ripeness with hydrolysis were statistically significant in fructose concentration. Fructose concentration rose considerably with hydrolysis, but only in juice extracted from ripe agave stems (early mature and castrated). This increase was statistically significant only with acid hydrolysis.

Empowerment in nurse leader groups in middle management: a quantitative comparative investigation.

PubMed

Spencer, Caroline; McLaren, Susan

2017-01-01

The aim was to investigate structural empowerment in nurse leaders in middle management positions. Objectives were to determine levels of empowerment of nurse leaders and to compare levels of empowerment between nurse leader groups. Access to formal and informal power, opportunity, resources, information and support are determinants of structural empowerment. Empowerment of nurse leaders in middle management positions is vital given their roles in enabling nursing teams to deliver high-quality care, benefitting both patient and workforce outcomes. Quantitative component of a mixed methods study using survey principles. The Conditions of Work Effectiveness Questionnaire II was distributed to the total population (n = 517) of nurse leaders in an NHS Foundation Trust in England. Nurse leader groups comprised unit leaders (sisters, matrons) and senior staff nurses. Quantitative data entered on spss v 17/18, were analysed using descriptive and inferential statistics. Overall, the unit response rate was 44·1% (n = 228). Levels of total and global empowerment were moderate and moderate to high respectively. Groups did not differ significantly on these parameters or on five elements of total empowerment, but significantly higher scores were found for unit leaders' access to information. Significantly higher scores were found for senior staff nurses on selected aspects of informal power and access to resources, but scores were significantly lower than unit leaders for components of support. A moderately empowered population of nurse leaders differed in relation to access to information, aspects of support, resources and informal power, reflecting differences in roles, spheres of responsibility, hierarchical position and the constraints on empowerment imposed on unit leaders by financial and resource pressures. Empowerment of nurse leaders in middle management is vital in enabling nursing teams to deliver high-quality care. Roles, spheres of responsibility, hierarchical position and constraints imposed by financial and resource pressures influence nurse leader empowerment. Administrative support is needed to sustain practice engagement. © 2016 John Wiley & Sons Ltd.

Quantitative and Qualitative Differences in Morphological Traits Revealed between Diploid Fragaria Species

PubMed Central

SARGENT, DANIEL J.; GEIBEL, M.; HAWKINS, J. A.; WILKINSON, M. J.; BATTEY, N. H.; SIMPSON, D. W.

2004-01-01

• Background and Aims The aims of this investigation were to highlight the qualitative and quantitative diversity apparent between nine diploid Fragaria species and produce interspecific populations segregating for a large number of morphological characters suitable for quantitative trait loci analysis. • Methods A qualitative comparison of eight described diploid Fragaria species was performed and measurements were taken of 23 morphological traits from 19 accessions including eight described species and one previously undescribed species. A principal components analysis was performed on 14 mathematically unrelated traits from these accessions, which partitioned the species accessions into distinct morphological groups. Interspecific crosses were performed with accessions of species that displayed significant quantitative divergence and, from these, populations that should segregate for a range of quantitative traits were raised. • Key Results Significant differences between species were observed for all 23 morphological traits quantified and three distinct groups of species accessions were observed after the principal components analysis. Interspecific crosses were performed between these groups, and F2 and backcross populations were raised that should segregate for a range of morphological characters. In addition, the study highlighted a number of distinctive morphological characters in many of the species studied. • Conclusions Diploid Fragaria species are morphologically diverse, yet remain highly interfertile, making the group an ideal model for the study of the genetic basis of phenotypic differences between species through map-based investigation using quantitative trait loci. The segregating interspecific populations raised will be ideal for such investigations and could also provide insights into the nature and extent of genome evolution within this group. PMID:15469944

The efficacy of semi-quantitative urine protein-to-creatinine (P/C) ratio for the detection of significant proteinuria in urine specimens in health screening settings.

PubMed

Chang, Chih-Chun; Su, Ming-Jang; Ho, Jung-Li; Tsai, Yu-Hui; Tsai, Wei-Ting; Lee, Shu-Jene; Yen, Tzung-Hai; Chu, Fang-Yeh

2016-01-01

Urine protein detection could be underestimated using the conventional dipstick method because of variations in urine aliquots. This study aimed to assess the efficacy of the semi-quantitative urine protein-to-creatinine (P/C) ratio compared with other laboratory methods. Random urine samples were requested from patients undergoing chronic kidney disease screening. Significant proteinuria was determined by the quantitative P/C ratio of at least 150 mg protein/g creatinine. The semi-quantitative P/C ratio, dipstick protein and quantitative protein concentrations were compared and analyzed. In the 2932 urine aliquots, 156 (5.3 %) urine samples were considered as diluted and 60 (39.2 %) were found as significant proteinuria. The semi-quantitative P/C ratio testing had the best sensitivity (70.0 %) and specificity (95.9 %) as well as the lowest underestimation rate (0.37 %) when compared to other laboratory methods in the study. In the semi-quantitative P/C ratio test, 19 (12.2 %) had positive, 52 (33.3 %) had diluted, and 85 (54.5 %) had negative results. Of those with positive results, 7 (36.8 %) were positive detected by traditional dipstick urine protein test, and 9 (47.4 %) were positive detected by quantitative urine protein test. Additionally, of those with diluted results, 25 (48.1 %) had significant proteinuria, and all were assigned as no significant proteinuria by both tests. The semi-quantitative urine P/C ratio is clinically applicable based on its better sensitivity and screening ability for significant proteinuria than other laboratory methods, particularly in diluted urine samples. To establish an effective strategy for CKD prevention, urine protein screening with semi-quantitative P/C ratio could be considered.

The Effects of Servant Leader and Integrity of Principal Performance in Catholic Senior High Schools in North Sulawesi, Indonesia

ERIC Educational Resources Information Center

Malingkas, Melky; Senduk, Johanis Frans; Simandjuntak, Suddin; Binilang, Benny Blemy

2018-01-01

The aim of this research was to examine the effects of servant leader and integrity on principal performance in Catholic senior high schools in North Sulawesi, Indonesia. This quantitative research used questionnaire-gathered data from 75 teachers at 11 schools. The results of research show that the servant leader approach has significant positive…

Boys and Motivation

ERIC Educational Resources Information Center

Martin, Andrew J.

2003-01-01

This paper explores key gender differences in motivation from a quantitative perspective and presents findings from a qualitative study into boys' perceptions of motivating teachers and motivating pedagogy. Data collected from 3773 high school students suggest that girls score significantly higher than boys in their belief in the value of school,…

Appraising Teacher Performance: A Quantitative Approach.

ERIC Educational Resources Information Center

Wingate, James G.; Bowers, Fred

Following a brief research review regarding the relationship between teacher behavior and student outcomes, a model is proposed for identifying those teaching behaviors that are significantly related to high-quality student performance. The model's stages include: (1) delineation of questions; (2) establishment of a framework; (3) selection of an…

Proteomic Profiling of Recombinant Escherichia coli in High-Cell- Density Fermentations for Improved Production of an Antibody Fragment Biopharmaceutical

PubMed Central

Aldor, Ilana S.; Krawitz, Denise C.; Forrest, William; Chen, Christina; Nishihara, Julie C.; Joly, John C.; Champion, Kathleen M.

2005-01-01

By using two-dimensional polyacrylamide gel electrophoresis, a proteomic analysis over time was conducted with high-cell-density, industrial, phosphate-limited Escherichia coli fermentations at the 10-liter scale. During production, a recombinant, humanized antibody fragment was secreted and assembled in a soluble form in the periplasm. E. coli protein changes associated with culture conditions were distinguished from protein changes associated with heterologous protein expression. Protein spots were monitored quantitatively and qualitatively. Differentially expressed proteins were quantitatively assessed by using a t-test method with a 1% false discovery rate as a significance criterion. As determined by this criterion, 81 protein spots changed significantly between 14 and 72 h (final time) of the control fermentations (vector only). Qualitative (on-off) comparisons indicated that 20 more protein spots were present only at 14 or 72 h in the control fermentations. These changes reflected physiological responses to the culture conditions. In control and production fermentations at 72 h, 25 protein spots were significantly differentially expressed. In addition, 19 protein spots were present only in control or production fermentations at this time. The quantitative and qualitative changes were attributable to overexpression of recombinant protein. The physiological changes observed during the fermentations included the up-regulation of phosphate starvation proteins and the down-regulation of ribosomal proteins and nucleotide biosynthesis proteins. Synthesis of the stress protein phage shock protein A (PspA) was strongly correlated with synthesis of a recombinant product. This suggested that manipulation of PspA levels might improve the soluble recombinant protein yield in the periplasm for this bioprocess. Indeed, controlled coexpression of PspA during production led to a moderate, but statistically significant, improvement in the yield. PMID:15811994

QUANTITATIVE TESTS OF ELMS AS INTERMEDIATE N PEELING-BALOONING MODES

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

LAO,LL; SNYDER,PB; LEONARD,AW

2003-03-01

A271 QUANTITATIVE TESTS OF ELMS AS INTERMEDIATE N PEELING-BALOONING MODES. Several testable features of the working model of edge localized modes (ELMs) as intermediate toroidal mode number peeling-ballooning modes are evaluated quantitatively using DIII-D and JT-60U experimental data and the ELITE MHD stability code. These include the hypothesis that ELM sizes are related to the radial widths of the unstable MHD modes, the unstable modes have a strong ballooning character localized in the outboard bad curvature region, and ELM size generally becomes smaller at high edge collisionality. ELMs are triggered when the growth rates of the unstable MHD modes becomemore » significantly large. These testable features are consistent with many ELM observations in DIII-D and JT-60U discharges.« less

Trabecular bone class mapping across resolutions: translating methods from HR-pQCT to clinical CT

NASA Astrophysics Data System (ADS)

Valentinitsch, Alexander; Fischer, Lukas; Patsch, Janina M.; Bauer, Jan; Kainberger, Franz; Langs, Georg; DiFranco, Matthew

2015-03-01

Quantitative assessment of 3D bone microarchitecture in high-resolution peripheral quantitative computed tomography (HR-pQCT) has shown promise in fracture risk assessment and biomechanics, but is limited to the distal radius and tibia. Trabecular microarchitecture classes (TMACs), based on voxel-wise clustering texture and structure tensor features in HRpQCT, is extended in this paper to quantify trabecular bone classes in clinical multi-detector CT (MDCT) images. Our comparison of TMACs in 12 cadaver radii imaged using both HRpQCT and MDCT yields a mean Dice score of up to 0.717+/-0.40 and visually concordant bone quality maps. Further work to develop clinically viable bone quantitative imaging using HR-pQCT validation could have a significant impact on overall bone health assessment.

Infection Control in Retreatment Cases: In Vivo Antibacterial Effects of 2 Instrumentation Systems.

PubMed

Rodrigues, Renata C V; Antunes, Henrique S; Neves, Mônica A S; Siqueira, José F; Rôças, Isabela N

2015-10-01

This in vivo study compared the antibacterial effects of 2 instrumentation systems in root canal-treated teeth with apical periodontitis. Forty-eight teeth with a single root and a single canal showing post-treatment apical periodontitis were selected for this study. For retreatment, teeth were randomly divided into 2 groups according to the instrumentation system used: Self-Adjusting File (SAF; ReDent-Nova, Ra'anana, Israel) and Twisted File Adaptive (TFA; SybronEndo, Orange, CA). In both groups, 2.5% sodium hypochlorite was the irrigant. Bacteriological samples were taken before (S1) and after chemomechanical preparation (S2). In the TFA group, passive ultrasonic irrigation (PUI) was performed after instrumentation, and samples were also taken after this supplementary step (S2b). DNA was extracted from the clinical samples and subjected to quantitative real-time polymerase chain reaction to evaluate the levels of total bacteria, streptococci, and Enterococcus faecalis. Statistical analyses from quantitative real-time polymerase chain reaction data were performed within groups using the Wilcoxon matched pairs test and between groups using the Mann-Whitney U test and the Fisher exact test with the significance level set at P < .05. Bacteria were detected in S1 samples from 43 teeth, which were then included in the antibacterial experiment. Both SAF and TFA instrumentation protocols showed a highly significant intracanal bacterial reduction (P < .001). Intergroup quantitative comparisons disclosed no significant differences between TFA with or without PUI and SAF (P > .05). PUI did not result in significant improvement in disinfection (P > .05). Both instrumentation systems/treatment protocols were highly effective in significantly reducing the intracanal bacterial counts. No significant difference was observed between the 2 systems in disinfecting the canals of teeth with post-treatment apical periodontitis. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

How is good and poor sleep in older adults and college students related to daytime sleepiness, fatigue, and ability to concentrate?

PubMed

Alapin, I; Fichten, C S; Libman, E; Creti, L; Bailes, S; Wright, J

2000-11-01

We compared good sleepers with minimally and highly distressed poor sleepers on three measures of daytime functioning: self-reported fatigue, sleepiness, and cognitive inefficiency. In two samples (194 older adults, 136 college students), we tested the hypotheses that (1) poor sleepers experience more problems with daytime functioning than good sleepers, (2) highly distressed poor sleepers report greater impairment in functioning during the day than either good sleepers or minimally distressed poor sleepers, (3) daytime symptoms are more closely related to psychological adjustment and to psychologically laden sleep variables than to quantitative sleep parameters, and (4) daytime symptoms are more closely related to longer nocturnal wake times than to shorter sleep times. Results in both samples indicated that poor sleepers reported more daytime difficulties than good sleepers. While low- and high-distress poor sleepers did not differ on sleep parameters, highly distressed poor sleepers reported consistently more difficulty in functioning during the day and experienced greater tension and depression than minimally distressed poor sleepers. Severity of all three daytime problems was generally significantly and positively related to poor psychological adjustment, psychologically laden sleep variables, and, with the exception of sleepiness, to quantitative sleep parameters. Results are used to discuss discrepancies between experiential and quantitative measures of daytime functioning.

Reciprocal Hosts' Responses to Powdery Mildew Isolates Originating from Domesticated Wheats and Their Wild Progenitor.

PubMed

Ben-David, Roi; Dinoor, Amos; Peleg, Zvi; Fahima, Tzion

2018-01-01

The biotroph wheat powdery mildew, Blumeria graminis (DC.) E.O. Speer, f. sp. tritici Em. Marchal ( Bgt ), has undergone long and dynamic co-evolution with its hosts. In the last 10,000 years, processes involved in plant evolution under domestication, altered host-population structure. Recently both virulence and genomic profiling separated Bgt into two groups based on their origin from domestic host and from wild emmer wheat. While most studies focused on the Bgt pathogen, there is significant knowledge gaps in the role of wheat host diversity in this specification. This study aimed to fill this gap by exploring qualitatively and also quantitatively the disease response of diverse host panel to powdery mildew [105 domesticated wheat genotypes ( Triticum turgidum ssp. dicoccum, T. turgidum ssp. durum , and T. aestivum ) and 241 accessions of its direct progenitor, wild emmer wheat ( T. turgidum ssp. dicoccoides )]. A set of eight Bgt isolates, originally collected from domesticated and wild wheat was used for screening this wheat collection. The isolates from domesticated wheat elicited susceptible to moderate plant responses on domesticated wheat lines and high resistance on wild genotypes (51.7% of the tested lines were resistant). Isolates from wild emmer elicited reciprocal disease responses: high resistance of domesticated germplasm and high susceptibility of the wild material (their original host). Analysis of variance of the quantitative phenotypic responses showed a significant Isolates × Host species interaction [ P (F) < 0.0001] and further supported these findings. Furthermore, analysis of the range of disease severity values showed that when the group of host genotypes was inoculated with Bgt isolate from the reciprocal host, coefficient of variation was significantly higher than when inoculated with its own isolates. This trend was attributed to the role of major resistance genes in the latter scenario (high proportion of complete resistance). By testing the association between disease severity and geographical distance from the source of inoculum, we have found higher susceptibility in wild emmer close to the source. Both qualitative and quantitative assays showed a reciprocal resistance pattern in the wheat host and are well aligned with the recent findings of significant differentiation into wild-emmer and domesticated-wheat populations in the pathogen.

Comparative analysis of hospital energy use: pacific northwest and scandinavia.

PubMed

Burpee, Heather; McDade, Erin

2014-01-01

This study aimed to establish the potential for significant energy reduction in hospitals in the United States by providing evidence of Scandinavian operational precedents with high Interior Environmental Quality (IEQ) and substantially lower energy profiles than comparable U.S. facilities. These facilities set important precedents for design teams seeking operational examples for achieving aggressive energy and interior environmental quality goals. This examination of operational hospitals is intended to offer hospital owners, designers, and building managers a strong case and concrete framework for strategies to achieve exceptionally high performing buildings. Energy efficient hospitals have the potential to significantly impact the U.S.'s overall energy profile, and key stakeholders in the hospital industry need specific, operationally grounded precedents in order to successfully implement informed energy reduction strategies. This study is an outgrowth of previous research evaluating high quality, low energy hospitals that serve as examples for new high performance hospital design, construction, and operation. Through extensive interviews, numerous site visits, the development of case studies, and data collection, this team has established thorough qualitative and quantitative analyses of several contemporary hospitals in Scandinavia and the Pacific Northwest. Many Scandinavian hospitals demonstrate a low energy profile, and when analyzed in comparison with U.S. hospitals, such Scandinavian precedents help define the framework required to make significant changes in the U.S. hospital building industry. Eight hospitals, four Scandinavian and four Pacific Northwest, were quantitatively compared using the Environmental Protection Agency's Portfolio Manager, allowing researchers to answer specific questions about the impact of energy source and architectural and mechanical strategies on energy efficiency in operational hospitals. Specific architectural, mechanical, and plant systems make these Scandinavian hospitals more energy efficient than their Pacific Northwest counterparts. More importantly, synergistic systems integration allows for their significant reductions in energy consumption. This quantitative comparison of operational Scandinavian and Pacific Northwest hospitals resulted in compelling evidence of the potential for deep energy savings in the U.S., and allowed researchers to outline specific strategies for achieving such reductions. © 2014 Vendome Group, LLC.

Quantitative magnetic resonance imaging assessments of autosomal recessive polycystic kidney disease progression and response to therapy in an animal model.

PubMed

Erokwu, Bernadette O; Anderson, Christian E; Flask, Chris A; Dell, Katherine M

2018-05-01

BackgroundAutosomal recessive polycystic kidney disease (ARPKD) is associated with significant mortality and morbidity, and currently, there are no disease-specific treatments available for ARPKD patients. One major limitation in establishing new therapies for ARPKD is a lack of sensitive measures of kidney disease progression. Magnetic resonance imaging (MRI) can provide multiple quantitative assessments of the disease.MethodsWe applied quantitative image analysis of high-resolution (noncontrast) T2-weighted MRI techniques to study cystic kidney disease progression and response to therapy in the PCK rat model of ARPKD.ResultsSerial imaging over a 2-month period demonstrated that renal cystic burden (RCB, %)=[total cyst volume (TCV)/total kidney volume (TKV) × 100], TCV, and, to a lesser extent, TKV detected cystic kidney disease progression, as well as the therapeutic effect of octreotide, a clinically available medication shown previously to slow both kidney and liver disease progression in this model. All three MRI measures correlated significantly with histologic measures of renal cystic area, although the correlation of RCB and TCV was stronger than that of TKV.ConclusionThese preclinical MRI results provide a basis for applying these quantitative MRI techniques in clinical studies, to stage and measure progression in human ARPKD kidney disease.

A comparative study of qualitative and quantitative methods for the assessment of adhesive remnant after bracket debonding.

PubMed

Cehreli, S Burcak; Polat-Ozsoy, Omur; Sar, Cagla; Cubukcu, H Evren; Cehreli, Zafer C

2012-04-01

The amount of the residual adhesive after bracket debonding is frequently assessed in a qualitative manner, utilizing the adhesive remnant index (ARI). This study aimed to investigate whether quantitative assessment of the adhesive remnant yields more precise results compared to qualitative methods utilizing the 4- and 5-point ARI scales. Twenty debonded brackets were selected. Evaluation and scoring of the adhesive remnant on bracket bases were made consecutively using: 1. qualitative assessment (visual scoring) and 2. quantitative measurement (image analysis) on digital photographs. Image analysis was made on scanning electron micrographs (SEM) and high-precision elemental maps of the adhesive remnant as determined by energy dispersed X-ray spectrometry. Evaluations were made in accordance with the original 4-point and the modified 5-point ARI scales. Intra-class correlation coefficients (ICCs) were calculated, and the data were evaluated using Friedman test followed by Wilcoxon signed ranks test with Bonferroni correction. ICC statistics indicated high levels of agreement for qualitative visual scoring among examiners. The 4-point ARI scale was compliant with the SEM assessments but indicated significantly less adhesive remnant compared to the results of quantitative elemental mapping. When the 5-point scale was used, both quantitative techniques yielded similar results with those obtained qualitatively. These results indicate that qualitative visual scoring using the ARI is capable of generating similar results with those assessed by quantitative image analysis techniques. In particular, visual scoring with the 5-point ARI scale can yield similar results with both the SEM analysis and elemental mapping.

The future of targeted peptidomics.

PubMed

Findeisen, Peter

2013-12-01

Targeted MS is becoming increasingly important for sensitive and specific quantitative detection of proteins and respective PTMs. In this article, Ceglarek et al. [Proteomics Clin. Appl. 2013, 7, 794-801] present an LC-MS-based method for simultaneous quantitation of seven apolipoproteins in serum specimens. The assay fulfills many necessities of routine diagnostic applications, namely, low cost, high throughput, and good reproducibility. We anticipate that validation of new biomarkers will speed up with this technology and the palette of laboratory-based diagnostic tools will hopefully be augmented significantly in the near future. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bone microarchitecture is more severely affected in patients on hemodialysis than in those receiving peritoneal dialysis.

PubMed

Pelletier, Solenne; Vilayphiou, Nicolas; Boutroy, Stéphanie; Bacchetta, Justine; Sornay-Rendu, Elisabeth; Szulc, Pawel; Arkouche, Walid; Guebre-Egziabher, Fitsum; Fouque, Denis; Chapurlat, Roland

2012-09-01

We used high-resolution quantitative computed tomography to study the microarchitecture of bone in patients with chronic kidney disease on dialysis. We compared bone characteristics in 56 maintenance hemodialysis (21 women, 14 post-menopausal) and 23 peritoneal dialysis patients (9 women, 6 post-menopausal) to 79 healthy men and women from two cohorts matched for age, body mass index, gender, and menopausal status. All underwent dual-energy X-ray absorptiometry of the spine and hip to measure areal bone mineral density, and high-resolution peripheral quantitative computed tomography of the radius and tibia to measure volumetric bone mineral density and microarchitecture. When compared to their matched healthy controls, patients receiving hemodialysis and peritoneal dialysis had a significantly lower areal bone mineral density in the hip. Hemodialysis patients had significantly lower total, cortical, and trabecular volumetric bone mineral density at both sites. Hemodialysis patients had significantly lower trabecular volumetric bone mineral density and microarchitecture at the tibia than the peritoneal dialysis patients. Overall, peritoneal dialysis patients were less affected, their cortical thickness at the distal tibia being the only significant difference versus controls. Thus, we found more severe trabecular damage at the weight-bearing tibia in hemodialysis compared to peritoneal dialysis patients, but this latter finding needs confirmation in larger cohorts.

Quantitative coronary plaque analysis predicts high-risk plaque morphology on coronary computed tomography angiography: results from the ROMICAT II trial.

PubMed

Liu, Ting; Maurovich-Horvat, Pál; Mayrhofer, Thomas; Puchner, Stefan B; Lu, Michael T; Ghemigian, Khristine; Kitslaar, Pieter H; Broersen, Alexander; Pursnani, Amit; Hoffmann, Udo; Ferencik, Maros

2018-02-01

Semi-automated software can provide quantitative assessment of atherosclerotic plaques on coronary CT angiography (CTA). The relationship between established qualitative high-risk plaque features and quantitative plaque measurements has not been studied. We analyzed the association between quantitative plaque measurements and qualitative high-risk plaque features on coronary CTA. We included 260 patients with plaque who underwent coronary CTA in the Rule Out Myocardial Infarction/Ischemia Using Computer Assisted Tomography (ROMICAT) II trial. Quantitative plaque assessment and qualitative plaque characterization were performed on a per coronary segment basis. Quantitative coronary plaque measurements included plaque volume, plaque burden, remodeling index, and diameter stenosis. In qualitative analysis, high-risk plaque was present if positive remodeling, low CT attenuation plaque, napkin-ring sign or spotty calcium were detected. Univariable and multivariable logistic regression analyses were performed to assess the association between quantitative and qualitative high-risk plaque assessment. Among 888 segments with coronary plaque, high-risk plaque was present in 391 (44.0%) segments by qualitative analysis. In quantitative analysis, segments with high-risk plaque had higher total plaque volume, low CT attenuation plaque volume, plaque burden and remodeling index. Quantitatively assessed low CT attenuation plaque volume (odds ratio 1.12 per 1 mm 3 , 95% CI 1.04-1.21), positive remodeling (odds ratio 1.25 per 0.1, 95% CI 1.10-1.41) and plaque burden (odds ratio 1.53 per 0.1, 95% CI 1.08-2.16) were associated with high-risk plaque. Quantitative coronary plaque characteristics (low CT attenuation plaque volume, positive remodeling and plaque burden) measured by semi-automated software correlated with qualitative assessment of high-risk plaque features.

Demonstration of a diode-laser-based high spectral resolution lidar (HSRL) for quantitative profiling of clouds and aerosols.

PubMed

Hayman, Matthew; Spuler, Scott

2017-11-27

We present a demonstration of a diode-laser-based high spectral resolution lidar. It is capable of performing calibrated retrievals of aerosol and cloud optical properties at a 150 m range resolution with less than 1 minute integration time over an approximate range of 12 km during day and night. This instrument operates at 780 nm, a wavelength that is well established for reliable semiconductor lasers and detectors, and was chosen because it corresponds to the D2 rubidium absorption line. A heated vapor reference cell of isotopic rubidium 87 is used as an effective and reliable aerosol signal blocking filter in the instrument. In principle, the diode-laser-based high spectral resolution lidar can be made cost competitive with elastic backscatter lidar systems, yet delivers a significant improvement in data quality through direct retrieval of quantitative optical properties of clouds and aerosols.

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

Lincoln, D.E.

Preliminary analysis of two populations of Artemisia tridentata compared leaf chemical and physiological characteristics which influence herbivores. The proportion of sixteen of the volatile compounds differed significantly between the two populations; however, total yield of volatiles did not. This initial survey established the reliability of the procedure to quantitatively monitor plant responses to CO/sub 2/ enrichment and suggests that test samples be restricted to a single population. Four sesquiterpene lactones have been selected for the experimental quantitative HPLC analysis; all peaks have been assigned identities and have demonstrated high degree of reproducibility. Growth of Artemisia under high and low lightmore » at three CO/sub 2/ levels demonstrated that this species also undergoes a ''dilution'' of the leaf carbon content and is useful as test species for herbivory response to CO/sub 2/ induced effects. The initial experiment also showed that high irradiance is a necessary growth condition. 10 refs.« less

Real-time and quantitative isotropic spatial resolution susceptibility imaging for magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Pi, Shiqiang; Liu, Wenzhong; Jiang, Tao

2018-03-01

The magnetic transparency of biological tissue allows the magnetic nanoparticle (MNP) to be a promising functional sensor and contrast agent. The complex susceptibility of MNPs, strongly influenced by particle concentration, excitation magnetic field and their surrounding microenvironment, provides significant implications for biomedical applications. Therefore, magnetic susceptibility imaging of high spatial resolution will give more detailed information during the process of MNP-aided diagnosis and therapy. In this study, we present a novel spatial magnetic susceptibility extraction method for MNPs under a gradient magnetic field, a low-frequency drive magnetic field, and a weak strength high-frequency magnetic field. Based on this novel method, a magnetic particle susceptibility imaging (MPSI) of millimeter-level spatial resolution (<3 mm) was achieved using our homemade imaging system. Corroborated by the experimental results, the MPSI shows real-time (1 s per frame acquisition) and quantitative abilities, and isotropic high resolution.

Detection and semi-quantification of Strongylus vulgaris DNA in equine faeces by real-time quantitative PCR.

PubMed

Nielsen, Martin K; Peterson, David S; Monrad, Jesper; Thamsborg, Stig M; Olsen, Susanne N; Kaplan, Ray M

2008-03-01

Strongylus vulgaris is an important strongyle nematode with high pathogenic potential infecting horses world-wide. Several decades of intensive anthelmintic use has virtually eliminated clinical disease caused by S. vulgaris, but has also caused high levels of anthelmintic resistance in equine small strongyle (cyathostomin) nematodes. Recommendations aimed at limiting the development of anthelmintic resistance by reducing treatment intensity raises a simultaneous demand for reliable and accurate diagnostic tools for detecting important parasitic pathogens. Presently, the only means available to differentiate among strongyle species in a faecal sample is by identifying individual L3 larvae following a two week coproculture procedure. The aim of the present study is to overcome this diagnostic obstacle by developing a fluorescence-based quantitative PCR assay capable of identifying S. vulgaris eggs in faecal samples from horses. Species-specific primers and a TaqMan probe were designed by alignment of published ribosomal DNA sequences of the second internal transcribed spacer of cyathostomin and Strongylus spp. nematodes. The assay was tested for specificity and optimized using genomic DNA extracted from identified male worms of Strongylus and cyathostomin species. In addition, eggs were collected from adult female worms and used to evaluate the quantitative potential of the assay. Statistically significant linear relationships were found between egg numbers and cycle of threshold (Ct) values. PCR results were unaffected by the presence of cyathostomin DNA in the sample and there was no indication of PCR inhibition by faecal sources. A field evaluation on faecal samples obtained from four Danish horse farms revealed a good agreement with the traditional larval culture (kappa-value=0.78), but with a significantly higher performance of the PCR assay. An association between Ct values and S. vulgaris larval counts was statistically significant. The present assay can reliably and semi-quantitatively detect minute quantities of S. vulgaris eggs in faecal samples.

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics*

PubMed Central

Cai, Wenxuan; Guner, Huseyin; Gregorich, Zachery R.; Chen, Albert J.; Ayaz-Guner, Serife; Peng, Ying; Valeja, Santosh G.; Liu, Xiaowen; Ge, Ying

2016-01-01

Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics. PMID:26598644

What's the 411? High School Leaders' Perceptions of Inclusion Implementation

ERIC Educational Resources Information Center

Jamison, Arnella L.

2013-01-01

This quantitative, descriptive study explored and described urban and suburban school leaders' perceptions of the definition of "inclusion" and perceptions of their level of involvement in the implementation of inclusion. Additionally, the study determined if there was a significant difference in the urban and suburban school leaders'…

ELL to Go

ERIC Educational Resources Information Center

Demski, Jennifer

2011-01-01

Township High School District 214 in Arlington Heights, Illinois, and Comal Independent School District (ISD) in New Braunfels, Texas, are pioneers in the incorporation of mobile devices such as the iPad and iPod Touch in the English language learner (ELL) classroom. Though it's too soon to collect significant quantitative data regarding the…

[Quality evaluation of rhubarb dispensing granules based on multi-component simultaneous quantitative analysis and bioassay].

PubMed

Tan, Peng; Zhang, Hai-Zhu; Zhang, Ding-Kun; Wu, Shan-Na; Niu, Ming; Wang, Jia-Bo; Xiao, Xiao-He

2017-07-01

This study attempts to evaluate the quality of Chinese formula granules by combined use of multi-component simultaneous quantitative analysis and bioassay. The rhubarb dispensing granules were used as the model drug for demonstrative study. The ultra-high performance liquid chromatography (UPLC) method was adopted for simultaneously quantitative determination of the 10 anthraquinone derivatives (such as aloe emodin-8-O-β-D-glucoside) in rhubarb dispensing granules; purgative biopotency of different batches of rhubarb dispensing granules was determined based on compound diphenoxylate tablets-induced mouse constipation model; blood activating biopotency of different batches of rhubarb dispensing granules was determined based on in vitro rat antiplatelet aggregation model; SPSS 22.0 statistical software was used for correlation analysis between 10 anthraquinone derivatives and purgative biopotency, blood activating biopotency. The results of multi-components simultaneous quantitative analysisshowed that there was a great difference in chemical characterizationand certain differences inpurgative biopotency and blood activating biopotency among 10 batches of rhubarb dispensing granules. The correlation analysis showed that the intensity of purgative biopotency was significantly correlated with the content of conjugated anthraquinone glycosides (P<0.01), and the intensity of blood activating biopotency was significantly correlated with the content of free anthraquinone (P<0.01). In summary, the combined use of multi-component simultaneous quantitative analysis and bioassay can achieve objective quantification and more comprehensive reflection on overall quality difference among different batches of rhubarb dispensing granules. Copyright© by the Chinese Pharmaceutical Association.

Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits.

PubMed

Scheper, Carsten; Wensch-Dorendorf, Monika; Yin, Tong; Dressel, Holger; Swalve, Herrmann; König, Sven

2016-06-29

Intensified selection of polled individuals has recently gained importance in predominantly horned dairy cattle breeds as an alternative to routine dehorning. The status quo of the current polled breeding pool of genetically-closely related artificial insemination sires with lower breeding values for performance traits raises questions regarding the effects of intensified selection based on this founder pool. We developed a stochastic simulation framework that combines the stochastic simulation software QMSim and a self-designed R program named QUALsim that acts as an external extension. Two traits were simulated in a dairy cattle population for 25 generations: one quantitative (QMSim) and one qualitative trait with Mendelian inheritance (i.e. polledness, QUALsim). The assignment scheme for qualitative trait genotypes initiated realistic initial breeding situations regarding allele frequencies, true breeding values for the quantitative trait and genetic relatedness. Intensified selection for polled cattle was achieved using an approach that weights estimated breeding values in the animal best linear unbiased prediction model for the quantitative trait depending on genotypes or phenotypes for the polled trait with a user-defined weighting factor. Selection response for the polled trait was highest in the selection scheme based on genotypes. Selection based on phenotypes led to significantly lower allele frequencies for polled. The male selection path played a significantly greater role for a fast dissemination of polled alleles compared to female selection strategies. Fixation of the polled allele implies selection based on polled genotypes among males. In comparison to a base breeding scenario that does not take polledness into account, intensive selection for polled substantially reduced genetic gain for this quantitative trait after 25 generations. Reducing selection intensity for polled males while maintaining strong selection intensity among females, simultaneously decreased losses in genetic gain and achieved a final allele frequency of 0.93 for polled. A fast transition to a completely polled population through intensified selection for polled was in contradiction to the preservation of high genetic gain for the quantitative trait. Selection on male polled genotypes with moderate weighting, and selection on female polled phenotypes with high weighting, could be a suitable compromise regarding all important breeding aspects.

Diagnostic accuracy of stress perfusion CMR in comparison with quantitative coronary angiography: fully quantitative, semiquantitative, and qualitative assessment.

PubMed

Mordini, Federico E; Haddad, Tariq; Hsu, Li-Yueh; Kellman, Peter; Lowrey, Tracy B; Aletras, Anthony H; Bandettini, W Patricia; Arai, Andrew E

2014-01-01

This study's primary objective was to determine the sensitivity, specificity, and accuracy of fully quantitative stress perfusion cardiac magnetic resonance (CMR) versus a reference standard of quantitative coronary angiography. We hypothesized that fully quantitative analysis of stress perfusion CMR would have high diagnostic accuracy for identifying significant coronary artery stenosis and exceed the accuracy of semiquantitative measures of perfusion and qualitative interpretation. Relatively few studies apply fully quantitative CMR perfusion measures to patients with coronary disease and comparisons to semiquantitative and qualitative methods are limited. Dual bolus dipyridamole stress perfusion CMR exams were performed in 67 patients with clinical indications for assessment of myocardial ischemia. Stress perfusion images alone were analyzed with a fully quantitative perfusion (QP) method and 3 semiquantitative methods including contrast enhancement ratio, upslope index, and upslope integral. Comprehensive exams (cine imaging, stress/rest perfusion, late gadolinium enhancement) were analyzed qualitatively with 2 methods including the Duke algorithm and standard clinical interpretation. A 70% or greater stenosis by quantitative coronary angiography was considered abnormal. The optimum diagnostic threshold for QP determined by receiver-operating characteristic curve occurred when endocardial flow decreased to <50% of mean epicardial flow, which yielded a sensitivity of 87% and specificity of 93%. The area under the curve for QP was 92%, which was superior to semiquantitative methods: contrast enhancement ratio: 78%; upslope index: 82%; and upslope integral: 75% (p = 0.011, p = 0.019, p = 0.004 vs. QP, respectively). Area under the curve for QP was also superior to qualitative methods: Duke algorithm: 70%; and clinical interpretation: 78% (p < 0.001 and p < 0.001 vs. QP, respectively). Fully quantitative stress perfusion CMR has high diagnostic accuracy for detecting obstructive coronary artery disease. QP outperforms semiquantitative measures of perfusion and qualitative methods that incorporate a combination of cine, perfusion, and late gadolinium enhancement imaging. These findings suggest a potential clinical role for quantitative stress perfusion CMR. Copyright © 2014 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Rapid quantitative determination of maltose and total sugars in sweet potato (Ipomoea batatas L. [Lam.]) varieties using HPTLC.

PubMed

Lebot, Vincent

2017-03-01

When a raw sweet potato root is analysed, only sucrose, glucose and fructose are present but during cooking, starch is hydrolysed into maltose giving the sweet flavour to cooked roots. This study aimed at developing an HPTLC protocol for the rapid quantitative determination of maltose and total sugars in four commercial varieties and to compare them to 243 hybrids grouped by flesh colour (white, orange, purple). In commercial varieties, mean maltose content varied from 10.26 to 15.60% and total sugars from 17.83 to 27.77% on fresh weight basis. Hybrids showed significant variation in maltose content within each group, with means ranging from 7.65% for white-fleshed, to 8.53% in orange- and 11.98% in purple-fleshed. Total mean sugars content was 20.24, 22.11 and 26.84% respectively for white, orange and purple flesh hybrids. No significant correlations were detected between individual sugars but maltose and total sugars content were highly correlated. Compared to the best commercial variety ( Baby ), 25 hybrids (10.3%) presented a higher maltose content and 40 (16.5%) showed a higher total sugars content. HPTLC was observed as an attractive, cost efficient, high-throughput technique for quantitating maltose and total sugars in sweet potatoes. Perspectives for improving sweet potato quality for consumers' requirements are also discussed.

A correlative imaging based methodology for accurate quantitative assessment of bone formation in additive manufactured implants.

PubMed

Geng, Hua; Todd, Naomi M; Devlin-Mullin, Aine; Poologasundarampillai, Gowsihan; Kim, Taek Bo; Madi, Kamel; Cartmell, Sarah; Mitchell, Christopher A; Jones, Julian R; Lee, Peter D

2016-06-01

A correlative imaging methodology was developed to accurately quantify bone formation in the complex lattice structure of additive manufactured implants. Micro computed tomography (μCT) and histomorphometry were combined, integrating the best features from both, while demonstrating the limitations of each imaging modality. This semi-automatic methodology registered each modality using a coarse graining technique to speed the registration of 2D histology sections to high resolution 3D μCT datasets. Once registered, histomorphometric qualitative and quantitative bone descriptors were directly correlated to 3D quantitative bone descriptors, such as bone ingrowth and bone contact. The correlative imaging allowed the significant volumetric shrinkage of histology sections to be quantified for the first time (~15 %). This technique demonstrated the importance of location of the histological section, demonstrating that up to a 30 % offset can be introduced. The results were used to quantitatively demonstrate the effectiveness of 3D printed titanium lattice implants.

Quantitative micro-CT based coronary artery profiling using interactive local thresholding and cylindrical coordinates.

PubMed

Panetta, Daniele; Pelosi, Gualtiero; Viglione, Federica; Kusmic, Claudia; Terreni, Marianna; Belcari, Nicola; Guerra, Alberto Del; Athanasiou, Lambros; Exarchos, Themistoklis; Fotiadis, Dimitrios I; Filipovic, Nenad; Trivella, Maria Giovanna; Salvadori, Piero A; Parodi, Oberdan

2015-01-01

Micro-CT is an established imaging technique for high-resolution non-destructive assessment of vascular samples, which is gaining growing interest for investigations of atherosclerotic arteries both in humans and in animal models. However, there is still a lack in the definition of micro-CT image metrics suitable for comprehensive evaluation and quantification of features of interest in the field of experimental atherosclerosis (ATS). A novel approach to micro-CT image processing for profiling of coronary ATS is described, providing comprehensive visualization and quantification of contrast agent-free 3D high-resolution reconstruction of full-length artery walls. Accelerated coronary ATS has been induced by high fat cholesterol-enriched diet in swine and left coronary artery (LCA) harvested en bloc for micro-CT scanning and histologic processing. A cylindrical coordinate system has been defined on the image space after curved multiplanar reformation of the coronary vessel for the comprehensive visualization of the main vessel features such as wall thickening and calcium content. A novel semi-automatic segmentation procedure based on 2D histograms has been implemented and the quantitative results validated by histology. The potentiality of attenuation-based micro-CT at low kV to reliably separate arterial wall layers from adjacent tissue as well as identify wall and plaque contours and major tissue components has been validated by histology. Morphometric indexes from histological data corresponding to several micro-CT slices have been derived (double observer evaluation at different coronary ATS stages) and highly significant correlations (R2 > 0.90) evidenced. Semi-automatic morphometry has been validated by double observer manual morphometry of micro-CT slices and highly significant correlations were found (R2 > 0.92). The micro-CT methodology described represents a handy and reliable tool for quantitative high resolution and contrast agent free full length coronary wall profiling, able to assist atherosclerotic vessels morphometry in a preclinical experimental model of coronary ATS and providing a link between in vivo imaging and histology.

How to quantitatively evaluate safety of driver behavior upon accident? A biomechanical methodology

PubMed Central

Zhang, Wen; Cao, Jieer

2017-01-01

How to evaluate driver spontaneous reactions in various collision patterns in a quantitative way is one of the most important topics in vehicle safety. Firstly, this paper constructs representative numerical crash scenarios described by impact velocity, impact angle and contact position based on finite element (FE) computation platform. Secondly, a driver cabin model is extracted and described in the well validated multi-rigid body (MB) model to compute the value of weighted injury criterion to quantitatively assess drivers’ overall injury under certain circumstances. Furthermore, based on the coupling of FE and MB, parametric studies on various crash scenarios are conducted. It is revealed that the WIC (Weighted Injury Criteria) value variation law under high impact velocities is quite distinct comparing with the one in low impact velocities. In addition, the coupling effect can be elucidated by the fact that the difference of WIC value among three impact velocities under smaller impact angles tends to be distinctly higher than that under larger impact angles. Meanwhile, high impact velocity also increases the sensitivity of WIC under different collision positions and impact angles. Results may provide a new methodology to quantitatively evaluate driving behaviors and serve as a significant guiding step towards collision avoidance for autonomous driving vehicles. PMID:29240789

How to quantitatively evaluate safety of driver behavior upon accident? A biomechanical methodology.

PubMed

Zhang, Wen; Cao, Jieer; Xu, Jun

2017-01-01

How to evaluate driver spontaneous reactions in various collision patterns in a quantitative way is one of the most important topics in vehicle safety. Firstly, this paper constructs representative numerical crash scenarios described by impact velocity, impact angle and contact position based on finite element (FE) computation platform. Secondly, a driver cabin model is extracted and described in the well validated multi-rigid body (MB) model to compute the value of weighted injury criterion to quantitatively assess drivers' overall injury under certain circumstances. Furthermore, based on the coupling of FE and MB, parametric studies on various crash scenarios are conducted. It is revealed that the WIC (Weighted Injury Criteria) value variation law under high impact velocities is quite distinct comparing with the one in low impact velocities. In addition, the coupling effect can be elucidated by the fact that the difference of WIC value among three impact velocities under smaller impact angles tends to be distinctly higher than that under larger impact angles. Meanwhile, high impact velocity also increases the sensitivity of WIC under different collision positions and impact angles. Results may provide a new methodology to quantitatively evaluate driving behaviors and serve as a significant guiding step towards collision avoidance for autonomous driving vehicles.

Association Mapping of Quantitative Disease Resistance in a Natural Population of Loblolly Pine (Pinus taeda L.)

PubMed Central

Quesada, Tania; Gopal, Vikneswaran; Cumbie, W. Patrick; Eckert, Andrew J.; Wegrzyn, Jill L.; Neale, David B.; Goldfarb, Barry; Huber, Dudley A.; Casella, George; Davis, John M.

2010-01-01

Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants. Whereas resistance is often quantitative, there is limited information on the genes that underpin quantitative variation in disease resistance. We used a population genomic approach to identify genes in loblolly pine (Pinus taeda) that are associated with resistance to pitch canker, a disease incited by the necrotrophic pathogen Fusarium circinatum. A set of 498 largely unrelated, clonally propagated genotypes were inoculated with F. circinatum microconidia and lesion length, a measure of disease resistance, data were collected 4, 8, and 12 weeks after inoculation. Best linear unbiased prediction was used to adjust for imbalance in number of observations and to identify highly susceptible and highly resistant genotypes (“tails”). The tails were reinoculated to validate the results of the full population screen. Significant associations were detected in 10 single nucleotide polymorphisms (SNPs) (out of 3938 tested). As hypothesized for genes involved in quantitative resistance, the 10 SNPs had small effects and proposed roles in basal resistance, direct defense, and signal transduction. We also discovered associated genes with unknown function, which would have remained undetected in a candidate gene approach constrained by annotation for disease resistance or stress response. PMID:20628037

Quantitative PCR assay to determine prevalence and intensity of MSX (Haplosporidium nelsoni) in North Carolina and Rhode Island oysters Crassostrea virginica.

PubMed

Wilbur, Ami E; Ford, Susan E; Gauthier, Julie D; Gomez-Chiarri, Marta

2012-12-27

The continuing challenges to the management of both wild and cultured eastern oyster Crassostrea virginica populations resulting from protozoan parasites has stimulated interest in the development of molecular assays for their detection and quantification. For Haplosporidium nelsoni, the causative agent of multinucleated sphere unknown (MSX) disease, diagnostic evaluations depend extensively on traditional but laborious histological approaches and more recently on rapid and sensitive (but not quantitative) end-point polymerase chain reaction (PCR) assays. Here, we describe the development and application of a quantitative PCR (qPCR) assay for H. nelsoni using an Applied Biosystems TaqMan® assay designed with minor groove binder (MGB) probes. The assay was highly sensitive, detecting as few as 20 copies of cloned target DNA. Histologically evaluated parasite density was significantly correlated with the quantification cycle (Cq), regardless of whether quantification was categorical (r2 = 0.696, p < 0.0001) or quantitative (r2 = 0.797, p < 0.0001). Application in field studies conducted in North Carolina, USA (7 locations), revealed widespread occurrence of the parasite with moderate to high intensities noted in some locations. In Rhode Island, USA, application of the assay on oysters from 2 locations resulted in no positives.

Quantitative and qualitative comparison of MR imaging of the temporomandibular joint at 1.5 and 3.0 T using an optimized high-resolution protocol

PubMed Central

Spinner, Georg; Wyss, Michael; Erni, Stefan; Ettlin, Dominik A; Nanz, Daniel; Ulbrich, Erika J; Gallo, Luigi M; Andreisek, Gustav

2016-01-01

Objectives: To quantitatively and qualitatively compare MRI of the temporomandibular joint (TMJ) using an optimized high-resolution protocol at 3.0 T and a clinical standard protocol at 1.5 T. Methods: A phantom and 12 asymptomatic volunteers were MR imaged using a 2-channel surface coil (standard TMJ coil) at 1.5 and 3.0 T (Philips Achieva and Philips Ingenia, respectively; Philips Healthcare, Best, Netherlands). Imaging protocol consisted of coronal and oblique sagittal proton density-weighted turbo spin echo sequences. For quantitative evaluation, a spherical phantom was imaged. Signal-to-noise ratio (SNR) maps were calculated on a voxelwise basis. For qualitative evaluation, all volunteers underwent MRI of the TMJ with the jaw in closed position. Two readers independently assessed visibility and delineation of anatomical structures of the TMJ and overall image quality on a 5-point Likert scale. Quantitative and qualitative measurements were compared between field strengths. Results: The quantitative analysis showed similar SNR for the high-resolution protocol at 3.0 T compared with the clinical protocol at 1.5 T. The qualitative analysis showed significantly better visibility and delineation of clinically relevant anatomical structures of the TMJ, including the TMJ disc and pterygoid muscle as well as better overall image quality at 3.0 T than at 1.5 T. Conclusions: The presented results indicate that expected gains in SNR at 3.0 T can be used to increase the spatial resolution when imaging the TMJ, which translates into increased visibility and delineation of anatomical structures of the TMJ. Therefore, imaging at 3.0 T should be preferred over 1.5 T for imaging the TMJ. PMID:26371077

Quantitative and qualitative comparison of MR imaging of the temporomandibular joint at 1.5 and 3.0 T using an optimized high-resolution protocol.

PubMed

Manoliu, Andrei; Spinner, Georg; Wyss, Michael; Erni, Stefan; Ettlin, Dominik A; Nanz, Daniel; Ulbrich, Erika J; Gallo, Luigi M; Andreisek, Gustav

2016-01-01

To quantitatively and qualitatively compare MRI of the temporomandibular joint (TMJ) using an optimized high-resolution protocol at 3.0 T and a clinical standard protocol at 1.5 T. A phantom and 12 asymptomatic volunteers were MR imaged using a 2-channel surface coil (standard TMJ coil) at 1.5 and 3.0 T (Philips Achieva and Philips Ingenia, respectively; Philips Healthcare, Best, Netherlands). Imaging protocol consisted of coronal and oblique sagittal proton density-weighted turbo spin echo sequences. For quantitative evaluation, a spherical phantom was imaged. Signal-to-noise ratio (SNR) maps were calculated on a voxelwise basis. For qualitative evaluation, all volunteers underwent MRI of the TMJ with the jaw in closed position. Two readers independently assessed visibility and delineation of anatomical structures of the TMJ and overall image quality on a 5-point Likert scale. Quantitative and qualitative measurements were compared between field strengths. The quantitative analysis showed similar SNR for the high-resolution protocol at 3.0 T compared with the clinical protocol at 1.5 T. The qualitative analysis showed significantly better visibility and delineation of clinically relevant anatomical structures of the TMJ, including the TMJ disc and pterygoid muscle as well as better overall image quality at 3.0 T than at 1.5 T. The presented results indicate that expected gains in SNR at 3.0 T can be used to increase the spatial resolution when imaging the TMJ, which translates into increased visibility and delineation of anatomical structures of the TMJ. Therefore, imaging at 3.0 T should be preferred over 1.5 T for imaging the TMJ.

Feasibility of high-resolution quantitative perfusion analysis in patients with heart failure.

PubMed

Sammut, Eva; Zarinabad, Niloufar; Wesolowski, Roman; Morton, Geraint; Chen, Zhong; Sohal, Manav; Carr-White, Gerry; Razavi, Reza; Chiribiri, Amedeo

2015-02-12

Cardiac magnetic resonance (CMR) is playing an expanding role in the assessment of patients with heart failure (HF). The assessment of myocardial perfusion status in HF can be challenging due to left ventricular (LV) remodelling and wall thinning, coexistent scar and respiratory artefacts. The aim of this study was to assess the feasibility of quantitative CMR myocardial perfusion analysis in patients with HF. A group of 58 patients with heart failure (HF; left ventricular ejection fraction, LVEF ≤ 50%) and 33 patients with normal LVEF (LVEF >50%), referred for suspected coronary artery disease, were studied. All subjects underwent quantitative first-pass stress perfusion imaging using adenosine according to standard acquisition protocols. The feasibility of quantitative perfusion analysis was then assessed using high-resolution, 3 T kt perfusion and voxel-wise Fermi deconvolution. 30/58 (52%) subjects in the HF group had underlying ischaemic aetiology. Perfusion abnormalities were seen amongst patients with ischaemic HF and patients with normal LV function. No regional perfusion defect was observed in the non-ischaemic HF group. Good agreement was found between visual and quantitative analysis across all groups. Absolute stress perfusion rate, myocardial perfusion reserve (MPR) and endocardial-epicardial MPR ratio identified areas with abnormal perfusion in the ischaemic HF group (p = 0.02; p = 0.04; p = 0.02, respectively). In the Normal LV group, MPR and endocardial-epicardial MPR ratio were able to distinguish between normal and abnormal segments (p = 0.04; p = 0.02 respectively). No significant differences of absolute stress perfusion rate or MPR were observed comparing visually normal segments amongst groups. Our results demonstrate the feasibility of high-resolution voxel-wise perfusion assessment in patients with HF.

High-speed transport-of-intensity phase microscopy with an electrically tunable lens.

PubMed

Zuo, Chao; Chen, Qian; Qu, Weijuan; Asundi, Anand

2013-10-07

We present a high-speed transport-of-intensity equation (TIE) quantitative phase microscopy technique, named TL-TIE, by combining an electrically tunable lens with a conventional transmission microscope. This permits the specimen at different focus position to be imaged in rapid succession, with constant magnification and no physically moving parts. The simplified image stack collection significantly reduces the acquisition time, allows for the diffraction-limited through-focus intensity stack collection at 15 frames per second, making dynamic TIE phase imaging possible. The technique is demonstrated by profiling of microlens array using optimal frequency selection scheme, and time-lapse imaging of live breast cancer cells by inversion the defocused phase optical transfer function to correct the phase blurring in traditional TIE. Experimental results illustrate its outstanding capability of the technique for quantitative phase imaging, through a simple, non-interferometric, high-speed, high-resolution, and unwrapping-free approach with prosperous applications in micro-optics, life sciences and bio-photonics.

PTMScout, a Web Resource for Analysis of High Throughput Post-translational Proteomics Studies*

PubMed Central

Naegle, Kristen M.; Gymrek, Melissa; Joughin, Brian A.; Wagner, Joel P.; Welsch, Roy E.; Yaffe, Michael B.; Lauffenburger, Douglas A.; White, Forest M.

2010-01-01

The rate of discovery of post-translational modification (PTM) sites is increasing rapidly and is significantly outpacing our biological understanding of the function and regulation of those modifications. To help meet this challenge, we have created PTMScout, a web-based interface for viewing, manipulating, and analyzing high throughput experimental measurements of PTMs in an effort to facilitate biological understanding of protein modifications in signaling networks. PTMScout is constructed around a custom database of PTM experiments and contains information from external protein and post-translational resources, including gene ontology annotations, Pfam domains, and Scansite predictions of kinase and phosphopeptide binding domain interactions. PTMScout functionality comprises data set comparison tools, data set summary views, and tools for protein assignments of peptides identified by mass spectrometry. Analysis tools in PTMScout focus on informed subset selection via common criteria and on automated hypothesis generation through subset labeling derived from identification of statistically significant enrichment of other annotations in the experiment. Subset selection can be applied through the PTMScout flexible query interface available for quantitative data measurements and data annotations as well as an interface for importing data set groupings by external means, such as unsupervised learning. We exemplify the various functions of PTMScout in application to data sets that contain relative quantitative measurements as well as data sets lacking quantitative measurements, producing a set of interesting biological hypotheses. PTMScout is designed to be a widely accessible tool, enabling generation of multiple types of biological hypotheses from high throughput PTM experiments and advancing functional assignment of novel PTM sites. PTMScout is available at http://ptmscout.mit.edu. PMID:20631208

Buffering effect of workplace social capital on the association of job insecurity with psychological distress in Japanese employees: a cross-sectional study.

PubMed

Inoue, Akiomi; Kawakami, Norito; Eguchi, Hisashi; Tsutsumi, Akizumi

2016-09-30

The present study aimed to examine the buffering effect of workplace social capital (WSC) on the association of job insecurity with psychological distress in Japanese employees. 2,971 employees from two factories of a manufacturing company in Japan completed a self-administered questionnaire including the scales on job insecurity, WSC, psychological distress, demographic and occupational characteristics, and quantitative workload. Using psychological distress (defined as a total score of the K6 scale ≥5) as a dependent variable, multiple logistic regression analyses were conducted. In a series of analyses, interaction term of job insecurity×WSC was included in the model. After adjusting for demographic and occupational characteristics as well as for quantitative workload and interaction effect of quantitative workload×WSC, high job insecurity and low WSC were significantly associated with psychological distress. Furthermore, a significant interaction effect of job insecurity×WSC was observed. Specifically, the association of job insecurity with psychological distress was greater among those who perceived lower levels of WSC (prevalence odds ratio=3.79 [95% confidence interval=2.70-5.32] for high vs. low job insecurity subgroup) than among those who perceived higher levels of WSC (prevalence odds ratio=2.96 [95% confidence interval=2.19-4.01] for high vs. low job insecurity subgroup). These findings were replicated among permanent male employees in the gender-stratified analyses. The present study suggests that WSC has a buffering effect on the association of job insecurity with psychological distress at least among Japanese permanent male employees.

Buffering effect of workplace social capital on the association of job insecurity with psychological distress in Japanese employees: a cross-sectional study

PubMed Central

Inoue, Akiomi; Kawakami, Norito; Eguchi, Hisashi; Tsutsumi, Akizumi

2016-01-01

Objectives: The present study aimed to examine the buffering effect of workplace social capital (WSC) on the association of job insecurity with psychological distress in Japanese employees. Methods: 2,971 employees from two factories of a manufacturing company in Japan completed a self-administered questionnaire including the scales on job insecurity, WSC, psychological distress, demographic and occupational characteristics, and quantitative workload. Using psychological distress (defined as a total score of the K6 scale ≥5) as a dependent variable, multiple logistic regression analyses were conducted. In a series of analyses, interaction term of job insecurity×WSC was included in the model. Results: After adjusting for demographic and occupational characteristics as well as for quantitative workload and interaction effect of quantitative workload×WSC, high job insecurity and low WSC were significantly associated with psychological distress. Furthermore, a significant interaction effect of job insecurity×WSC was observed. Specifically, the association of job insecurity with psychological distress was greater among those who perceived lower levels of WSC (prevalence odds ratio=3.79 [95% confidence interval=2.70-5.32] for high vs. low job insecurity subgroup) than among those who perceived higher levels of WSC (prevalence odds ratio=2.96 [95% confidence interval=2.19-4.01] for high vs. low job insecurity subgroup). These findings were replicated among permanent male employees in the gender-stratified analyses. Conclusions: The present study suggests that WSC has a buffering effect on the association of job insecurity with psychological distress at least among Japanese permanent male employees. PMID:27488045

Quantitative Molecular Detection of Putative Periodontal Pathogens in Clinically Healthy and Periodontally Diseased Subjects

PubMed Central

Göhler, André; Hetzer, Adrian; Holtfreter, Birte; Geisel, Marie Henrike; Schmidt, Carsten Oliver; Steinmetz, Ivo; Kocher, Thomas

2014-01-01

Periodontitis is a multi-microbial oral infection with high prevalence among adults. Putative oral pathogens are commonly found in periodontally diseased individuals. However, these organisms can be also detected in the oral cavity of healthy subjects. This leads to the hypothesis, that alterations in the proportion of these organisms relative to the total amount of oral microorganisms, namely their abundance, rather than their simple presence might be important in the transition from health to disease. Therefore, we developed a quantitative molecular method to determine the abundance of various oral microorganisms and the portion of bacterial and archaeal nucleic acid relative to the total nucleic acid extracted from individual samples. We applied quantitative real-time PCRs targeting single-copy genes of periodontal bacteria and 16S-rRNA genes of Bacteria and Archaea. Testing tongue scrapings of 88 matched pairs of periodontally diseased and healthy subjects revealed a significantly higher abundance of P. gingivalis and a higher total bacterial abundance in diseased subjects. In fully adjusted models the risk of being periodontally diseased was significantly higher in subjects with high P. gingivalis and total bacterial abundance. Interestingly, we found that moderate abundances of A. actinomycetemcomitans were associated with reduced risk for periodontal disease compared to subjects with low abundances, whereas for high abundances, this protective effect leveled off. Moderate archaeal abundances were health associated compared to subjects with low abundances. In conclusion, our methodological approach unraveled associations of the oral flora with periodontal disease, which would have gone undetected if only qualitative data had been determined. PMID:25029268

MR Imaging of the Prostate and Adjacent Anatomic Structures before, during, and after Ejaculation: Qualitative and Quantitative Evaluation1

PubMed Central

Medved, Milica; Sammet, Steffen; Yousuf, Ambereen; Oto, Aytekin

2015-01-01

Purpose To determine the possibility of obtaining high-quality magnetic resonance (MR) images before, during, and immediately after ejaculation and detecting measurable changes in quantitative MR imaging parameters after ejaculation. Materials and Methods In this prospective, institutional review board–approved, HIPAA-compliant study, eight young healthy volunteers (median age, 22.5 years), after providing informed consent, underwent MR imaging while masturbating to the point of ejaculation. A 1.5-T MR imaging unit was used, with an eight-channel surface coil and a dynamic single-shot fast spin-echo sequence. In addition, a quantitative MR imaging protocol that allowed calculation of T1, T2, and apparent diffusion coefficient (ADC) values was applied before and after ejaculation. Volumes of the prostate and seminal vesicles (SV) were calculated by using whole-volume segmentation on T2-weighted images, both before and after ejaculation. Pre- and postejaculation changes in quantitative MR parameters and measured volumes were evaluated by using the Wilcoxon signed rank test with Bonferroni adjustment. Results There was no significant change in prostate volumes on pre- and postejaculation images, while the SV contracted by 41% on average (median, 44.5%; P = .004). No changes before and after ejaculation were observed in T1 values or in T2 and ADC values in the central gland, while T2 and ADC values were significantly reduced in the peripheral zone by 12% and 14%, respectively (median, 13% and 14.5%, respectively; P = .004). Conclusion Successful dynamic MR imaging of ejaculation events and the ability to visualize internal sphincter closure, passage of ejaculate, and significant changes in SV volumes were demonstrated. Significant changes in peripheral zone T2 and ADC values were observed. PMID:24495265

Plasma cytokine profiling in sibling pairs discordant for autism spectrum disorder

PubMed Central

2013-01-01

Objective Converging lines of evidence point to the existence of immune dysfunction in autism spectrum disorder (ASD), which could directly affect several key neurodevelopmental processes. Previous studies have shown higher cytokine levels in patients with autism compared with matched controls or subjects with other developmental disorders. In the current study, we used plasma-cytokine profiling for 25 discordant sibling pairs to evaluate whether these alterations occur within families with ASD. Methods Plasma-cytokine profiling was conducted using an array-based multiplex sandwich ELISA for simultaneous quantitative measurement of 40 unique targets. We also analyzed the correlations between cytokine levels and clinically relevant quantitative traits (Vineland Adaptive Behavior Scale in Autism (VABS) composite score, Social Responsiveness Scale (SRS) total T score, head circumference, and full intelligence quotient (IQ)). In addition, because of the high phenotypic heterogeneity of ASD, we defined four subgroups of subjects (those who were non-verbal, those with gastrointestinal issues, those with regressive autism, and those with a history of allergies), which encompass common and/or recurrent endophenotypes in ASD, and tested the cytokine levels in each group. Results None of the measured parameters showed significant differences between children with ASD and their related typically developing siblings. However, specific target levels did correlate with quantitative clinical traits, and these were significantly different when the ASD subgroups were analyzed. It is notable that these differences seem to be attributable to a predisposing immunogenetic background, as no other significant differences were noticed between discordant sibling pairs. Interleukin-1β appears to be the cytokine most involved in quantitative traits and clinical subgroups of ASD. Conclusions In the present study, we found a lack of significant differences in plasma-cytokine levels between children with ASD and in their related non-autistic siblings. Thus, our results support the evidence that the immune profiles of children with autism do not differ from their typically developing siblings. However, the significant association of cytokine levels with the quantitative traits and the clinical subgroups analyzed suggests that altered immune responses may affect core feature of ASD. PMID:23497090

Phasegram Analysis of Vocal Fold Vibration Documented With Laryngeal High-speed Video Endoscopy.

PubMed

Herbst, Christian T; Unger, Jakob; Herzel, Hanspeter; Švec, Jan G; Lohscheller, Jörg

2016-11-01

In a recent publication, the phasegram, a bifurcation diagram over time, has been introduced as an intuitive visualization tool for assessing the vibratory states of oscillating systems. Here, this nonlinear dynamics approach is augmented with quantitative analysis parameters, and it is applied to clinical laryngeal high-speed video (HSV) endoscopic recordings of healthy and pathological phonations. HSV data from a total of 73 females diagnosed as healthy (n = 42), or with functional dysphonia (n = 15) or with unilateral vocal fold paralysis (n = 16), were quantitatively analyzed. Glottal area waveforms (GAW) and left and right hemi-GAWs (hGAW) were extracted from the HSV recordings. Based on Poincaré sections through phase space-embedded signals, two novel quantitative parameters were computed: the phasegram entropy (PE) and the phasegram complexity estimate (PCE), inspired by signal entropy and correlation dimension computation, respectively. Both PE and PCE assumed higher average values (suggesting more irregular vibrations) for the pathological as compared with the healthy participants, thus significantly discriminating healthy group from the paralysis group (P = 0.02 for both PE and PCE). Comparisons of individual PE or PCE data for the left and the right hGAW within each subject resulted in asymmetry measures for the regularity of vocal fold vibration. The PCE-based asymmetry measure revealed significant differences between the healthy group and the paralysis group (P = 0.03). Quantitative phasegram analysis of GAW and hGAW data is a promising tool for the automated processing of HSV data in research and in clinical practice. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Participation in High-Impact Sports Predicts Bone Mineral Density in Senior Olympic Athletes

PubMed Central

Leigey, Daniel; Irrgang, James; Francis, Kimberly; Cohen, Peter; Wright, Vonda

2009-01-01

Background: Loss of bone mineral density (BMD) and resultant fractures increase with age in both sexes. Participation in resistance or high-impact sports is a known contributor to bone health in young athletes; however, little is known about the effect of participation in impact sports on bone density as people age. Hypothesis: To test the hypothesis that high-impact sport participation will predict BMD in senior athletes, this study evaluated 560 athletes during the 2005 National Senior Games (the Senior Olympics). Study Design: Cross-sectional methods. The athletes completed a detailed health history questionnaire and underwent calcaneal quantitative ultrasound to measure BMD. Athletes were classified as participating in high impact sports (basketball, road race [running], track and field, triathalon, and volleyball) or non-high-impact sports. Stepwise linear regression was used to determine the influence of high-impact sports on BMD. Results: On average, participants were 65.9 years old (range, 50 to 93). There were 298 women (53.2%) and 289 men (51.6%) who participated in high-impact sports. Average body mass index was 25.6 ± 3.9. The quantitative ultrasound-generated T scores, a quantitative measure of BMD, averaged 0.4 ± 1.3 and −0.1 ± 1.4 for the high-impact and non-high-impact groups, respectively. After age, sex, obesity, and use of osteoporosis medication were controlled, participation in high-impact sports was a significant predictor of BMD (R2 change 3.2%, P < .001). Conclusions: This study represents the largest sample of BMD data in senior athletes to date. Senior participation in high-impact sports positively influenced bone health, even in the oldest athletes. Clinical Relevance: These data imply that high-impact exercise is a vital tool to maintain healthy BMD with active aging. PMID:23015914

A short insertion mutation disrupts genesis of miR-16 and causes increased body weight in domesticated chicken.

PubMed

Jia, Xinzheng; Lin, Huiran; Nie, Qinghua; Zhang, Xiquan; Lamont, Susan J

2016-11-03

Body weight is one of the most important quantitative traits with high heritability in chicken. We previously mapped a quantitative trait locus (QTL) for body weight by genome-wide association study (GWAS) in an F2 chicken resource population. To identify the causal mutations linked to this QTL, expression profiles were determined on livers of high-weight and low-weight chicken lines by microarray. Combining the expression pattern with SNP effects by GWAS, miR-16 was identified as the most likely potential candidate with a 3.8-fold decrease in high-weight lines. Re-sequencing revealed that a 54-bp insertion mutation in the upstream region of miR-15a-16 displayed high allele frequencies in high-weight commercial broiler line. This mutation resulted in lower miR-16 expression by introducing three novel splicing sites instead of the missing 5' terminal splicing of mature miR-16. Elevating miR-16 significantly inhibited DF-1 chicken embryo cell proliferation, consistent with a role in suppression of cellular growth. The 54-bp insertion was significantly associated with increased body weight, bone size and muscle mass. Also, the insertion mutation tended towards fixation in commercial broilers (Fst > 0.4). Our findings revealed a novel causative mutation for body weight regulation that aids our basic understanding of growth regulation in birds.

A short insertion mutation disrupts genesis of miR-16 and causes increased body weight in domesticated chicken

PubMed Central

Jia, Xinzheng; Lin, Huiran; Nie, Qinghua; Zhang, Xiquan; Lamont, Susan J.

2016-01-01

Body weight is one of the most important quantitative traits with high heritability in chicken. We previously mapped a quantitative trait locus (QTL) for body weight by genome-wide association study (GWAS) in an F2 chicken resource population. To identify the causal mutations linked to this QTL, expression profiles were determined on livers of high-weight and low-weight chicken lines by microarray. Combining the expression pattern with SNP effects by GWAS, miR-16 was identified as the most likely potential candidate with a 3.8-fold decrease in high-weight lines. Re-sequencing revealed that a 54-bp insertion mutation in the upstream region of miR-15a-16 displayed high allele frequencies in high-weight commercial broiler line. This mutation resulted in lower miR-16 expression by introducing three novel splicing sites instead of the missing 5′ terminal splicing of mature miR-16. Elevating miR-16 significantly inhibited DF-1 chicken embryo cell proliferation, consistent with a role in suppression of cellular growth. The 54-bp insertion was significantly associated with increased body weight, bone size and muscle mass. Also, the insertion mutation tended towards fixation in commercial broilers (Fst > 0.4). Our findings revealed a novel causative mutation for body weight regulation that aids our basic understanding of growth regulation in birds. PMID:27808177

High-throughput process development: determination of dynamic binding capacity using microtiter filter plates filled with chromatography resin.

PubMed

Bergander, Tryggve; Nilsson-Välimaa, Kristina; Oberg, Katarina; Lacki, Karol M

2008-01-01

Steadily increasing demand for more efficient and more affordable biomolecule-based therapies put a significant burden on biopharma companies to reduce the cost of R&D activities associated with introduction of a new drug to the market. Reducing the time required to develop a purification process would be one option to address the high cost issue. The reduction in time can be accomplished if more efficient methods/tools are available for process development work, including high-throughput techniques. This paper addresses the transitions from traditional column-based process development to a modern high-throughput approach utilizing microtiter filter plates filled with a well-defined volume of chromatography resin. The approach is based on implementing the well-known batch uptake principle into microtiter plate geometry. Two variants of the proposed approach, allowing for either qualitative or quantitative estimation of dynamic binding capacity as a function of residence time, are described. Examples of quantitative estimation of dynamic binding capacities of human polyclonal IgG on MabSelect SuRe and of qualitative estimation of dynamic binding capacity of amyloglucosidase on a prototype of Capto DEAE weak ion exchanger are given. The proposed high-throughput method for determination of dynamic binding capacity significantly reduces time and sample consumption as compared to a traditional method utilizing packed chromatography columns without sacrificing the accuracy of data obtained.

Multimedia Instructional Tools and Student Learning in an Integrated Business Applications Course

ERIC Educational Resources Information Center

Wells, Sandra H.

2018-01-01

The purpose of this quantitative descriptive comparative study was to investigate and explore the usage of multimedia instructional tools (MMITs) in an integrated business applications course to determine if there was a statistically significant difference in the gain scores between the pretest and posttest scores of high school students who used…

Access to Music Education with Regard to Race in Two Urban Areas

ERIC Educational Resources Information Center

Salvador, Karen; Allegood, Kristen

2014-01-01

This quantitative study examined access to school music instruction with regard to race in two urban areas: Detroit, Michigan, and Washington, DC, in 2009-2010. We found significant differences in the provision of music instruction between schools with high and low proportions of nonwhite enrollment, in categories including curricular offerings,…

Quantitative Evaluation of Flexibility in Undergraduate Engineering Curricula in the United Arab Emirates

ERIC Educational Resources Information Center

Darwish, Naif A.; Qasim, Muhammad

2016-01-01

In academia, smooth progression of students significantly depends on the way curricula are developed and organized. Curricula or study plans with high degree of interconnectivity between courses, multiple prerequisites, and hierarchically structured courses tend to complicate the smooth progress of the enrolled students. In this work, a rigorous…

Aligning Career Expectations with the Practice of Medicine: Physician Satisfaction

ERIC Educational Resources Information Center

Gibson, Denise D.; Borges, Nicole J.

2009-01-01

This study examined physicians' level of satisfaction with their job and the match between expectations and actual practice of specialty. Quantitative results suggested that physicians (N = 211) had a moderately high level of overall job satisfaction with no significant differences found between men and women physicians. Among those in primary…

Evaluating Serious Games through User Experience and Performance Assessment

ERIC Educational Resources Information Center

Barton, Irving Gary, Jr.

2017-01-01

Military education is held to high standards for our servicemen and women. The purpose of this quantitative, comparative study was to determine if significant differences existed in learning styles relative to military experience as determined by learning in a serious game environment. Study results are expected to advance the state of research in…

High School Students' Informal Reasoning on a Socio-Scientific Issue: Qualitative and Quantitative Analyses

ERIC Educational Resources Information Center

Wu, Ying-Tien; Tsai, Chin-Chung

2007-01-01

Recently, the significance of learners' informal reasoning on socio-scientific issues has received increasing attention among science educators. To gain deeper insights into this important issue, an integrated analytic framework was developed in this study. With this framework, 71 Grade 10 students' informal reasoning about nuclear energy usage…

Quantitative analysis of 18F-NaF dynamic PET/CT cannot differentiate malignant from benign lesions in multiple myeloma

PubMed Central

Sachpekidis, Christos; Hillengass, Jens; Goldschmidt, Hartmut; Anwar, Hoda; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-01-01

A renewed interest has been recently developed for the highly sensitive bone-seeking radiopharmaceutical 18F-NaF. Aim of the present study is to evaluate the potential utility of quantitative analysis of 18F-NaF dynamic PET/CT data in differentiating malignant from benign degenerative lesions in multiple myeloma (MM). 80 MM patients underwent whole-body PET/CT and dynamic PET/CT scanning of the pelvis with 18F-NaF. PET/CT data evaluation was based on visual (qualitative) assessment, semi-quantitative (SUV) calculations, and absolute quantitative estimations after application of a 2-tissue compartment model and a non-compartmental approach leading to the extraction of fractal dimension (FD). In total 263 MM lesions were demonstrated on 18F-NaF PET/CT. Semi-quantitative and quantitative evaluations were performed for 25 MM lesions as well as for 25 benign, degenerative and traumatic lesions. Mean SUVaverage for MM lesions was 11.9 and mean SUVmax was 23.2. Respectively, SUVaverage and SUVmax for degenerative lesions were 13.5 and 20.2. Kinetic analysis of 18F-NaF revealed the following mean values for MM lesions: K1 = 0.248 (1/min), k3 = 0.359 (1/min), influx (Ki) = 0.107 (1/min), FD = 1.382, while the respective values for degenerative lesions were: K1 = 0.169 (1/min), k3 = 0.422 (1/min), influx (Ki) = 0.095 (1/min), FD = 1. 411. No statistically significant differences between MM and benign degenerative disease regarding SUVaverage, SUVmax, K1, k3 and influx (Ki) were demonstrated. FD was significantly higher in degenerative than in malignant lesions. The present findings show that quantitative analysis of 18F-NaF PET data cannot differentiate malignant from benign degenerative lesions in MM patients, supporting previously published results, which reflect the limited role of 18F-NaF PET/CT in the diagnostic workup of MM. PMID:28913153

Tissue-based quantitative proteome analysis of human hepatocellular carcinoma using tandem mass tags.

PubMed

Megger, Dominik Andre; Rosowski, Kristin; Ahrens, Maike; Bracht, Thilo; Eisenacher, Martin; Schlaak, Jörg F; Weber, Frank; Hoffmann, Andreas-Claudius; Meyer, Helmut E; Baba, Hideo A; Sitek, Barbara

2017-03-01

Human hepatocellular carcinoma (HCC) is a severe malignant disease, and accurate and reliable diagnostic markers are still needed. This study was aimed for the discovery of novel marker candidates by quantitative proteomics. Proteomic differences between HCC and nontumorous liver tissue were studied by mass spectrometry. Among several significantly upregulated proteins, translocator protein 18 (TSPO) and Ras-related protein Rab-1A (RAB1A) were selected for verification by immunohistochemistry in an independent cohort. For RAB1A, a high accuracy for the discrimination of HCC and nontumorous liver tissue was observed. RAB1A was verified to be a potent biomarker candidate for HCC.

Quantitative assessment of anthrax vaccine immunogenicity using the dried blood spot matrix.

PubMed

Schiffer, Jarad M; Maniatis, Panagiotis; Garza, Ilana; Steward-Clark, Evelene; Korman, Lawrence T; Pittman, Phillip R; Mei, Joanne V; Quinn, Conrad P

2013-03-01

The collection, processing and transportation to a testing laboratory of large numbers of clinical samples during an emergency response situation present significant cost and logistical issues. Blood and serum are common clinical samples for diagnosis of disease. Serum preparation requires significant on-site equipment and facilities for immediate processing and cold storage, and significant costs for cold-chain transport to testing facilities. The dried blood spot (DBS) matrix offers an alternative to serum for rapid and efficient sample collection with fewer on-site equipment requirements and considerably lower storage and transport costs. We have developed and validated assay methods for using DBS in the quantitative anti-protective antigen IgG enzyme-linked immunosorbent assay (ELISA), one of the primary assays for assessing immunogenicity of anthrax vaccine and for confirmatory diagnosis of Bacillus anthracis infection in humans. We have also developed and validated high-throughput data analysis software to facilitate data handling for large clinical trials and emergency response. Published by Elsevier Ltd.

Association between periodontal condition and subgingival microbiota in women during pregnancy: a longitudinal study.

PubMed

Borgo, Priscila Viola; Rodrigues, Viviane Aparecida Arenas; Feitosa, Alfredo Carlos Rodrigues; Xavier, Karla Correa Barcelos; Avila-Campos, Mario Julio

2014-01-01

In this study, the gingival conditions and the quantitative detection for Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Porphyromonas gingivalis and Prevotella intermedia in pregnant women were determined. Quantitative determinations of periodontal bacteria by using a SyBr green system in women during pregnancy were performed. Women at the 2nd and 3rd trimesters of pregnancy and non-pregnant women were included in this study. A. actinomycetemcomitans was observed in high numbers in women at the 2nd and 3rd trimesters of pregnancy with a significant difference (p<0.05). F. nucleatum and P. intermedia were also observed in high levels. Our results show that pregnant women are more susceptible to gingivitis, and the presence of A. actinomycetemcomitans in subgingival biofilm might be taken into account for the treatment of periodontal disease.

Effects of quantitative electroencephalography based neurofeedback training on autonomous regulations in patients with alcohol use disorder.

PubMed

Ko, Sangjin; Park, Wanju

2018-06-02

The study investigated whether neurofeedback training can normalize the excessive high-beta and low alpha waves indicative of hyperarousal, and subsequently improve autonomous regulation based on the self-determination theory in alcohol use disorders. A nonequivalent control group pretest-posttest design was used. Data were collected using self-report questionnaires from 36 Korean inpatients who met the Alcohol Use Disorder Identification Test in Korea criteria. Data were collected from quantitative electroencephalography to assess alpha (8-12 Hz) and high-beta (21-30 Hz) waves for hyperarousal. The questionnaires included Basic Psychological Need Satisfaction scales that assessed autonomy, competence, and relatedness, and the Alcohol Abstinence Self-Efficacy Scale and Treatment Self-Regulation Questionnaire. The experimental group underwent 10 sessions of neurofeedback training over four weeks. Data were analyzed using the chi-squared, Mann-Whitney U, and Wilcoxon signed-rank tests. In the experimental group, the alpha wave was increased in 15 of 19 sites and high-beta waves were decreased in 15 of 19 sites, but this difference was not significant. However, high-beta waves were increased in 15 of 19 sites in the control group, with seven sites (Fz, Cz, Pz, Fp2, F4, C4, and P4) showing significant increases. The experimental group showed a significant increase in basic psychological need satisfaction, alcohol abstinence self-efficacy, and self-regulation compared with the control group. Neurofeedback training is recommended for improving autonomous regulation in alcohol use disorder as a nursing intervention. However, for significantly attenuating hyperarousal through brain wave correction, it may be necessary to increase the number of neurofeedback sessions. Copyright © 2018. Published by Elsevier B.V.

Stochastic optical reconstruction microscopy-based relative localization analysis (STORM-RLA) for quantitative nanoscale assessment of spatial protein organization.

PubMed

Veeraraghavan, Rengasayee; Gourdie, Robert G

2016-11-07

The spatial association between proteins is crucial to understanding how they function in biological systems. Colocalization analysis of fluorescence microscopy images is widely used to assess this. However, colocalization analysis performed on two-dimensional images with diffraction-limited resolution merely indicates that the proteins are within 200-300 nm of each other in the xy-plane and within 500-700 nm of each other along the z-axis. Here we demonstrate a novel three-dimensional quantitative analysis applicable to single-molecule positional data: stochastic optical reconstruction microscopy-based relative localization analysis (STORM-RLA). This method offers significant advantages: 1) STORM imaging affords 20-nm resolution in the xy-plane and <50 nm along the z-axis; 2) STORM-RLA provides a quantitative assessment of the frequency and degree of overlap between clusters of colabeled proteins; and 3) STORM-RLA also calculates the precise distances between both overlapping and nonoverlapping clusters in three dimensions. Thus STORM-RLA represents a significant advance in the high-throughput quantitative assessment of the spatial organization of proteins. © 2016 Veeraraghavan and Gourdie. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Prognostic significance of normal quantitative planar thallium-201 stress scintigraphy in patients with chest pain

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

Wackers, F.J.; Russo, D.J.; Russo, D.

The prognostic significance of normal quantitative planar thallium-201 stress scintigraphy was evaluated in patients with a chest pain syndrome. The prevalence of cardiac events during follow-up was related to the pretest (that is, before stress scintigraphy) likelihood of coronary artery disease determined on the basis of symptoms, age, sex and stress electrocardiography. In a consecutive series of 344 patients who had adequate thallium-201 stress scintigrams, 95 had unequivocally normal studies by quantitative analysis. The pretest likelihood of coronary artery disease in the 95 patients had a bimodal distribution. During a mean follow-up period of 22 +/- 3 months, no patientmore » died. Three patients (3%) had a cardiac event: two of these patients (pretest likelihood of coronary artery disease 54 and 94%) had a nonfatal myocardial infarction 8 and 22 months, respectively, after stress scintigraphy, and one patient (pretest likelihood 98%) underwent percutaneous transluminal coronary angioplasty 16 months after stress scintigraphy for persisting anginal complaints. Three patients were lost to follow-up; all three had a low pretest likelihood of coronary artery disease. It is concluded that patients with chest pain and normal findings on quantitative thallium-201 scintigraphy have an excellent prognosis. Cardiac events are rare (infarction rate 1% per year) and occur in patients with a moderate to high pretest likelihood of coronary artery disease.« less

Quantitative agreement between [(15)O]H2O PET and model free QUASAR MRI-derived cerebral blood flow and arterial blood volume.

PubMed

Heijtel, D F R; Petersen, E T; Mutsaerts, H J M M; Bakker, E; Schober, P; Stevens, M F; van Berckel, B N M; Majoie, C B L M; Booij, J; van Osch, M J P; van Bavel, E T; Boellaard, R; Lammertsma, A A; Nederveen, A J

2016-04-01

The purpose of this study was to assess whether there was an agreement between quantitative cerebral blood flow (CBF) and arterial cerebral blood volume (CBVA) measurements by [(15)O]H2O positron emission tomography (PET) and model-free QUASAR MRI. Twelve healthy subjects were scanned within a week in separate MRI and PET imaging sessions, after which quantitative and qualitative agreement between both modalities was assessed for gray matter, white matter and whole brain region of interests (ROI). The correlation between CBF measurements obtained with both modalities was moderate to high (r(2): 0.28-0.60, P < 0.05), although QUASAR significantly underestimated CBF by 30% (P < 0.001). CBVA was moderately correlated (r(2): 0.28-0.43, P < 0.05), with QUASAR yielding values that were only 27% of the [(15)O]H2O-derived values (P < 0.001). Group-wise voxel statistics identified minor areas with significant contrast differences between [(15)O]H2O PET and QUASAR MRI, indicating similar qualitative CBVA and CBF information by both modalities. In conclusion, the results of this study demonstrate that QUASAR MRI and [(15)O]H2O PET provide similar CBF and CBVA information, but with systematic quantitative discrepancies. Copyright © 2016 John Wiley & Sons, Ltd.

Comparative quantitative proteomics analysis of the ABA response of roots of drought-sensitive and drought-tolerant wheat varieties identifies proteomic signatures of drought adaptability.

PubMed

Alvarez, Sophie; Roy Choudhury, Swarup; Pandey, Sona

2014-03-07

Wheat is one of the most highly cultivated cereals in the world. Like other cultivated crops, wheat production is significantly affected by abiotic stresses such as drought. Multiple wheat varieties suitable for different geographical regions of the world have been developed that are adapted to different environmental conditions; however, the molecular basis of such adaptations remains unknown in most cases. We have compared the quantitative proteomics profile of the roots of two different wheat varieties, Nesser (drought-tolerant) and Opata (drought-sensitive), in the absence and presence of abscisic acid (ABA, as a proxy for drought). A labeling LC-based quantitative proteomics approach using iTRAQ was applied to elucidate the changes in protein abundance levels. Quantitative differences in protein levels were analyzed for the evaluation of inherent differences between the two varieties as well as the overall and variety-specific effect of ABA on the root proteome. This study reveals the most elaborate ABA-responsive root proteome identified to date in wheat. A large number of proteins exhibited inherently different expression levels between Nesser and Opata. Additionally, significantly higher numbers of proteins were ABA-responsive in Nesser roots compared with Opata roots. Furthermore, several proteins showed variety-specific regulation by ABA, suggesting their role in drought adaptation.

Joint association of sleep problems and psychosocial working conditions with registered long-term sickness absence. A Danish cohort study.

PubMed

Madsen, Ida Eh; Larsen, Ann D; Thorsen, Sannie V; Pejtersen, Jan H; Rugulies, Reiner; Sivertsen, Børge

2016-07-01

Sleep problems and adverse psychosocial working conditions are associated with increased risk of long-term sickness absence. Because sleep problems affect role functioning they may also exacerbate any effects of psychosocial working conditions and vice versa. We examined whether sleep problems and psychosocial working conditions interact in their associations with long-term sickness absence. We linked questionnaire data from participants to two surveys of random samples of the Danish working population (N=10 752) with registries on long-term sick leave during five years after questionnaire response. We defined sleep problems by self-reported symptoms and/or register data on hypnotics purchases of hypnotics. Psychosocial working conditions included quantitative and emotional demands, influence, supervisor recognition and social support, leadership quality, and social support from colleagues. Using time-to-event models, we calculated hazard ratios (HR) and differences and examined interaction as departure from multiplicativity and additivity. During 40 165 person-years of follow-up, we identified 2313 episodes of long-terms sickness absence. Sleep problems predicted risk of long-term sickness absence [HR 1.54, 95% confidence interval (95% CI) 1.38-1.73]. This association was statistically significantly stronger among participants with high quantitative demands and weaker among those with high supervisor recognition (P<0.0001). High quantitative demands exacerbated the association of sleep problems with risk of long-term sickness absence whereas high supervisor recognition buffered this association. To prevent long-term sickness absence among employees with sleep problems, workplace modifications focusing on quantitative demands and supervisor recognition may be considered. Workplace interventions for these factors may more effectively prevent sickness absence when targeted at this group. The efficacy and effectiveness of such interventions needs to be established in future studies.

Time-resolved magnetic resonance angiography (MRA) at 3.0 Tesla for evaluation of hemodynamic characteristics of vascular malformations: description of distinct subgroups.

PubMed

Hammer, Simone; Uller, Wibke; Manger, Florentine; Fellner, Claudia; Zeman, Florian; Wohlgemuth, Walter A

2017-01-01

Quantitative evaluation of hemodynamic characteristics of arteriovenous and venous malformations using time-resolved magnetic resonance angiography (MRA) at 3.0 Tesla. Time-resolved MRA with interleaved stochastic trajectories (TWIST) at 3.0 Tesla was studied in 83 consecutive patients with venous malformations (VM) and arteriovenous malformations (AVM). Enhancement characteristics were calculated as percentage increase of signal intensity above baseline over time. Maximum percentage signal intensity increase (signal max ), time intervals between onset of arterial enhancement and lesion enhancement (t onset ), and time intervals between beginning of lesion enhancement and maximum percentage of lesion enhancement (t max ) were analyzed. All AVMs showed a high-flow hemodynamic pattern. Two significantly different (p < 0.001) types of venous malformations emerged: VMs with arteriovenous fistulas (AVF) (median signal max 737 %, IQR [interquartile range] = 511 - 1182 %; median t onset 5 s, IQR = 5 - 10 s; median t max 35 s, IQR = 26 - 40 s) and without AVFs (median signal max 284 %, IQR = 177-432 %; median t onset 23 s, IQR = 15 - 30 s; median t max 60 s, IQR = 55 - 75 s). Quantitative evaluation of time-resolved MRA at 3.0 Tesla provides hemodynamic characterization of vascular malformations. VMs can be subclassified into two hemodynamic subgroups due to presence or absence of AVFs. • Time-resolved MRA at 3.0 Tesla provides quantitative hemodynamic characterization of vascular malformations. • Malformations significantly differ in time courses of enhancement and signal intensity increase. • AVMs show a distinctive high-flow hemodynamic pattern. • Two significantly different types of VMs emerged: VMs with and without AVFs.

Teaching science in a technology rich environment: Probeware's effect on student attitude and achievement

NASA Astrophysics Data System (ADS)

Zelmanowicz, Marc

Purpose The use of technology in the science classroom has been a major part of the initiative toward increasing student attitude and achievement in Science, Technology, Education and Math [STEM] education in the United States. The purpose of this study was to determine the extent to which the use of probeware in a high school science living environment classroom impacts student attitude towards science and/or student achievement on standards-based assessments. This study sought to answer the following quantitative questions with a qualitative component: To what extent does the use of probeware in a high school level living environment course influence student attitudes toward science compared to students who are not using probeware? What is the impact, if any, on student achievement in a living environment course, as measured by New York State Living Environment Regents [NYSLER] exam grades, between students who use probeware and students who do not? Is there a significant difference between the two groups with regard to achieving mastery on the NYSLER exam? Sample The participants in the study were Living Environment students of a suburban high school outside of New York City. Methods The quasiexperimental study examined the effects of the replacement of traditional scientific equipment with probeware on student attitude and achievement in a living environment classroom. Student attitude was measured by the modified Attitude Toward Science Inventory [mATSI] and student achievement was measured by the New York State Living Environment Regents [NSLER] Exam. Descriptive statistics, ANCOVA and hierarchical regression analysis were conducted to answer the research questions in this study. A qualitative component was included to enhance the understanding of the quantitative analysis. Major Findings Through this study, results demonstrated a statistically significant impact of probeware on student attitude, but did not show a statistically significant impact of probeware on student achievement or achievement of mastery; The qualitative component confirmed that probeware positively impact student attitude and achievement. With regards to achievement, the qualitative interviews contradicted the quantitative analysis. Significance Results from this study add to the body of research that probeware can impact student attitude towards science education.

TROP2 correlates with microvessel density and poor prognosis in hilar cholangiocarcinoma.

PubMed

Ning, Shanglei; Guo, Sen; Xie, Jianjun; Xu, Yunfei; Lu, Xiaofei; Chen, Yuxin

2013-02-01

Trophoblast cell surface antigen 2 (TROP2) was found to be associated with tumor progression and poor prognosis in a variety of epithelial carcinomas. The aim of the study was to investigate TROP2 expression and its prognostic impact in hilar cholangiocarcinoma. Immunohistochemistry and quantitative real-time PCR were used to determine TROP2 expression in surgical specimens from 70 hilar cholangiocarcinoma patients receiving radical resection. The relationship between TROP2 expression and microvessel density was investigated and standard statistical analysis was used to evaluate TROP2 prognosis significance in hilar cholangiocarcinoma. High TROP2 expression by immunohistochemistry was found in 43 (61.4 %) of the 70 tumor specimens. Quantitative real-time PCR confirmed that TROP2 level in tumor was significantly higher than in non-tumoral biliary tissues (P = 0.001). Significant correlations were found between TROP2 expression and histological differentiation (P = 0.016) and tumor T stage (P = 0.031) in hilar cholangiocarcinoma. TROP2 expression correlated with microvessel density in hilar cholangiocarcinoma (P = 0.026). High TROP2 expression patients had a significantly poorer overall survival rate than those with low TROP2 expression (30 vs. 68.5 %, P = 0.001), and multivariate Cox regression analysis indicated TROP2 as an independent prognostic factor for hilar cholangiocarcinoma (P = 0.004). TROP2 expression correlates with microvessel density significantly and is an independent prognostic factor in human hilar cholangiocarcinoma.

Genetic Control of Fruit Vitamin C Contents1

PubMed Central

Davey, Mark W.; Kenis, Katrien; Keulemans, Johan

2006-01-01

An F1 progeny derived from a cross between the apple (Malus x domestica) cultivars Telamon and Braeburn was used to identify quantitative trait loci (QTL) linked to the vitamin C (l-ascorbate [l-AA]) contents of fruit skin and flesh (cortex) tissues. We identified up to three highly significant QTLs for both the mean l-AA and the mean total l-AA contents of fruit flesh on both parental genetic linkage maps, confirming the quantitative nature of these traits. These QTLs account for up to a maximum of 60% of the total population variation observed in the progeny, and with a maximal individual contribution of 31% per QTL. QTLs common to both parents were identified on linkage groups (LGs) 6, 10, and 11 of the Malus reference map, while each parent also had additional unique QTLs on other LGs. Interestingly, one strong QTL on LG-17 of the Telamon linkage map colocalized with a highly significant QTL associated with flesh browning, and a minor QTL for dehydroascorbate content, supporting earlier work that links fruit l-AA contents with the susceptibility of hardfruit to postharvest browning. We also found significant minor QTLs for skin l-AA and total l-AA (l-AA + dehydroascorbate) contents in Telamon. Currently, little is known about the genetic determinants underlying tissue l-AA homeostasis, but the presence of major, highly significant QTL in both these apple genotypes under field conditions suggests the existence of common control mechanisms, allelic heterozygosity, and helps outline strategies and the potential for the molecular breeding of these traits. PMID:16844833

Reactivity to stress and the cognitive components of math disability in grade 1 children.

PubMed

MacKinnon McQuarrie, Maureen A; Siegel, Linda S; Perry, Nancy E; Weinberg, Joanne

2014-01-01

This study investigated the relationship among working memory, processing speed, math performance, and reactivity to stress in 83 Grade 1 children. Specifically, 39 children with math disability (MD) were compared to 44 children who are typically achieving (TA) in mathematics. It is the first study to use a physiological index of stress (salivary cortisol levels) to measure children's reactivity while completing tasks that assess the core components of MD: working memory for numbers, working memory for words, digits backward, letter number sequence, digit span forward, processing speed for numbers and words, block rotation, and math tasks. Grade 1 children with MD obtained significantly lower scores on the letter number sequence and quantitative concepts tasks. Higher levels of reactivity significantly predicted poorer performance on the working memory for numbers, working memory for words, and quantitative concepts tasks for Grade 1 children, regardless of math ability. Grade 1 children with MD and higher reactivity had significantly lower scores on the letter number sequence task than the children with MD and low reactivity. The findings suggest that high reactivity impairs performance in working memory and math tasks in Grade 1 children, and young children with high reactivity may benefit from interventions aimed at lowering anxiety in stressful situations, which may improve learning. © Hammill Institute on Disabilities 2012.

Reactivity to Stress and the Cognitive Components of Math Disability in Grade 1 Children

PubMed Central

MacKinnon McQuarrie, Maureen A.; Siegel, Linda S.; Perry, Nancy E.; Weinberg, Joanne

2016-01-01

This study investigated the relationship among working memory, processing speed, math performance, and reactivity to stress in 83 Grade 1 children. Specifically, 39 children with math disability (MD) were compared to 44 children who are typically achieving (TA) in mathematics. It is the first study to use a physiological index of stress (salivary cortisol levels) to measure children’s reactivity while completing tasks that assess the core components of MD: working memory for numbers, working memory for words, digits backward, letter number sequence, digit span forward, processing speed for numbers and words, block rotation, and math tasks. Grade 1 children with MD obtained significantly lower scores on the letter number sequence and quantitative concepts tasks. Higher levels of reactivity significantly predicted poorer performance on the working memory for numbers, working memory for words, and quantitative concepts tasks for Grade 1 children, regardless of math ability. Grade 1 children with MD and higher reactivity had significantly lower scores on the letter number sequence task than the children with MD and low reactivity. The findings suggest that high reactivity impairs performance in working memory and math tasks in Grade 1 children, and young children with high reactivity may benefit from interventions aimed at lowering anxiety in stressful situations, which may improve learning. PMID:23124381

Improving chemical education from high school to college using a more hands-on approach

NASA Astrophysics Data System (ADS)

Ruddick, Kristie Winfield

In this work, various alternative teaching methods and activities for chemical education are developed, presented, and evaluated. In the first study, an original hands-on activity using LEGO® blocks to model ionic chemical formulas is presented together with quantitative and qualitative data regarding its educational effectiveness. Students explore cation to anion ratios using LEGO® blocks to represent trivalent, divalent and monovalent cations and anions. High school chemistry students who participated in the LEGO® lab showed significantly higher post-test scores than other students. The second study grows out of the creation of a computational lab module that is shown to significantly increase student learning in the subject of molecular orbital theory in first semester college General Chemistry. The third and final study presented is a course redesign project for college CHEM 1100, Preparation for General Chemistry. In this project the classroom is “flipped”. Students watch video lectures at home, and spend class time working with peers and the instructor on problem solving activities. The results presented here are one of the first quantitative studies showing the effectiveness of “flipping the classroom”. Students who were taught using the Reverse-Instruction (RI) method had significantly higher success in both the Preparation for General Chemistry course and traditionally taught General Chemistry I the following semester.

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

PubMed Central

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-01-01

Local surface charge density of lipid membranes influences membrane–protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values. PMID:27561322

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

NASA Astrophysics Data System (ADS)

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-08-01

Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy.

PubMed

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-08-26

Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

Qualitative and quantitative analyses of flavonoids in Spirodela polyrrhiza by high-performance liquid chromatography coupled with mass spectrometry.

PubMed

Qiao, Xue; He, Wen-ni; Xiang, Cheng; Han, Jian; Wu, Li-jun; Guo, De-an; Ye, Min

2011-01-01

Spirodela polyrrhiza (L.) Schleid. is a traditional Chinese herbal medicine for the treatment of influenza. Despite its wide use in Chinese medicine, no report on quality control of this herb is available so far. To establish qualitative and quantitative analytical methods by high-performance liquid chromatography (HPLC) coupled with mass spectrometry (MS) for the quality control of S. polyrrhiza. The methanol extract of S. polyrrhiza was analysed by HPLC/ESI-MS(n). Flavonoids were identified by comparing with reference standards or according to their MS(n) (n = 2-4) fragmentation behaviours. Based on LC/MS data, a standardised HPLC fingerprint was established by analysing 15 batches of commercial herbal samples. Furthermore, quantitative analysis was conducted by determining five major flavonoids, namely luteolin 8-C-glucoside, apigenin 8-C-glucoside, luteolin 7-O-glucoside, apigenin 7-O-glucoside and luteolin. A total of 18 flavonoids were identified by LC/MS, and 14 of them were reported from this herb for the first time. The HPLC fingerprints contained 10 common peaks, and could differentiate good quality batches from counterfeits. The total contents of five major flavonoids in S. polyrrhiza varied significantly from 4.28 to 19.87 mg/g. Qualitative LC/MS and quantitative HPLC analytical methods were established for the comprehensive quality control of S. polyrrhiza. Copyright © 2011 John Wiley & Sons, Ltd.

Digital pathology and image analysis for robust high-throughput quantitative assessment of Alzheimer disease neuropathologic changes.

PubMed

Neltner, Janna Hackett; Abner, Erin Lynn; Schmitt, Frederick A; Denison, Stephanie Kay; Anderson, Sonya; Patel, Ela; Nelson, Peter T

2012-12-01

Quantitative neuropathologic methods provide information that is important for both research and clinical applications. The technologic advancement of digital pathology and image analysis offers new solutions to enable valid quantification of pathologic severity that is reproducible between raters regardless of experience. Using an Aperio ScanScope XT and its accompanying image analysis software, we designed algorithms for quantitation of amyloid and tau pathologies on 65 β-amyloid (6F/3D antibody) and 48 phospho-tau (PHF-1)-immunostained sections of human temporal neocortex. Quantitative digital pathologic data were compared with manual pathology counts. There were excellent correlations between manually counted and digitally analyzed neuropathologic parameters (R² = 0.56-0.72). Data were highly reproducible among 3 participants with varying degrees of expertise in neuropathology (intraclass correlation coefficient values, >0.910). Digital quantification also provided additional parameters, including average plaque area, which shows statistically significant differences when samples are stratified according to apolipoprotein E allele status (average plaque area, 380.9 μm² in apolipoprotein E [Latin Small Letter Open E]4 carriers vs 274.4 μm² for noncarriers; p < 0.001). Thus, digital pathology offers a rigorous and reproducible method for quantifying Alzheimer disease neuropathologic changes and may provide additional insights into morphologic characteristics that were previously more challenging to assess because of technical limitations.

Digital histologic analysis reveals morphometric patterns of age-related involution in breast epithelium and stroma.

PubMed

Sandhu, Rupninder; Chollet-Hinton, Lynn; Kirk, Erin L; Midkiff, Bentley; Troester, Melissa A

2016-02-01

Complete age-related regression of mammary epithelium, often termed postmenopausal involution, is associated with decreased breast cancer risk. However, most studies have qualitatively assessed involution. We quantitatively analyzed epithelium, stroma, and adipose tissue from histologically normal breast tissue of 454 patients in the Normal Breast Study. High-resolution digital images of normal breast hematoxylin and eosin-stained slides were partitioned into epithelium, adipose tissue, and nonfatty stroma. Percentage area and nuclei per unit area (nuclear density) were calculated for each component. Quantitative data were evaluated in association with age using linear regression and cubic spline models. Stromal area decreased (P = 0.0002), and adipose tissue area increased (P < 0.0001), with an approximate 0.7% change in area for each component, until age 55 years when these area measures reached a steady state. Although epithelial area did not show linear changes with age, epithelial nuclear density decreased linearly beginning in the third decade of life. No significant age-related trends were observed for stromal or adipose nuclear density. Digital image analysis offers a high-throughput method for quantitatively measuring tissue morphometry and for objectively assessing age-related changes in adipose tissue, stroma, and epithelium. Epithelial nuclear density is a quantitative measure of age-related breast involution that begins to decline in the early premenopausal period. Copyright © 2015 Elsevier Inc. All rights reserved.

LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data.

PubMed

Zhang, Wei; Zhang, Jiyang; Xu, Changming; Li, Ning; Liu, Hui; Ma, Jie; Zhu, Yunping; Xie, Hongwei

2012-12-01

Database searching based methods for label-free quantification aim to reconstruct the peptide extracted ion chromatogram based on the identification information, which can limit the search space and thus make the data processing much faster. The random effect of the MS/MS sampling can be remedied by cross-assignment among different runs. Here, we present a new label-free fast quantitative analysis tool, LFQuant, for high-resolution LC-MS/MS proteomics data based on database searching. It is designed to accept raw data in two common formats (mzXML and Thermo RAW), and database search results from mainstream tools (MASCOT, SEQUEST, and X!Tandem), as input data. LFQuant can handle large-scale label-free data with fractionation such as SDS-PAGE and 2D LC. It is easy to use and provides handy user interfaces for data loading, parameter setting, quantitative analysis, and quantitative data visualization. LFQuant was compared with two common quantification software packages, MaxQuant and IDEAL-Q, on the replication data set and the UPS1 standard data set. The results show that LFQuant performs better than them in terms of both precision and accuracy, and consumes significantly less processing time. LFQuant is freely available under the GNU General Public License v3.0 at http://sourceforge.net/projects/lfquant/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Is quantitative oestrogen receptor expression useful in the evaluation of the clinical prognosis? Analysis of a homogeneous series of 797 patients with prospective determination of the ER status using simultaneous EIA and IHC.

PubMed

Mazouni, Chafika; Bonnier, Pascal; Goubar, Aïcha; Romain, Sylvie; Martin, Pierre-Marie

2010-10-01

Oestrogen receptor (ER) determination in breast cancer (BC) is a major yardstick for the prognosis and for response to hormonal therapy (HT). As several techniques have been proposed for ER quantification, the purpose of our study was to assess whether the qualitative or quantitative analysis of ER expression might influence the prognosis and response to treatment. We analysed overall survival (OS) and disease-free survival (DFS) in 797 primary BC cases with ER determination by enzyme immunoassay (EIA) and immunohistochemistry (IHC). The clinical impact according to qualitative or quantitative analysis of ER expression was assessed. Response to HT was evaluated according to quantitative EIA-determined ER expression levels. According to the qualitative analysis of ER expression, patients with EIA-determined and IHC-determined ER-positive tumours had significantly longer OS and DFS (p<0.001). The analysis stratified on quartiles of ER levels showed significantly different outcomes according to EIA- and IHC-determined subgroups. In the group of patients who received adjuvant treatment, 5-year OS was significantly different between the groups, with a clear benefit for the highest EIA-determined ER quartiles (p<0.001). Comparatively, in terms of 5-year DFS, a clear separation was noted between groups for adjuvant treatment (p<0.001). The group with moderate ER+ values was clearly distinct from the ER-negative population. Quantitative ER expression helped to better distinguish the beneficial or detrimental effect of HT within quartiles of ER-expressing tumours. Based on the STEPP analysis which showed a trend towards an ER effect on DFS as a function of HT assignment, we confirm the benefit of HT in patients with a very high EIA-determined ER level and a detrimental impact on negative and weakly positive groups. Quantitative ER expression in BC helps to better discriminate heterogeneity in clinical outcome and response to HT. Copyright © 2010 Elsevier Ltd. All rights reserved.

Quantitative evaluation of protocorm growth and fungal colonization in Bletilla striata (Orchidaceae) reveals less-productive symbiosis with a non-native symbiotic fungus.

PubMed

Yamamoto, Tatsuki; Miura, Chihiro; Fuji, Masako; Nagata, Shotaro; Otani, Yuria; Yagame, Takahiro; Yamato, Masahide; Kaminaka, Hironori

2017-02-21

In nature, orchid plants depend completely on symbiotic fungi for their nutrition at the germination and the subsequent seedling (protocorm) stages. However, only limited quantitative methods for evaluating the orchid-fungus interactions at the protocorm stage are currently available, which greatly constrains our understanding of the symbiosis. Here, we aimed to improve and integrate quantitative evaluations of the growth and fungal colonization in the protocorms of a terrestrial orchid, Blettila striata, growing on a plate medium. We achieved both symbiotic and asymbiotic germinations for the terrestrial orchid B. striata. The protocorms produced by the two germination methods grew almost synchronously for the first three weeks. At week four, however, the length was significantly lower in the symbiotic protocorms. Interestingly, the dry weight of symbiotic protocorms did not significantly change during the growth period, which implies that there was only limited transfer of carbon compounds from the fungus to the protocorms in this relationship. Next, to evaluate the orchid-fungus interactions, we developed an ink-staining method to observe the hyphal coils in protocorms without preparing thin sections. Crushing the protocorm under the coverglass enables us to observe all hyphal coils in the protocorms with high resolution. For this observation, we established a criterion to categorize the stages of hyphal coils, depending on development and degradation. By counting the symbiotic cells within each stage, it was possible to quantitatively evaluate the orchid-fungus symbiosis. We describe a method for quantitative evaluation of orchid-fungus symbiosis by integrating the measurements of plant growth and fungal colonization. The current study revealed that although fungal colonization was observed in the symbiotic protocorms, the weight of the protocorm did not significantly increase, which is probably due to the incompatibility of the fungus in this symbiosis. These results suggest that fungal colonization and nutrition transfer can be differentially regulated in the symbiosis. The evaluation methods developed in this study can be used to study various quantitative aspects of the orchid-fungus symbiosis.

Putting tools in the toolbox: Development of a free, open-source toolbox for quantitative image analysis of porous media.

NASA Astrophysics Data System (ADS)

Iltis, G.; Caswell, T. A.; Dill, E.; Wilkins, S.; Lee, W. K.

2014-12-01

X-ray tomographic imaging of porous media has proven to be a valuable tool for investigating and characterizing the physical structure and state of both natural and synthetic porous materials, including glass bead packs, ceramics, soil and rock. Given that most synchrotron facilities have user programs which grant academic researchers access to facilities and x-ray imaging equipment free of charge, a key limitation or hindrance for small research groups interested in conducting x-ray imaging experiments is the financial cost associated with post-experiment data analysis. While the cost of high performance computing hardware continues to decrease, expenses associated with licensing commercial software packages for quantitative image analysis continue to increase, with current prices being as high as $24,000 USD, for a single user license. As construction of the Nation's newest synchrotron accelerator nears completion, a significant effort is being made here at the National Synchrotron Light Source II (NSLS-II), Brookhaven National Laboratory (BNL), to provide an open-source, experiment-to-publication toolbox that reduces the financial and technical 'activation energy' required for performing sophisticated quantitative analysis of multidimensional porous media data sets, collected using cutting-edge x-ray imaging techniques. Implementation focuses on leveraging existing open-source projects and developing additional tools for quantitative analysis. We will present an overview of the software suite that is in development here at BNL including major design decisions, a demonstration of several test cases illustrating currently available quantitative tools for analysis and characterization of multidimensional porous media image data sets and plans for their future development.

Symposium Proceedings on Quantitative Feedback Theory Held in Fairborn, Ohio on 2-4 August 1992.

DTIC Science & Technology

1992-08-01

modification. This permits a drastic reduction in the cost of feedback, in terms of loop bandwidth and effect of sensor noise . This is the first...High- frequency Bound ( UHB ) but its main use is to ensure that at high frequencies the controlled system cannot go unstable and has sufficient noise ...a 5-cascaded multiple-loop feedback system giving significant reductions in sensor noise amplification (peak reduced by a factor of 4), is

Quantitative phenotyping of X-disease resistance in chokecherry using real-time PCR.

PubMed

Huang, Danqiong; Walla, James A; Dai, Wenhao

2014-03-01

A quantitative real-time SYBR Green PCR (qPCR) assay has been developed to detect and quantify X-disease phytoplasmas in chokecherry. An X-disease phytoplasma-specific and high sensitivity primer pair was designed based on the 16S rRNA gene sequence of X-disease phytoplasmas. This primer pair was specific to the 16SrIII group (X-disease) phytoplasmas. The qPCR method can quantify phytoplasmas from a DNA mix (a mix of both chokecherry and X-disease phytoplasma DNA) at as low as 0.001 ng, 10-fold lower than conventional PCR using the same primer pair. A significant correlation between the copy number of phytoplasmas and visual phenotypic rating scores of X-disease resistance in chokecherry plants was observed. Disease resistant chokecherries had a significantly lower titer of X-disease phytoplasmas than susceptible plants. This suggests that the qPCR assay provides a more objective tool to phenotype phytoplasma disease severity, particularly for early evaluation of host resistance; therefore, this method will facilitate quantitative phenotyping of disease resistance and has great potential in enhancing plant breeding. Copyright © 2013 Elsevier B.V. All rights reserved.

Examining the Impact of Leadership Style and School Climate on Student Achievement

ERIC Educational Resources Information Center

Robinson, Tina

2010-01-01

The purpose of this quantitative study was to investigate whether or not leadership style and school climate are significant predictors of student achievement. The target population consisted of elementary and high school teachers from Virginia public schools who had taught under the leadership of their respective current principals for at least 4…

The Effects of Teacher Participation in the Time to Teach Classroom Management Program on Ninth Grade Student Behavior

ERIC Educational Resources Information Center

Houck, T. Chad

2017-01-01

In high school settings the behavior of students can have significant impacts on educational outcomes. This study tests Bronfrenbrenner's ecological systems theory by quantitatively studying academic and discipline measures of 9th grade students before and after teachers participated in the Time To Teach (TTT) professional development training.…

Quantitative x-ray phase imaging at the nanoscale by multilayer Laue lenses

PubMed Central

Yan, Hanfei; Chu, Yong S.; Maser, Jörg; Nazaretski, Evgeny; Kim, Jungdae; Kang, Hyon Chol; Lombardo, Jeffrey J.; Chiu, Wilson K. S.

2013-01-01

For scanning x-ray microscopy, many attempts have been made to image the phase contrast based on a concept of the beam being deflected by a specimen, the so-called differential phase contrast imaging (DPC). Despite the successful demonstration in a number of representative cases at moderate spatial resolutions, these methods suffer from various limitations that preclude applications of DPC for ultra-high spatial resolution imaging, where the emerging wave field from the focusing optic tends to be significantly more complicated. In this work, we propose a highly robust and generic approach based on a Fourier-shift fitting process and demonstrate quantitative phase imaging of a solid oxide fuel cell (SOFC) anode by multilayer Laue lenses (MLLs). The high sensitivity of the phase to structural and compositional variations makes our technique extremely powerful in correlating the electrode performance with its buried nanoscale interfacial structures that may be invisible to the absorption and fluorescence contrasts. PMID:23419650

Reciprocal Hosts' Responses to Powdery Mildew Isolates Originating from Domesticated Wheats and Their Wild Progenitor

PubMed Central

Ben-David, Roi; Dinoor, Amos; Peleg, Zvi; Fahima, Tzion

2018-01-01

The biotroph wheat powdery mildew, Blumeria graminis (DC.) E.O. Speer, f. sp. tritici Em. Marchal (Bgt), has undergone long and dynamic co-evolution with its hosts. In the last 10,000 years, processes involved in plant evolution under domestication, altered host-population structure. Recently both virulence and genomic profiling separated Bgt into two groups based on their origin from domestic host and from wild emmer wheat. While most studies focused on the Bgt pathogen, there is significant knowledge gaps in the role of wheat host diversity in this specification. This study aimed to fill this gap by exploring qualitatively and also quantitatively the disease response of diverse host panel to powdery mildew [105 domesticated wheat genotypes (Triticum turgidum ssp. dicoccum, T. turgidum ssp. durum, and T. aestivum) and 241 accessions of its direct progenitor, wild emmer wheat (T. turgidum ssp. dicoccoides)]. A set of eight Bgt isolates, originally collected from domesticated and wild wheat was used for screening this wheat collection. The isolates from domesticated wheat elicited susceptible to moderate plant responses on domesticated wheat lines and high resistance on wild genotypes (51.7% of the tested lines were resistant). Isolates from wild emmer elicited reciprocal disease responses: high resistance of domesticated germplasm and high susceptibility of the wild material (their original host). Analysis of variance of the quantitative phenotypic responses showed a significant Isolates × Host species interaction [P(F) < 0.0001] and further supported these findings. Furthermore, analysis of the range of disease severity values showed that when the group of host genotypes was inoculated with Bgt isolate from the reciprocal host, coefficient of variation was significantly higher than when inoculated with its own isolates. This trend was attributed to the role of major resistance genes in the latter scenario (high proportion of complete resistance). By testing the association between disease severity and geographical distance from the source of inoculum, we have found higher susceptibility in wild emmer close to the source. Both qualitative and quantitative assays showed a reciprocal resistance pattern in the wheat host and are well aligned with the recent findings of significant differentiation into wild-emmer and domesticated-wheat populations in the pathogen. PMID:29527213

Tumor aggressiveness and patient outcome in cancer of the pancreas assessed by dynamic 18F-FDG PET/CT.

PubMed

Epelbaum, Ron; Frenkel, Alex; Haddad, Riad; Sikorski, Natalia; Strauss, Ludwig G; Israel, Ora; Dimitrakopoulou-Strauss, Antonia

2013-01-01

This study aimed to assess the role of a quantitative dynamic PET model in pancreatic cancer as a potential index of tumor aggressiveness and predictor of survival. Seventy-one patients with (18)F-FDG-avid adenocarcinoma of the pancreas before treatment were recruited, including 27 with localized tumors (11 underwent pancreatectomy, and 16 had localized nonresectable tumors) and 44 with metastatic disease. Dynamic (18)F-FDG PET images were acquired over a 60-min period, followed by a whole-body PET/CT study. Quantitative data measurements were based on a 2-compartment model, and the following variables were calculated: VB (fractional blood volume in target area), K(1) and k(2) (kinetic membrane transport parameters), k(3) and k(4) (intracellular (18)F-FDG phosphorylation and dephosphorylation parameters, respectively), and (18)F-FDG INF (global (18)F-FDG influx). The single significant variable for overall survival (OS) in patients with localized disease was (18)F-FDG INF. Patients with a high (18)F-FDG INF (>0.033 min(-1)) had a median OS of 6 and 5 mo for nonresectable and resected tumors, respectively, versus 15 and 19 mo for a low (18)F-FDG INF in nonresectable and resected tumors, respectively (P < 0.04). In metastatic disease, multivariate analysis found VB, K(1), and k(3) to be significant variables for OS (P < 0.043, <0.031, and <0.009, respectively). Prognostic factors for OS in the entire group of patients that were significant at multivariate analysis were stage of disease, VB, K(1), and (18)F-FDG INF (P < 0.00035, <0.03, <0.024, and <0.008, respectively). Median OS for all patients with a high (18)F-FDG INF, low VB, and high K(1) was 3 mo, as opposed to 14 mo in patients with a low (18)F-FDG INF, high VB, and low K(1) (P < 0.021), irrespective of stage and resectability. Quantitative (18)F-FDG kinetic parameters measured by dynamic PET in newly diagnosed pancreatic cancer correlated with the aggressiveness of disease. The (18)F-FDG INF was the single most significant variable for OS in patients with localized disease, whether resectable or not.

Mapping morphological shape as a high-dimensional functional curve

PubMed Central

Fu, Guifang; Huang, Mian; Bo, Wenhao; Hao, Han; Wu, Rongling

2018-01-01

Abstract Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits. After quantifying morphological shape via a radius centroid contour approach, each shape, as a phenotype, was characterized as a high-dimensional curve, varying as angle θ runs clockwise with the first point starting from angle zero. We then modeled the dynamic trajectories of three mean curves and variation patterns as functions of θ. Our framework led to the detection of a few significant QTLs regulating the variation of leaf shape collected from a natural population of poplar, Populus szechuanica var tibetica. This population, distributed at altitudes 2000–4500 m above sea level, is an evolutionarily important plant species. This is the first work in the quantitative genetic shape mapping area that emphasizes a sense of ‘function’ instead of decomposing the shape into a few discrete principal components, as the majority of shape studies do. PMID:28062411

Tunable, Quantitative Fenton-RAFT Polymerization via Metered Reagent Addition.

PubMed

Nothling, Mitchell D; McKenzie, Thomas G; Reyhani, Amin; Qiao, Greg G

2018-05-10

A continuous supply of radical species is a key requirement for activating chain growth and accessing quantitative monomer conversions in reversible addition-fragmentation chain transfer (RAFT) polymerization. In Fenton-RAFT, activation is provided by hydroxyl radicals, whose indiscriminate reactivity and short-lived nature poses a challenge to accessing extended polymerization times and quantitative monomer conversions. Here, an alternative Fenton-RAFT procedure is presented, whereby radical generation can be finely controlled via metered dosing of a component of the Fenton redox reaction (H 2 O 2 ) using an external pumping system. By limiting the instantaneous flux of radicals and ensuring sustained radical generation over tunable time periods, metered reagent addition reduces unwanted radical "wasting" reactions and provides access to consistent quantitative monomer conversions with high chain-end fidelity. Fine tuning of radical concentration during polymerization is achieved simply via adjustment of reagent dose rate, offering significant potential for automation. This modular strategy holds promise for extending traditional RAFT initiation toward more tightly regulated radical concentration profiles and affords excellent prospects for the automation of Fenton-RAFT polymerization. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative profiling of CpG island methylation in human stool for colorectal cancer detection.

PubMed

Elliott, Giles O; Johnson, Ian T; Scarll, Jane; Dainty, Jack; Williams, Elizabeth A; Garg, D; Coupe, Amanda; Bradburn, David M; Mathers, John C; Belshaw, Nigel J

2013-01-01

The aims of this study were to investigate the use of quantitative CGI methylation data from stool DNA to classify colon cancer patients and to relate stool CGI methylation levels to those found in corresponding tissue samples. We applied a quantitative methylation-specific PCR assay to determine CGI methylation levels of six genes, previously shown to be aberrantly methylated during colorectal carcinogenesis. Assays were performed on DNA from biopsies of "normal" mucosa and stool samples from 57 patients classified as disease-free, adenoma, or cancer by endoscopy, and in tumour tissue from cancer patients. Additionally, CGI methylation was analysed in stool DNA from an asymptomatic population of individuals covering a broad age range (mean = 47 ± 24 years) CGI methylation levels in stool DNA were significantly higher than in DNA from macroscopically normal mucosa, and a significant correlation between stool and mucosa was observed for ESR1 only. Multivariate statistical analyses using the methylation levels of each CGI in stool DNA as a continuous variable revealed a highly significant (p = 0.003) classification of cancer vs. non-cancer (adenoma + disease-free) patients (sensitivity = 65 %, specificity = 81 %). CGI methylation profiling of stool DNA successfully identified patients with cancer despite the methylation status of CGIs in stool DNA not generally reflecting those in DNA from the colonic mucosa.

Quantitative phosphoproteome on the silkworm (Bombyx mori) cells infected with baculovirus.

PubMed

Shobahah, Jauharotus; Xue, Shengjie; Hu, Dongbing; Zhao, Cui; Wei, Ming; Quan, Yanping; Yu, Wei

2017-06-19

Bombyx mori has become an important model organism for many fundamental studies. Bombyx mori nucleopolyhedrovirus (BmNPV) is a significant pathogen to Bombyx mori, yet also an efficient vector for recombinant protein production. A previous study indicated that acetylation plays many vital roles in several cellular processes of Bombyx mori while global phosphorylation pattern upon BmNPV infection remains elusive. Employing tandem mass tag (TMT) labeling and phosphorylation affinity enrichment followed by high-resolution LC-MS/MS analysis and intensive bioinformatics analysis, the quantitative phosphoproteome in Bombyx mori cells infected by BmNPV at 24 hpi with an MOI of 10 was extensively examined. Totally, 6480 phosphorylation sites in 2112 protein groups were identified, among which 4764 sites in 1717 proteins were quantified. Among the quantified proteins, 81 up-regulated and 25 down-regulated sites were identified with significant criteria (the quantitative ratio above 1.3 was considered as up-regulation and below 0.77 was considered as down-regulation) and with significant p-value (p < 0.05). Some proteins of BmNPV were also hyperphosphorylated during infection, such as P6.9, 39 K, LEF-6, Ac58-like protein, Ac82-like protein and BRO-D. The phosphorylated proteins were primary involved in several specific functions, out of which, we focused on the binding activity, protein synthesis, viral replication and apoptosis through kinase activity.

Bilaterally Asymmetric Effects of Quantitative Trait Loci (QTLs): QTLs That Affect Laxity in the Right Versus Left Coxofemoral (Hip) Joints of the Dog (Canis familiaris)

PubMed Central

Chase, Kevin; Lawler, Dennis F.; Adler, Fred R.; Ostrander, Elaine A.; Lark, Karl G.

2009-01-01

In dogs hip joint laxity that can lead to degenerative joint disease (DJD) is frequent and heritable, providing a genetic model for some aspects of the human disease. We have used Portuguese water dogs (PWDs) to identify Quantitative trait loci (QTLs) that regulate laxity in the hip joint.A population of 286 PWDs, each characterized by ca. 500 molecular genetic markers, was analyzed for subluxation of the hip joint as measured by the Norberg angle, a quantitative radiographic measure of laxity. A significant directed asymmetry was observed, such that greater laxity was observed in the left than the right hip. This asymmetry was not heritable. However, the average Norberg angle was highly heritable as were the Norberg angles of either the right or left hips. After correction for pedigree effects, two QTLs were identified using the metrics of the left and right hips as separate data sets. Both are on canine chromosome 1 (CFA1), separated by about 95 Mb. One QTL, associated with the SSR marker FH2524 was significant for the left, but not the right hip. The other, associated with FH2598, was significant for the right but not the left hip. For both QTLs, some extreme phenotypes were best explained by specific interactions between haplotypes. PMID:14708095

Bilaterally asymmetric effects of quantitative trait loci (QTLs): QTLs that affect laxity in the right versus left coxofemoral (hip) joints of the dog (Canis familiaris).

PubMed

Chase, Kevin; Lawler, Dennis F; Adler, Fred R; Ostrander, Elaine A; Lark, Karl G

2004-01-30

In dogs hip joint laxity that can lead to degenerative joint disease (DJD) is frequent and heritable, providing a genetic model for some aspects of the human disease. We have used Portuguese water dogs (PWDs) to identify Quantitative trait loci (QTLs) that regulate laxity in the hip joint. A population of 286 PWDs, each characterized by ca. 500 molecular genetic markers, was analyzed for subluxation of the hip joint as measured by the Norberg angle, a quantitative radiographic measure of laxity. A significant directed asymmetry was observed, such that greater laxity was observed in the left than the right hip. This asymmetry was not heritable. However, the average Norberg angle was highly heritable as were the Norberg angles of either the right or left hips. After correction for pedigree effects, two QTLs were identified using the metrics of the left and right hips as separate data sets. Both are on canine chromosome 1 (CFA1), separated by about 95 Mb. One QTL, associated with the SSR marker FH2524 was significant for the left, but not the right hip. The other, associated with FH2598, was significant for the right but not the left hip. For both QTLs, some extreme phenotypes were best explained by specific interactions between haplotypes. Copyright 2003 Wiley-Liss, Inc.

Association between periodontal condition and subgingival microbiota in women during pregnancy: a longitudinal study

PubMed Central

BORGO, Priscila Viola; RODRIGUES, Viviane Aparecida Arenas; FEITOSA, Alfredo Carlos Rodrigues; XAVIER, Karla Correa Barcelos; AVILA-CAMPOS, Mario Julio

2014-01-01

Objectivo In this study, the gingival conditions and the quantitative detection for Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Porphyromonas gingivalis and Prevotella intermedia in pregnant women were determined. Material and Methods Quantitative determinations of periodontal bacteria by using a SyBr green system in women during pregnancy were performed. Women at the 2nd and 3rd trimesters of pregnancy and non-pregnant women were included in this study. A. actinomycetemcomitans was observed in high numbers in women at the 2nd and 3rd trimesters of pregnancy with a significant difference (p<0.05). F. nucleatum and P. intermedia were also observed in high levels. Results and Conclusion Our results show that pregnant women are more susceptible to gingivitis, and the presence of A. actinomycetemcomitans in subgingival biofilm might be taken into account for the treatment of periodontal disease. PMID:25591021

Multicenter trial of the proficiency of smart quantitative sensation tests.

PubMed

Dyck, Peter J; Argyros, Barbara; Russell, James W; Gahnstrom, Linde E; Nalepa, Susan; Albers, James W; Lodermeier, Karen A; Zafft, Andrew J; Dyck, P James B; Klein, Christopher J; Litchy, William J; Davies, Jenny L; Carter, Rickey E; Melton, L Joseph

2014-05-01

We assessed proficiency (accuracy and intra- and intertest reproducibility) of smart quantitative sensation tests (smart QSTs) in subjects without and with diabetic sensorimotor polyneuropathy (DSPN). Technologists from 3 medical centers using different but identical QSTs independently assessed 6 modalities of sensation of the foot (or leg) twice in patients without (n = 6) and with (n = 6) DSPN using smart computer assisted QSTs. Low rates of test abnormalities were observed in health and high rates in DSPN. Very high intraclass correlations were obtained between continuous measures of QSTs and neuropathy signs, symptoms, or nerve conductions (NCs). No significant intra- or intertest differences were observed. These results provide proof of concept that smart QSTs provide accurate assessment of sensation loss without intra- or intertest differences useful for multicenter trials. Smart technology makes possible efficient testing of body surface area sensation loss in symmetric length-dependent sensorimotor polyneuropathies. Copyright © 2013 Wiley Periodicals, Inc.

A Multicenter Trial of the Proficiency of Smart Quantitative Sensation Tests

PubMed Central

Dyck, Peter J.; Argyros, Barbara; Russell, James W.; Gahnstrom, Linde E.; Nalepa, Susan; Albers, James W.; Lodermeier, Karen A.; Zafft, Andrew J.; Dyck, P. James B.; Klein, Christopher J.; Litchy, William J.; Davies, Jenny L.; Carter, Rickey E.; Melton, L. Joseph

2014-01-01

Introduction We assessed proficiency (accuracy and intra- and inter-test reproducibility) of smart quantitative sensation tests (smart QSTs) in subjects without and with diabetic polyneuropathy (DSPN). Methods Technologists from 3 medical centers using different but identical QSTs assessed independently 6 modalities of sensation of foot (or leg) twice in patients without (n = 6) and with (n = 6) DSPN using smart computer assisted QSTs. Results Low rates of test abnormalities were observed in health and high rates in DSPN. Very high intra-class correlations were obtained between continuous measures of QSTs and neuropathy signs, symptoms, or nerve conductions (NCs). No significant intra- or inter-test differences were observed. Discussion These results provide proof of concept that smart QSTs provide accurate assessment of sensation loss without intra- or inter-test differences useful for multicenter trials. Smart technology makes possible efficient testing of body surface area sensation loss in symmetric length-dependent sensorimotor polyneuropathies. PMID:23929701

Evaluation of the capabilities of satellite imagery for monitoring regional air pollution episodes

NASA Technical Reports Server (NTRS)

Barnes, J. C.; Bowley, C. J.; Burke, H. H. K.

1979-01-01

A comparative analysis of satellite visible channel imagery and ground based aerosol measurements is carried out for three cases representing a significant pollution episodes based on low surface visibility and high sulfate levels. The feasibility of detecting pollution episodes from space is also investigated using a simulation model. The model results are compared to quantitative information derived from digitized satellite data. The results show that when levels are or = 30 micrograms/cu, a haze pattern that correlates closely with the area of reported low surface visibilities and high micrograms sulfate levels can be detected in satellite visible channel imagery. The model simulation demonstrates the potential of the satellite to monitor the magnitude and areal extent of pollution episodes. Quantitative information on total aerosol amount derived from the satellite digitized data using the atmospheric radiative transfer model agrees well with the results obtained from the ground based measurements.

Three-dimensional drift kinetic response of high-β plasmas in the DIII-D tokamak.

PubMed

Wang, Z R; Lanctot, M J; Liu, Y Q; Park, J-K; Menard, J E

2015-04-10

A quantitative interpretation of the experimentally measured high-pressure plasma response to externally applied three-dimensional (3D) magnetic field perturbations, across the no-wall Troyon β limit, is achieved. The self-consistent inclusion of the drift kinetic effects in magnetohydrodynamic (MHD) modeling [Y. Q. Liu et al., Phys. Plasmas 15, 112503 (2008)] successfully resolves an outstanding issue of the ideal MHD model, which significantly overpredicts the plasma-induced field amplification near the no-wall limit, as compared to experiments. The model leads to quantitative agreement not only for the measured field amplitude and toroidal phase but also for the measured internal 3D displacement of the plasma. The results can be important to the prediction of the reliable plasma behavior in advanced fusion devices, such as ITER [K. Ikeda, Nucl. Fusion 47, S1 (2007)].

Comparison of 18F-FDG PET/CT and PET/MRI in patients with multiple myeloma

PubMed Central

Sachpekidis, Christos; Hillengass, Jens; Goldschmidt, Hartmut; Mosebach, Jennifer; Pan, Leyun; Schlemmer, Heinz-Peter; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2015-01-01

PET/MRI represents a promising hybrid imaging modality with several potential clinical applications. Although PET/MRI seems highly attractive in the diagnostic approach of multiple myeloma (MM), its role has not yet been evaluated. The aims of this prospective study are to evaluate the feasibility of 18F-FDG PET/MRI in detection of MM lesions, and to investigate the reproducibility of bone marrow lesions detection and quantitative data of 18F-FDG uptake between the functional (PET) component of PET/CT and PET/MRI in MM patients. The study includes 30 MM patients. All patients initially underwent 18F-FDG PET/CT (60 min p.i.), followed by PET/MRI (120 min p.i.). PET/CT and PET/MRI data were assessed and compared based on qualitative (lesion detection) and quantitative (SUV) evaluation. The hybrid PET/MRI system provided good image quality in all cases without artefacts. PET/MRI identified 65 of the 69 lesions, which were detectable with PET/CT (94.2%). Quantitative PET evaluations showed the following mean values in MM lesions: SUVaverage=5.5 and SUVmax=7.9 for PET/CT; SUVaverage=3.9 and SUVmax=5.8 for PET/MRI. Both SUVaverage and SUVmax were significantly higher on PET/CT than on PET/MRI. Spearman correlation analysis demonstrated a strong correlation between both lesional SUVaverage (r=0.744) and lesional SUVmax (r=0.855) values derived from PET/CT and PET/MRI. Regarding detection of myeloma skeletal lesions, PET/MRI exhibited equivalent performance to PET/CT. In terms of tracer uptake quantitation, a significant correlation between the two techniques was demonstrated, despite the statistically significant differences in lesional SUVs between PET/CT and PET/MRI. PMID:26550538

Variants in TTC25 affect autistic trait in patients with autism spectrum disorder and general population.

PubMed

Vojinovic, Dina; Brison, Nathalie; Ahmad, Shahzad; Noens, Ilse; Pappa, Irene; Karssen, Lennart C; Tiemeier, Henning; van Duijn, Cornelia M; Peeters, Hilde; Amin, Najaf

2017-08-01

Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder with a complex genetic architecture. To identify genetic variants underlying ASD, we performed single-variant and gene-based genome-wide association studies using a dense genotyping array containing over 2.3 million single-nucleotide variants in a discovery sample of 160 families with at least one child affected with non-syndromic ASD using a binary (ASD yes/no) phenotype and a quantitative autistic trait. Replication of the top findings was performed in Psychiatric Genomics Consortium and Erasmus Rucphen Family (ERF) cohort study. Significant association of quantitative autistic trait was observed with the TTC25 gene at 17q21.2 (effect size=10.2, P-value=3.4 × 10 -7 ) in the gene-based analysis. The gene also showed nominally significant association in the cohort-based ERF study (effect=1.75, P-value=0.05). Meta-analysis of discovery and replication improved the association signal (P-value meta =1.5 × 10 -8 ). No genome-wide significant signal was observed in the single-variant analysis of either the binary ASD phenotype or the quantitative autistic trait. Our study has identified a novel gene TTC25 to be associated with quantitative autistic trait in patients with ASD. The replication of association in a cohort-based study and the effect estimate suggest that variants in TTC25 may also be relevant for broader ASD phenotype in the general population. TTC25 is overexpressed in frontal cortex and testis and is known to be involved in cilium movement and thus an interesting candidate gene for autistic trait.

The effects of inquiry instruction on student learning in technology-based undergraduate chemistry laboratories

NASA Astrophysics Data System (ADS)

Meade, Karen Marie

The purpose of this study was to identify conceptual and attitudinal effects of inquiry learning in technology-based undergraduate chemistry laboratories. There were 428 participants who were registered in general chemistry laboratory at the University of Iowa in the Spring of 2002. Conceptual and attitudinal pretest and posttest results were quantitative in nature. Qualitative results were collected from questionnaires and focus groups. Quantitative data were analyzed using a repeated measures analysis of variance to identify differences between treatment groups. A high-inquiry treatment group was open-ended and required student decisions regarding data collection, data representation, and interpretation. The low-inquiry treatment involved collaboration and traditional learning strategies. Major findings of this study were: (1) Pretest to posttest conceptual gains were significant for both treatment groups. Low-inquiry students performed significantly better on exploration questions than high-inquiry students. (2) Process skills developed at higher levels for high-inquiry students than low-inquiry students. (3) Positive attitudes decreased significantly for all students from pretest to posttest. More favorable attitudes toward science enjoyment and the ability to do well in science were found for high-inquiry students. More favorable attitudes toward science enjoyment and the ability to do well in science were found for low-inquiry males and high-inquiry females. (4) More favorable attitudes toward the nature of science caused by use of the learning cycle were reported by high-inquiry students. (5) Low-inquiry students reported more favorable attitudes toward technologies in the laboratory than did high-inquiry students. Favorable attitudes toward the use of infrared spectrometers and unfavorable attitudes toward the use of pH meters were reported by both treatment groups. (6) More formal reasoning skills were reported by high-inquiry students. Both groups reported that looking for patterns was a common theme in the laboratories. Hypotheses were reported as rarely used by both treatment groups. These findings are significant because they indicate that inquiry activities positively affect attitudes toward science, gender equality, and contribute to the development of formal reasoning skills and process skills.

How to Combine ChIP with qPCR.

PubMed

Asp, Patrik

2018-01-01

Chromatin immunoprecipitation (ChIP) coupled with quantitative PCR (qPCR) has in the last 15 years become a basic mainstream tool in genomic research. Numerous commercially available ChIP kits, qPCR kits, and real-time PCR systems allow for quick and easy analysis of virtually anything chromatin-related as long as there is an available antibody. However, the highly accurate quantitative dimension added by using qPCR to analyze ChIP samples significantly raises the bar in terms of experimental accuracy, appropriate controls, data analysis, and data presentation. This chapter will address these potential pitfalls by providing protocols and procedures that address the difficulties inherent in ChIP-qPCR assays.

Is multidetector CT-based bone mineral density and quantitative bone microstructure assessment at the spine still feasible using ultra-low tube current and sparse sampling?

PubMed

Mei, Kai; Kopp, Felix K; Bippus, Rolf; Köhler, Thomas; Schwaiger, Benedikt J; Gersing, Alexandra S; Fehringer, Andreas; Sauter, Andreas; Münzel, Daniela; Pfeiffer, Franz; Rummeny, Ernst J; Kirschke, Jan S; Noël, Peter B; Baum, Thomas

2017-12-01

Osteoporosis diagnosis using multidetector CT (MDCT) is limited to relatively high radiation exposure. We investigated the effect of simulated ultra-low-dose protocols on in-vivo bone mineral density (BMD) and quantitative trabecular bone assessment. Institutional review board approval was obtained. Twelve subjects with osteoporotic vertebral fractures and 12 age- and gender-matched controls undergoing routine thoracic and abdominal MDCT were included (average effective dose: 10 mSv). Ultra-low radiation examinations were achieved by simulating lower tube currents and sparse samplings at 50%, 25% and 10% of the original dose. BMD and trabecular bone parameters were extracted in T10-L5. Except for BMD measurements in sparse sampling data, absolute values of all parameters derived from ultra-low-dose data were significantly different from those derived from original dose images (p<0.05). BMD, apparent bone fraction and trabecular thickness were still consistently lower in subjects with than in those without fractures (p<0.05). In ultra-low-dose scans, BMD and microstructure parameters were able to differentiate subjects with and without vertebral fractures, suggesting osteoporosis diagnosis is feasible. However, absolute values differed from original values. BMD from sparse sampling appeared to be more robust. This dose-dependency of parameters should be considered for future clinical use. • BMD and quantitative bone parameters are assessable in ultra-low-dose in vivo MDCT scans. • Bone mineral density does not change significantly when sparse sampling is applied. • Quantitative trabecular bone microstructure measurements are sensitive to dose reduction. • Osteoporosis subjects could be differentiated even at 10% of original dose. • Radiation exposure should be considered when comparing quantitative bone parameters.

Low-frequency quantitative ultrasound imaging of cell death in vivo

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

Sadeghi-Naini, Ali; Falou, Omar; Czarnota, Gregory J.

Purpose: Currently, no clinical imaging modality is used routinely to assess tumor response to cancer therapies within hours to days of the delivery of treatment. Here, the authors demonstrate the efficacy of ultrasound at a clinically relevant frequency to quantitatively detect changes in tumors in response to cancer therapies using preclinical mouse models.Methods: Conventional low-frequency and corresponding high-frequency ultrasound (ranging from 4 to 28 MHz) were used along with quantitative spectroscopic and signal envelope statistical analyses on data obtained from xenograft tumors treated with chemotherapy, x-ray radiation, as well as a novel vascular targeting microbubble therapy.Results: Ultrasound-based spectroscopic biomarkers indicatedmore » significant changes in cell-death associated parameters in responsive tumors. Specifically changes in the midband fit, spectral slope, and 0-MHz intercept biomarkers were investigated for different types of treatment and demonstrated cell-death related changes. The midband fit and 0-MHz intercept biomarker derived from low-frequency data demonstrated increases ranging approximately from 0 to 6 dBr and 0 to 8 dBr, respectively, depending on treatments administrated. These data paralleled results observed for high-frequency ultrasound data. Statistical analysis of ultrasound signal envelope was performed as an alternative method to obtain histogram-based biomarkers and provided confirmatory results. Histological analysis of tumor specimens indicated up to 61% cell death present in the tumors depending on treatments administered, consistent with quantitative ultrasound findings indicating cell death. Ultrasound-based spectroscopic biomarkers demonstrated a good correlation with histological morphological findings indicative of cell death (r{sup 2}= 0.71, 0.82; p < 0.001).Conclusions: In summary, the results provide preclinical evidence, for the first time, that quantitative ultrasound used at a clinically relevant frequency, in addition to high-frequency ultrasound, can detect tissue changes associated with cell death in vivo in response to cancer treatments.« less

Quantitative Changes in Cerebral Perfusion during Urinary Urgency in Women with Overactive Bladder

PubMed Central

Weissbart, Steven J.; Xu, Sihua; Bhavsar, Rupal; Rao, Hengyi

2017-01-01

Purpose To quantitatively measure changes in cerebral perfusion in select regions of interest in the brain during urinary urgency in women with overactive bladder (OAB) using arterial spin labeling (ASL). Methods Twelve women with OAB and 10 controls underwent bladder filling and rated urinary urgency (scale 0–10). ASL fMRI scans were performed (1) in the low urgency state after voiding and (2) high urgency state after drinking oral fluids. Absolute regional cerebral blood flow (rCBF) in select regions of interest was compared between the low and high urgency states. Results There were no significant differences in rCBF between the low and high urgency states in the control group. In the OAB group, rCBF (mean ± SE, ml/100 g/min) increased by 10–14% from the low to the high urgency state in the right anterior cingulate cortex (ACC) (44.56 ± 0.59 versus 49.52 ± 1.49, p < 0.05), left ACC (49.29 ± 0.85 versus 54.02 ± 1.46, p < 0.05), and left insula (50.46 ± 1.72 versus 54.99 ± 1.09, p < 0.05). Whole-brain analysis identified additional areas of activation in the right insula, right dorsolateral prefrontal cortex, and pons/midbrain area. Conclusions Urinary urgency is associated with quantitative increase in cerebral perfusion in regions of the brain associated with processing emotional response to discomfort. PMID:28904950

Longitudinal spatial coherence gated high-resolution tomography and quantitative phase microscopy of biological cells and tissues with uniform illumination

NASA Astrophysics Data System (ADS)

Mehta, Dalip Singh; Ahmad, Azeem; Dubey, Vishesh; Singh, Veena; Butola, Ankit; Mohanty, Tonmoy; Nandi, Sreyankar

2018-02-01

We report longitudinal spatial coherence (LSC) gated high-resolution tomography and quantitative phase microscopy of biological cells and tissues with uniform illumination using laser as a light source. To accomplish this a pseudo thermal light source was synthesized by passing laser beams through an optical system, which is basically a speckle reduction system with combined effect of spatial, temporal, angular and polarisation diversity. The longitudinal spatial coherence length of such light was significantly reduced by synthesizing a pseudo thermal source with the combined effect of spatial, angular and temporal diversity. This results in a low spatially coherent (i.e., broad angular frequency spectrum) light source with narrow temporal frequency spectrum. Light from such a pseudo thermal light source was passed through an interference microscope with varying magnification, such as, 10X and 50X. The interference microscope was used for full-field OCT imaging of multilayer objects and topography of industrial objects. Experimental results of optical sectioning of multilayer biological objects with high axial-resolution less than 10μm was achieved which is comparable to broadband white light source. The synthesized light source with reduced speckles having uniform illumination on the sample, which can be very useful for fluorescence microscopy as well as quantitative phase microscopy with less phase noise. The present system does not require any dispersion compensation optical system for biological samples as a highly monochromatic light source is used.

Towards quantitative assessment of calciphylaxis

NASA Astrophysics Data System (ADS)

Deserno, Thomas M.; Sárándi, István.; Jose, Abin; Haak, Daniel; Jonas, Stephan; Specht, Paula; Brandenburg, Vincent

2014-03-01

Calciphylaxis is a rare disease that has devastating conditions associated with high morbidity and mortality. Calciphylaxis is characterized by systemic medial calcification of the arteries yielding necrotic skin ulcerations. In this paper, we aim at supporting the installation of multi-center registries for calciphylaxis, which includes a photographic documentation of skin necrosis. However, photographs acquired in different centers under different conditions using different equipment and photographers cannot be compared quantitatively. For normalization, we use a simple color pad that is placed into the field of view, segmented from the image, and its color fields are analyzed. In total, 24 colors are printed on that scale. A least-squares approach is used to determine the affine color transform. Furthermore, the card allows scale normalization. We provide a case study for qualitative assessment. In addition, the method is evaluated quantitatively using 10 images of two sets of different captures of the same necrosis. The variability of quantitative measurements based on free hand photography is assessed regarding geometric and color distortions before and after our simple calibration procedure. Using automated image processing, the standard deviation of measurements is significantly reduced. The coefficients of variations yield 5-20% and 2-10% for geometry and color, respectively. Hence, quantitative assessment of calciphylaxis becomes practicable and will impact a better understanding of this rare but fatal disease.

Culture-free, highly sensitive, quantitative detection of bacteria from minimally processed samples using fluorescence imaging by smartphone.

PubMed

Shrivastava, Sajal; Lee, Won-Il; Lee, Nae-Eung

2018-06-30

A critical unmet need in the diagnosis of bacterial infections, which remain a major cause of human morbidity and mortality, is the detection of scarce bacterial pathogens in a variety of samples in a rapid and quantitative manner. Herein, we demonstrate smartphone-based detection of Staphylococcus aureus in a culture-free, rapid, quantitative manner from minimally processed liquid samples using aptamer-functionalized fluorescent magnetic nanoparticles. The tagged S. aureus cells were magnetically captured in a detection cassette, and then fluorescence was imaged using a smartphone camera with a light-emitting diode as the excitation source. Our results showed quantitative detection capability with a minimum detectable concentration as low as 10 cfu/ml by counting individual bacteria cells, efficiently capturing S. aureus cells directly from a peanut milk sample within 10 min. When the selectivity of detection was investigated using samples spiked with other pathogenic bacteria, no significant non-specific detection occurred. Furthermore, strains of S. aureus from various origins showed comparable results, ensuring that the approach can be widely adopted. Therefore, the quantitative fluorescence imaging platform on a smartphone could allow on-site detection of bacteria, providing great potential assistance during major infectious disease outbreaks in remote and resource-limited settings. Copyright © 2018 Elsevier B.V. All rights reserved.

Comparative study of standard space and real space analysis of quantitative MR brain data.

PubMed

Aribisala, Benjamin S; He, Jiabao; Blamire, Andrew M

2011-06-01

To compare the robustness of region of interest (ROI) analysis of magnetic resonance imaging (MRI) brain data in real space with analysis in standard space and to test the hypothesis that standard space image analysis introduces more partial volume effect errors compared to analysis of the same dataset in real space. Twenty healthy adults with no history or evidence of neurological diseases were recruited; high-resolution T(1)-weighted, quantitative T(1), and B(0) field-map measurements were collected. Algorithms were implemented to perform analysis in real and standard space and used to apply a simple standard ROI template to quantitative T(1) datasets. Regional relaxation values and histograms for both gray and white matter tissues classes were then extracted and compared. Regional mean T(1) values for both gray and white matter were significantly lower using real space compared to standard space analysis. Additionally, regional T(1) histograms were more compact in real space, with smaller right-sided tails indicating lower partial volume errors compared to standard space analysis. Standard space analysis of quantitative MRI brain data introduces more partial volume effect errors biasing the analysis of quantitative data compared to analysis of the same dataset in real space. Copyright © 2011 Wiley-Liss, Inc.

Novel Autism Subtype-Dependent Genetic Variants Are Revealed by Quantitative Trait and Subphenotype Association Analyses of Published GWAS Data

PubMed Central

Hu, Valerie W.; Addington, Anjene; Hyman, Alexander

2011-01-01

The heterogeneity of symptoms associated with autism spectrum disorders (ASDs) has presented a significant challenge to genetic analyses. Even when associations with genetic variants have been identified, it has been difficult to associate them with a specific trait or characteristic of autism. Here, we report that quantitative trait analyses of ASD symptoms combined with case-control association analyses using distinct ASD subphenotypes identified on the basis of symptomatic profiles result in the identification of highly significant associations with 18 novel single nucleotide polymorphisms (SNPs). The symptom categories included deficits in language usage, non-verbal communication, social development, and play skills, as well as insistence on sameness or ritualistic behaviors. Ten of the trait-associated SNPs, or quantitative trait loci (QTL), were associated with more than one subtype, providing partial replication of the identified QTL. Notably, none of the novel SNPs is located within an exonic region, suggesting that these hereditary components of ASDs are more likely related to gene regulatory processes (or gene expression) than to structural or functional changes in gene products. Seven of the QTL reside within intergenic chromosomal regions associated with rare copy number variants that have been previously reported in autistic samples. Pathway analyses of the genes associated with the QTL identified in this study implicate neurological functions and disorders associated with autism pathophysiology. This study underscores the advantage of incorporating both quantitative traits as well as subphenotypes into large-scale genome-wide analyses of complex disorders. PMID:21556359

A quantitative method for optimized placement of continuous air monitors.

PubMed

Whicker, Jeffrey J; Rodgers, John C; Moxley, John S

2003-11-01

Alarming continuous air monitors (CAMs) are a critical component for worker protection in facilities that handle large amounts of hazardous materials. In nuclear facilities, continuous air monitors alarm when levels of airborne radioactive materials exceed alarm thresholds, thus prompting workers to exit the room to reduce inhalation exposures. To maintain a high level of worker protection, continuous air monitors are required to detect radioactive aerosol clouds quickly and with good sensitivity. This requires that there are sufficient numbers of continuous air monitors in a room and that they are well positioned. Yet there are no published methodologies to quantitatively determine the optimal number and placement of continuous air monitors in a room. The goal of this study was to develop and test an approach to quantitatively determine optimal number and placement of continuous air monitors in a room. The method we have developed uses tracer aerosol releases (to simulate accidental releases) and the measurement of the temporal and spatial aspects of the dispersion of the tracer aerosol through the room. The aerosol dispersion data is then analyzed to optimize continuous air monitor utilization based on simulated worker exposure. This method was tested in a room within a Department of Energy operated plutonium facility at the Savannah River Site in South Carolina, U.S. Results from this study show that the value of quantitative airflow and aerosol dispersion studies is significant and that worker protection can be significantly improved while balancing the costs associated with CAM programs.

Teacher Self-Efficacy: A Link to Student Achievement in English Language and Mathematics in Belizean Primary Schools

ERIC Educational Resources Information Center

Alvarez-Nunez, Tanya Mae

2012-01-01

Scope and Method of Study: This quantitative, non-experimental study sought to determine if a statistically significant difference existed in student achievement on the PSE exam in Belizean primary schools for students who have teachers with varying levels of self-efficacy (high, medium and low). The Teacher Efficacy Scale (TES), which captures…

The Effects of the Project Champion's Leadership Style on Global Information Technology User Acceptance and Use

ERIC Educational Resources Information Center

Ekiko, Mbong C.

2014-01-01

The research problem was the lack of knowledge about the effect of leadership style of the project champion on global information technology (IT) project outcomes, resulting in a high failure rate of IT projects accompanied by significant waste of resources. The purpose of this quantitative, nonexperimental study was to evaluate the relationship…

A Meta-Analysis of School-Based Interventions Aimed to Prevent or Reduce Violence in Teen Dating Relationships

ERIC Educational Resources Information Center

De La Rue, Lisa; Polanin, Joshua R.; Espelage, Dorothy L.; Pigott, Terri D.

2017-01-01

The incidence of violence in dating relationships has a significant impact on young people, including decreased mental and physical health. This review is the first to provide a quantitative synthesis of empirical evaluations of school-based programs implemented in middle and high schools that sought to prevent or reduce incidents of dating…

Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy.

PubMed

Cartagena, Alexander; Hernando-Pérez, Mercedes; Carrascosa, José L; de Pablo, Pedro J; Raman, Arvind

2013-06-07

Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the study of structure-property-function relationships. We present an in vitro dynamic AFM technique operating in the intermittent contact regime which synthesizes anharmonic Lorentz-force excited AFM cantilevers to map quantitatively at nanometer resolution the local electro-mechanical force gradient, adhesion, and hydration layer viscosity within individual φ29 virions. Furthermore, the changes in material properties over the entire φ29 virion provoked by the local disruption of its shell are studied, providing evidence of bacteriophage depressurization. The technique significantly generalizes recent multi-harmonic theory (A. Raman, et al., Nat. Nanotechnol., 2011, 6, 809-814) and enables high-resolution in vitro quantitative mapping of multiple material properties within weakly bonded viruses and nanoparticles with complex structure that otherwise cannot be observed using standard AFM techniques.

COTS-Based Fault Tolerance in Deep Space: Qualitative and Quantitative Analyses of a Bus Network Architecture

NASA Technical Reports Server (NTRS)

Tai, Ann T.; Chau, Savio N.; Alkalai, Leon

2000-01-01

Using COTS products, standards and intellectual properties (IPs) for all the system and component interfaces is a crucial step toward significant reduction of both system cost and development cost as the COTS interfaces enable other COTS products and IPs to be readily accommodated by the target system architecture. With respect to the long-term survivable systems for deep-space missions, the major challenge for us is, under stringent power and mass constraints, to achieve ultra-high reliability of the system comprising COTS products and standards that are not developed for mission-critical applications. The spirit of our solution is to exploit the pertinent standard features of a COTS product to circumvent its shortcomings, though these standard features may not be originally designed for highly reliable systems. In this paper, we discuss our experiences and findings on the design of an IEEE 1394 compliant fault-tolerant COTS-based bus architecture. We first derive and qualitatively analyze a -'stacktree topology" that not only complies with IEEE 1394 but also enables the implementation of a fault-tolerant bus architecture without node redundancy. We then present a quantitative evaluation that demonstrates significant reliability improvement from the COTS-based fault tolerance.

Tracking antibiotic resistome during wastewater treatment using high throughput quantitative PCR.

PubMed

An, Xin-Li; Su, Jian-Qiang; Li, Bing; Ouyang, Wei-Ying; Zhao, Yi; Chen, Qing-Lin; Cui, Li; Chen, Hong; Gillings, Michael R; Zhang, Tong; Zhu, Yong-Guan

2018-05-08

Wastewater treatment plants (WWTPs) contain diverse antibiotic resistance genes (ARGs), and thus are considered as a major pathway for the dissemination of these genes into the environments. However, comprehensive evaluations of ARGs dynamic during wastewater treatment process lack extensive investigations on a broad spectrum of ARGs. Here, we investigated the dynamics of ARGs and bacterial community structures in 114 samples from eleven Chinese WWTPs using high-throughput quantitative PCR and 16S rRNA-based Illumina sequencing analysis. Significant shift of ARGs profiles was observed and wastewater treatment process could significantly reduce the abundance and diversity of ARGs, with the removal of ARGs concentration by 1-2 orders of magnitude. Whereas, a considerable number of ARGs were detected and enriched in effluents compared with influents. In particular, seven ARGs mainly conferring resistance to beta-lactams and aminoglycosides and three mobile genetic elements persisted in all WWTPs samples after wastewater treatment. ARGs profiles varied with wastewater treatment processes, seasons and regions. This study tracked the footprint of ARGs during wastewater treatment process, which would support the assessment on the spread of ARGs from WWTPs and provide data for identifying management options to improve ARG mitigation in WWTPs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Modifiable lifestyle factors affecting bone health using calcaneus quantitative ultrasound in adolescent girls.

PubMed

Robinson, M L; Winters-Stone, K; Gabel, K; Dolny, D

2007-08-01

One hundred and fourteen girls were measured for calcaneus QUS (stiffness index score), calcium intake, weight, and total hours spent in physical activity (moderate to high-impact activities and low to no-impact activities). Multiple regression analysis indicated that hours spent in moderate to high-impact activities, current calcium intake, and weight significantly predicted SI. To determine the influence of modifiable lifestyle factors on adolescent girls' bone health measured by calcaneus quantitative ultrasound (QUS). One hundred and fourteen girls, ages 14-18 (15.97 +/- .7), enrolled in high school physical education classes, were measured for calcaneus QUS (stiffness index score), height, weight, current calcium intake from 2-3 day food records, and estimated total hours spent in physical activity from kindergarten to present. Cumulative physical activity hours were separated into two classifications (according to their estimated strain from ground reaction force): moderate to high-impact activities and low to no-impact activities. Pearson correlations between stiffness index (SI) and age, height, weight, current calcium intake, and hours spent in moderate to high-impact versus low to no-impact activities indicated a positive relationships between SI and weight (r = .259, p = .005), current calcium intake (r = .286, p = .002), and hours spent in moderate to high-impact activities (r = .451, p < .001). Multiple regression between SI and the above independent variables indicated that collectively, hours spent in moderate to high-impact activities, current calcium intake, and weight (r (2) = .363, p = <.001) significantly predicted SI. Our data indicate that moderate to high-impact activities, current calcium intake, and weight positively influence bone properties of the calcaneus in adolescent girls.

Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS

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

Gritsenko, Marina A.; Xu, Zhe; Liu, Tao

Comprehensive, quantitative information on abundances of proteins and their post-translational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labelling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification andmore » quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples, and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.« less

Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS.

PubMed

Gritsenko, Marina A; Xu, Zhe; Liu, Tao; Smith, Richard D

2016-01-01

Comprehensive, quantitative information on abundances of proteins and their posttranslational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labeling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification and quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.

Critical Thinking Skills of Students through Mathematics Learning with ASSURE Model Assisted by Software Autograph

NASA Astrophysics Data System (ADS)

Kristianti, Y.; Prabawanto, S.; Suhendra, S.

2017-09-01

This study aims to examine the ability of critical thinking and students who attain learning mathematics with learning model ASSURE assisted Autograph software. The design of this study was experimental group with pre-test and post-test control group. The experimental group obtained a mathematics learning with ASSURE-assisted model Autograph software and the control group acquired the mathematics learning with the conventional model. The data are obtained from the research results through critical thinking skills tests. This research was conducted at junior high school level with research population in one of junior high school student in Subang Regency of Lesson Year 2016/2017 and research sample of class VIII student in one of junior high school in Subang Regency for 2 classes. Analysis of research data is administered quantitatively. Quantitative data analysis was performed on the normalized gain level between the two sample groups using a one-way anova test. The results show that mathematics learning with ASSURE assisted model Autograph software can improve the critical thinking ability of junior high school students. Mathematical learning using ASSURE-assisted model Autograph software is significantly better in improving the critical thinking skills of junior high school students compared with conventional models.

Chemokine Receptor CXCR4 Expression in Patients With Melanoma and Colorectal Cancer Liver Metastases and the Association With Disease Outcome

PubMed Central

Kim, Joseph; Mori, Takuji; Chen, Steven L.; Amersi, Farin F.; Martinez, Steve R.; Kuo, Christine; Turner, Roderick R.; Ye, Xing; Bilchik, Anton J.; Morton, Donald L.; Hoon, Dave S. B.

2006-01-01

Objective: To determine the role of chemokine receptor (CR) expression in patients with melanoma and colorectal cancer (CRC) liver metastases. Summary Background Data: Murine and in vitro models have identified CR as potential factors in organ-specific metastasis of multiple cancers. Chemokines via their respective receptors have been shown to promote cell migration to distant organs. Methods: Patients who underwent hepatic surgery for melanoma or CRC liver metastases were assessed. Screening cDNA microarrays of melanoma/CRC cell lines and tumor specimens were analyzed to identify CR. Microarray data were validated by quantitative real-time RT-PCR (qRT) in paraffin-embedded liver metastases. Migration assays and immunohistochemistry were performed to verify CR function and confirm CR expression, respectively. Results: Microarray analysis identified CXCR4 as the most common CR expressed by both cancers. qRT demonstrated CXCR4 expression in 24 of 27 (89%) melanoma and 28 of 29 (97%) CRC liver metastases. In vitro treatment of melanoma or CRC cells with CXCL12, the ligand for CXCR4, significantly increased cell migration (P < 0.001). Low versus high CXCR4 expression in CRC liver metastases correlated with a significant difference in overall survival (median 27 months vs. 10 months, respectively; P = 0.036). In melanoma, low versus high CXCR4 expression in liver metastases demonstrated no difference in overall survival (median 11 months vs. 8 months, respectively; P = not significant). Conclusions: CXCR4 is expressed and functional on melanoma and CRC cells. The ligand for CXCR4 is highly expressed in liver and may specifically attract melanoma and CRC CXCR4 (+) cells. Quantitative analysis of CXCR4 gene expression in patients with liver metastases has prognostic significance for disease outcome. PMID:16794396

The Impact of Acquisition Dose on Quantitative Breast Density Estimation with Digital Mammography: Results from ACRIN PA 4006.

PubMed

Chen, Lin; Ray, Shonket; Keller, Brad M; Pertuz, Said; McDonald, Elizabeth S; Conant, Emily F; Kontos, Despina

2016-09-01

Purpose To investigate the impact of radiation dose on breast density estimation in digital mammography. Materials and Methods With institutional review board approval and Health Insurance Portability and Accountability Act compliance under waiver of consent, a cohort of women from the American College of Radiology Imaging Network Pennsylvania 4006 trial was retrospectively analyzed. All patients underwent breast screening with a combination of dose protocols, including standard full-field digital mammography, low-dose digital mammography, and digital breast tomosynthesis. A total of 5832 images from 486 women were analyzed with previously validated, fully automated software for quantitative estimation of density. Clinical Breast Imaging Reporting and Data System (BI-RADS) density assessment results were also available from the trial reports. The influence of image acquisition radiation dose on quantitative breast density estimation was investigated with analysis of variance and linear regression. Pairwise comparisons of density estimations at different dose levels were performed with Student t test. Agreement of estimation was evaluated with quartile-weighted Cohen kappa values and Bland-Altman limits of agreement. Results Radiation dose of image acquisition did not significantly affect quantitative density measurements (analysis of variance, P = .37 to P = .75), with percent density demonstrating a high overall correlation between protocols (r = 0.88-0.95; weighted κ = 0.83-0.90). However, differences in breast percent density (1.04% and 3.84%, P < .05) were observed within high BI-RADS density categories, although they were significantly correlated across the different acquisition dose levels (r = 0.76-0.92, P < .05). Conclusion Precision and reproducibility of automated breast density measurements with digital mammography are not substantially affected by variations in radiation dose; thus, the use of low-dose techniques for the purpose of density estimation may be feasible. (©) RSNA, 2016 Online supplemental material is available for this article.

The Impact of Acquisition Dose on Quantitative Breast Density Estimation with Digital Mammography: Results from ACRIN PA 4006

PubMed Central

Chen, Lin; Ray, Shonket; Keller, Brad M.; Pertuz, Said; McDonald, Elizabeth S.; Conant, Emily F.

2016-01-01

Purpose To investigate the impact of radiation dose on breast density estimation in digital mammography. Materials and Methods With institutional review board approval and Health Insurance Portability and Accountability Act compliance under waiver of consent, a cohort of women from the American College of Radiology Imaging Network Pennsylvania 4006 trial was retrospectively analyzed. All patients underwent breast screening with a combination of dose protocols, including standard full-field digital mammography, low-dose digital mammography, and digital breast tomosynthesis. A total of 5832 images from 486 women were analyzed with previously validated, fully automated software for quantitative estimation of density. Clinical Breast Imaging Reporting and Data System (BI-RADS) density assessment results were also available from the trial reports. The influence of image acquisition radiation dose on quantitative breast density estimation was investigated with analysis of variance and linear regression. Pairwise comparisons of density estimations at different dose levels were performed with Student t test. Agreement of estimation was evaluated with quartile-weighted Cohen kappa values and Bland-Altman limits of agreement. Results Radiation dose of image acquisition did not significantly affect quantitative density measurements (analysis of variance, P = .37 to P = .75), with percent density demonstrating a high overall correlation between protocols (r = 0.88–0.95; weighted κ = 0.83–0.90). However, differences in breast percent density (1.04% and 3.84%, P < .05) were observed within high BI-RADS density categories, although they were significantly correlated across the different acquisition dose levels (r = 0.76–0.92, P < .05). Conclusion Precision and reproducibility of automated breast density measurements with digital mammography are not substantially affected by variations in radiation dose; thus, the use of low-dose techniques for the purpose of density estimation may be feasible. © RSNA, 2016 Online supplemental material is available for this article. PMID:27002418

Differences in mitochondrial gene expression profiles, enzyme activities and myosin heavy chain types in yak versus bovine skeletal muscles.

PubMed

Lin, Y Q; Xu, Y O; Yue, Y; Jin, S Y; Qu, Y; Dong, F; Li, Y P; Zheng, Y C

2012-08-29

Hypoxia can affect energy metabolism. We examined gene expression and enzyme activity related to mitochondrial energy metabolism, as well as myosin heavy chain (MyHC) types in yaks (Bos grunniens) living at high altitudes. Real-time quantitative PCR assays indicated that the yak has significantly lower levels of carnitine palmitoyltransferase (CPT) mRNA in the biceps femoris and lower levels of uncoupling protein 3 (UCP3) mRNA in both biceps femoris and longissimus dorsi than in Yellow cattle. No significant differences between yak and Yellow cattle were observed in the activities of mitochondrial β-hydroxyacyl-CoA dehydrogenase, isocitrate dehydrogenase and cytochrome oxidase in the same muscles. Semi-quantitative RT-PCR analysis showed that the MyHC 1 mRNA levels in yak biceps femoris was lower than in Yellow cattle. We conclude that the yak has significantly lower mRNA levels of CPT, UCP3, and MyHC 1 in biceps femoris than in Yellow cattle, suggesting that the yak biceps femoris has lower fatty acid oxidation capacity and greater glycolytic metabolic potential.

Iris pigmentation as a quantitative trait: variation in populations of European, East Asian and South Asian ancestry and association with candidate gene polymorphisms.

PubMed

Edwards, Melissa; Cha, David; Krithika, S; Johnson, Monique; Cook, Gillian; Parra, Esteban J

2016-03-01

In this study, we present a new quantitative method to measure iris colour based on high-resolution photographs. We applied this method to analyse iris colour variation in a sample of individuals of East Asian, European and South Asian ancestry. We show that measuring iris colour using the coordinates of the CIELAB colour space uncovers a significant amount of variation that is not captured using conventional categorical classifications, such as 'brown', 'blue' or 'green'. We tested the association of a selected panel of polymorphisms with iris colour in each population group. Six markers showed significant associations with iris colour in the European sample, three in the South Asian sample and two in the East Asian sample. We also observed that the marker HERC2 rs12913832, which is the main determinant of 'blue' versus 'brown' iris colour in European populations, is also significantly associated with central heterochromia in the European sample. © 2015 The Authors. Pigment Cell & Melanoma Research Published by John Wiley & Sons Ltd.

A Quantitative MR Imaging Assessment of Leukoencephalopathy in Children Treated for Acute Lymphoblastic Leukemia without Irradiation

PubMed Central

Reddick, Wilburn E.; Glass, John O.; Helton, Kathleen J.; Langston, James W.; Li, Chin-Shang; Pui, Ching-Hon

2008-01-01

PURPOSE Intravenous methotrexate (IV-MTX), an effective treatment for acute lymphoblastic leukemia (ALL), has a significant toxic effect on the central nervous system, with leukoencephalopathy (LE) being the most common form. The purpose of this study was to use objective quantitative MR imaging to prospectively assess the temporal evolution of LE extent and intensity. METHODS Forty-five children (low-risk, 10 mol/L/12F; mean age, 5.0 years at diagnosis; standard/high-risk, 11 mol/L/12F; mean age, 9.2 years at diagnosis) treated for ALL on a single institutional protocol were evaluated longitudinally to assess the extent of LE (proportion of white matter impacted) through tissue segmentation and the relative intensity of LE through relative elevations in T1 and T2 relaxation rates. One-sided Wilcoxon-Mann-Whitney tests were used to assess differences in quantitative measures at 4 different points in therapy both within and between risk arms. RESULTS The proportion of white matter affected in both patient groups increased significantly with additional courses of IV-MTX, whereas the intensity of LE also increased steadily; however, both the intensity and extent of LE declined significantly ∼1.5 years after completion of IV-MTX. Increases in the T1 and T2 relaxation rates above normal-appearing white matter were significantly correlated with each other and were dependent on the proportion of white matter affected. CONCLUSION Higher doses and more courses of IV-MTX were associated with increased intensity and extent of LE. There was a significant reduction in both the intensity and extent of LE after completion of therapy. The impact of these changes on neurocognitive functioning and quality of life in survivors remains to be determined. PMID:16219848

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung.

PubMed

Holman, Beverley F; Cuplov, Vesna; Hutton, Brian F; Groves, Ashley M; Thielemans, Kris

2016-04-21

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant (18)F-FDG and (18)F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

Correlation of visual in vitro cytotoxicity ratings of biomaterials with quantitative in vitro cell viability measurements.

PubMed

Bhatia, Sujata K; Yetter, Ann B

2008-08-01

Medical devices and implanted biomaterials are often assessed for biological reactivity using visual scores of cell-material interactions. In such testing, biomaterials are assigned cytotoxicity ratings based on visual evidence of morphological cellular changes, including cell lysis, rounding, spreading, and proliferation. For example, ISO 10993 cytotoxicity testing of medical devices allows the use of a visual grading scale. The present study compared visual in vitro cytotoxicity ratings to quantitative in vitro cytotoxicity measurements for biomaterials to determine the level of correlation between visual scoring and a quantitative cell viability assay. Biomaterials representing a spectrum of biological reactivity levels were evaluated, including organo-tin polyvinylchloride (PVC; a known cytotoxic material), ultra-high molecular weight polyethylene (a known non-cytotoxic material), and implantable tissue adhesives. Each material was incubated in direct contact with mouse 3T3 fibroblast cell cultures for 24 h. Visual scores were assigned to the materials using a 5-point rating scale; the scorer was blinded to the material identities. Quantitative measurements of cell viability were performed using a 3-(4,5-dimethylthiozol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) colorimetric assay; again, the assay operator was blinded to material identities. The investigation revealed a high degree of correlation between visual cytotoxicity ratings and quantitative cell viability measurements; a Pearson's correlation gave a correlation coefficient of 0.90 between the visual cytotoxicity score and the percent viable cells. An equation relating the visual cytotoxicity score and the percent viable cells was derived. The results of this study are significant for the design and interpretation of in vitro cytotoxicity studies of novel biomaterials.

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung

NASA Astrophysics Data System (ADS)

Holman, Beverley F.; Cuplov, Vesna; Hutton, Brian F.; Groves, Ashley M.; Thielemans, Kris

2016-04-01

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant 18F-FDG and 18F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

Qualitative and quantitative analysis of the diuretic component ergone in Polyporus umbellatus by HPLC with fluorescence detection and HPLC-APCI-MS/MS.

PubMed

Zhao, Ying-Yong; Zhao, Ye; Zhang, Yong-Min; Lin, Rui-Chao; Sun, Wen-Ji

2009-06-01

Polyporus umbellatus is a widely used anti-aldosteronic diuretic in Traditional Chinese medicine (TCM). A new, sensitive and selective high-performance liquid chromatography-fluorescence detector (HPLC-FLD) and high-performance liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (HPLC-APCI-MS/MS) method for quantitative and qualitative determination of ergosta-4,6,8(14),22-tetraen-3-one(ergone), which is the main diuretic component, was provided for quality control of P. umbellatus crude drug. The ergone in the ethanolic extract of P. umbellatus was unambiguously characterized by HPLC-APCI, and further confirmed by comparing with a standard compound. The trace ergone was detected by the sensitive and selective HPLC-FLD. Linearity (r2 > 0.9998) and recoveries of low, medium and high concentration (100.5%, 100.2% and 100.4%) were consistent with the experimental criteria. The limit of detection (LOD) of ergone was around 0.2 microg/mL. Our results indicated that the content of ergone in P. umbellatus varied significantly from habitat to habitat with contents ranging from 2.13 +/- 0.02 to 59.17 +/- 0.05 microg/g. Comparison among HPLC-FLD and HPLC-UV or HPLC-APCI-MS/MS demonstrated that the HPLC-FLD and HPLC-APCI-MS/MS methods gave similar quantitative results for the selected herb samples, the HPLC-UV methods gave lower quantitative results than HPLC-FLD and HPLC-APCI-MS/MS methods. The established new HPLC-FLD method has the advantages of being rapid, simple, selective and sensitive, and could be used for the routine analysis of P. umbellatus crude drug.

Quantitative effects of cyanogenesis on an adapted herbivore.

PubMed

Ballhorn, D J; Heil, M; Pietrowski, A; Lieberei, R

2007-12-01

Plant cyanogenesis means the release of gaseous hydrogen cyanide (HCN) in response to cell damage and is considered as an effective defense against generalist herbivores. In contrast, specialists are generally believed not to be affected negatively by this trait. However, quantitative data on long-term effects of cyanogenesis on specialists are rare. In this study, we used lima bean accessions (Fabaceae: Phaseolus lunatus L.) with high quantitative variability of cyanogenic features comprising cyanogenic potential (HCNp; concentration of cyanogenic precursors) and cyanogenic capacities (HCNc; release of gaseous HCN per unit time). In feeding trials, we analyzed performance of herbivorous Mexican bean beetle (Coleoptera: Coccinellidae: Epilachna varivestis Mulsant) on selected lines characterized by high (HC-plants) and low HCNp (LC-plants). Larval and adult stages of this herbivore feed on a narrow range of legumes and prefer cyanogenic lima bean as host plant. Nevertheless, we found that performance of beetles (larval weight gain per time and body mass of adult beetles) was significantly affected by lima bean HCNp: Body weight decreased and developmental period of larvae and pupae increased on HC-plants during the first generation of beetles and then remained constant for four consecutive generations. In addition, we found continuously decreasing numbers of eggs and larval hatching as inter-generational effects on HC-plants. In contrast to HC-plants, constantly high performance was observed among four generations on LC-plants. Our results demonstrate that Mexican bean beetle, although preferentially feeding on lima bean, is quantitatively affected by the HCNp of its host plant. Effects can only be detected when considering more than one generation. Thus, cyanide-containing precursors can have negative effects even on herbivores adapted to feed on cyanogenic plants.

Genetic approaches in comparative and evolutionary physiology

PubMed Central

Bridgham, Jamie T.; Kelly, Scott A.; Garland, Theodore

2015-01-01

Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology. PMID:26041111

Genetic approaches in comparative and evolutionary physiology.

PubMed

Storz, Jay F; Bridgham, Jamie T; Kelly, Scott A; Garland, Theodore

2015-08-01

Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology. Copyright © 2015 the American Physiological Society.

A mixed model for the relationship between climate and human cranial form.

PubMed

Katz, David C; Grote, Mark N; Weaver, Timothy D

2016-08-01

We expand upon a multivariate mixed model from quantitative genetics in order to estimate the magnitude of climate effects in a global sample of recent human crania. In humans, genetic distances are correlated with distances based on cranial form, suggesting that population structure influences both genetic and quantitative trait variation. Studies controlling for this structure have demonstrated significant underlying associations of cranial distances with ecological distances derived from climate variables. However, to assess the biological importance of an ecological predictor, estimates of effect size and uncertainty in the original units of measurement are clearly preferable to significance claims based on units of distance. Unfortunately, the magnitudes of ecological effects are difficult to obtain with distance-based methods, while models that produce estimates of effect size generally do not scale to high-dimensional data like cranial shape and form. Using recent innovations that extend quantitative genetics mixed models to highly multivariate observations, we estimate morphological effects associated with a climate predictor for a subset of the Howells craniometric dataset. Several measurements, particularly those associated with cranial vault breadth, show a substantial linear association with climate, and the multivariate model incorporating a climate predictor is preferred in model comparison. Previous studies demonstrated the existence of a relationship between climate and cranial form. The mixed model quantifies this relationship concretely. Evolutionary questions that require population structure and phylogeny to be disentangled from potential drivers of selection may be particularly well addressed by mixed models. Am J Phys Anthropol 160:593-603, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Bevacizumab impairs oxidative energy metabolism and shows antitumoral effects in recurrent glioblastomas: a 31P/1H MRSI and quantitative magnetic resonance imaging study.

PubMed

Hattingen, Elke; Jurcoane, Alina; Bähr, Oliver; Rieger, Johannes; Magerkurth, Jörg; Anti, Sandra; Steinbach, Joachim P; Pilatus, Ulrich

2011-12-01

Bevacizumab shows unprecedented rates of response in recurrent glioblastomas (GBM), but the detailed mechanisms are still unclear. We employed in vivo magnetic resonance spectroscopic imaging (MRSI) and quantitative magnetic resonance imaging to investigate whether bevacizumab alters oxygen and energy metabolism and whether this effect has antitumoral activity in recurrent GBM. (31)P and (1)H MRSI, apparent diffusion coefficient (ADC), and high-resolution T2 and T2' mapping (indirect marker of oxygen extraction) were investigated in 16 patients with recurrent GBM at 3 Tesla before and 1.5-2 months after initiation of therapy with bevacizumab. Changes of metabolite concentrations and of the quantitative values in the tumor and normal appearing brain tissue were calculated. The Wilcoxon signed-ranks test was used to evaluate differences for tumor/edema versus control as well as changes before versus after commencement of therapy. Survival analyses were performed for significant parameters. Tumor T2', pH, ADC, and T2 decreased significantly in patients responding to bevacizumab therapy (n = 10). Patients with at least 25% T2' decrease during treatment showed longer progression-free and overall survival durations. Levels of high-energy metabolites were lower at baseline; these persisted under therapy. Glycerophosphoethanolamine as catabolic phospholipid metabolite increased in responders. The MRSI data support the hypothesis that bevacizumab induces relative tumor hypoxia (T2' decrease) and affects energy homeostasis in recurrent GBM, suggesting that bevacizumab impairs vascular function. The antiangiogenic effect of bevacizumab is predictive of better outcome and seems to induce antitumoral activity in the responding GBMs.

δ-aminolevulinic acid–induced protoporphyrin IX concentration correlates with histopathologic markers of malignancy in human gliomas: the need for quantitative fluorescence-guided resection to identify regions of increasing malignancy

PubMed Central

Valdés, Pablo A.; Kim, Anthony; Brantsch, Marco; Niu, Carolyn; Moses, Ziev B.; Tosteson, Tor D.; Wilson, Brian C.; Paulsen, Keith D.; Roberts, David W.; Harris, Brent T.

2011-01-01

Extent of resection is a major goal and prognostic factor in the treatment of gliomas. In this study we evaluate whether quantitative ex vivo tissue measurements of δ-aminolevulinic acid–induced protoporphyrin IX (PpIX) identify regions of increasing malignancy in low- and high-grade gliomas beyond the capabilities of current fluorescence imaging in patients undergoing fluorescence-guided resection (FGR). Surgical specimens were collected from 133 biopsies in 23 patients and processed for ex vivo neuropathological analysis: PpIX fluorimetry to measure PpIX concentrations (CPpIX) and Ki-67 immunohistochemistry to assess tissue proliferation. Samples displaying visible levels of fluorescence showed significantly higher levels of CPpIX and tissue proliferation. CPpIX was strongly correlated with histopathological score (nonparametric) and tissue proliferation (parametric), such that increasing levels of CPpIX were identified with regions of increasing malignancy. Furthermore, a large percentage of tumor-positive biopsy sites (∼40%) that were not visibly fluorescent under the operating microscope had levels of CPpIX greater than 0.1 µg/mL, which indicates that significant PpIX accumulation exists below the detection threshold of current fluorescence imaging. Although PpIX fluorescence is recognized as a visual biomarker for neurosurgical resection guidance, these data show that it is quantitatively related at the microscopic level to increasing malignancy in both low- and high-grade gliomas. This work suggests a need for improved PpIX fluorescence detection technologies to achieve better sensitivity and quantification of PpIX in tissue during surgery. PMID:21798847

Pannus invasion and cartilage degradation in rheumatoid arthritis: involvement of MMP-3 and interleukin-1beta.

PubMed

Ainola, M M; Mandelin, J A; Liljeström, M P; Li, T F; Hukkanen, M V J; Konttinen, Y T

2005-01-01

Synovial inflammation in rheumatoid arthritis (RA) leads to pannus tissue invasion and destruction of cartilage/bone matrix by proteinases. Our intention was to analyze some of the key matrix metalloproteinases (MMPs) in pannus tissue overlying evolving cartilage erosions in RA. Frozen tissue samples of pannus and synovium from advanced RA and synovium from osteoarthritic patients were used for immunohistochemical, western blotting and quantitative reverse transcriptase polymerase chain reaction (RT-PCR) analysis of MMP-1, -3, -13 and -14. Synovial fibroblast cultures, stimulated with tumour necrosis factor alpha (TNF-alpha) and interleukin-1 beta (IL-1beta), were analyzed with enzyme-linked immunosorbent assays (ELISA) and quantitative RT-PCR. MMP-3 was highly expressed in pannus tissue compared with significantly lower expression levels of MMP-1, -13 and -14. In fibroblast cultures IL-1beta was a potent stimulus for MMP-3, whereas TNF-alpha was more potent for MMP-1. This is the first study to demonstrate quantitatively in real time that MMP-3 mRNA expression is clearly higher in advanced RA pannus tissue compared to parallel RA or osteoarthritic synovium. MMP-3 mRNA levels were also clearly overexpressed in RA pannus compared to MMP-1, -13 and -14. Advanced RA has previously been found to overexpress IL-1beta. The high expression of MMP-3 in pannus and IL-1beta, mediated stimulation of MMP-3 suggest that MMP-3 plays a significant role in the progression of erosions through the proteoglycan-rich cartilage matrix.

Piezoelectricity above the Curie temperature? Combining flexoelectricity and functional grading to enable high-temperature electromechanical coupling

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

Mbarki, R.; Baccam, N.; Dayal, Kaushik

Most technologically relevant ferroelectrics typically lose piezoelectricity above the Curie temperature. This limits their use to relatively low temperatures. In this Letter, exploiting a combination of flexoelectricity and simple functional grading, we propose a strategy for high-temperature electromechanical coupling in a standard thin film configuration. We use continuum modeling to quantitatively demonstrate the possibility of achieving apparent piezoelectric materials with large and temperature-stable electromechanical coupling across a wide temperature range that extends significantly above the Curie temperature. With Barium and Strontium Titanate, as example materials, a significant electromechanical coupling that is potentially temperature-stable up to 900 °C is possible.

Quantitative analysis of 18F-NaF dynamic PET/CT cannot differentiate malignant from benign lesions in multiple myeloma.

PubMed

Sachpekidis, Christos; Hillengass, Jens; Goldschmidt, Hartmut; Anwar, Hoda; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-01-01

A renewed interest has been recently developed for the highly sensitive bone-seeking radiopharmaceutical 18 F-NaF. Aim of the present study is to evaluate the potential utility of quantitative analysis of 18 F-NaF dynamic PET/CT data in differentiating malignant from benign degenerative lesions in multiple myeloma (MM). 80 MM patients underwent whole-body PET/CT and dynamic PET/CT scanning of the pelvis with 18 F-NaF. PET/CT data evaluation was based on visual (qualitative) assessment, semi-quantitative (SUV) calculations, and absolute quantitative estimations after application of a 2-tissue compartment model and a non-compartmental approach leading to the extraction of fractal dimension (FD). In total 263 MM lesions were demonstrated on 18 F-NaF PET/CT. Semi-quantitative and quantitative evaluations were performed for 25 MM lesions as well as for 25 benign, degenerative and traumatic lesions. Mean SUV average for MM lesions was 11.9 and mean SUV max was 23.2. Respectively, SUV average and SUV max for degenerative lesions were 13.5 and 20.2. Kinetic analysis of 18 F-NaF revealed the following mean values for MM lesions: K 1 = 0.248 (1/min), k 3 = 0.359 (1/min), influx (K i ) = 0.107 (1/min), FD = 1.382, while the respective values for degenerative lesions were: K 1 = 0.169 (1/min), k 3 = 0.422 (1/min), influx (K i ) = 0.095 (1/min), FD = 1. 411. No statistically significant differences between MM and benign degenerative disease regarding SUV average , SUV max , K 1 , k 3 and influx (K i ) were demonstrated. FD was significantly higher in degenerative than in malignant lesions. The present findings show that quantitative analysis of 18 F-NaF PET data cannot differentiate malignant from benign degenerative lesions in MM patients, supporting previously published results, which reflect the limited role of 18 F-NaF PET/CT in the diagnostic workup of MM.

Conceptual development and retention within the learning cycle

NASA Astrophysics Data System (ADS)

McWhirter, Lisa Jo

1998-12-01

This research was designed to achieve two goals: (1) examine concept development and retention within the learning cycle and (2) examine how students' concept development is mediated by classroom discussions and the students' small cooperative learning group. Forty-eight sixth-grade students and one teacher at an urban middle school participated in the study. The research utilized both quantitative and qualitative analyses. Quantitative assessments included a concept mapping technique as well as teacher generated multiple choice tests. Preliminary quantitative analysis found that students' reading levels had an effect on students' pretest scores in both the concept mapping and the multiple-choice assessment. Therefore, a covariant design was implemented for the quantitative analyses. Quantitative analysis techniques were used to examine concept development and retention, it was discovered that the students' concept knowledge increased significantly from the time of the conclusion of the term introduction phase to the conclusion of the expansion phase. These findings would indicate that all three phases of the learning cycle are necessary for conceptual development. However, quantitative analyses of concept maps indicated that this is not true for all students. Individual students showed evidence of concept development and integration at each phase. Therefore, concept development is individualized and all phases of the learning cycle are not necessary for all students. As a result, individual's assimilation, disequilibration, accommodation and organization may not correlate with the phases of the learning cycle. Quantitative analysis also indicated a significant decrease in the retention of concepts over time. Qualitative analyses were used to examine how students' concept development is mediated by classroom discussions and the students' small cooperative learning group. It was discovered that there was a correlation between teacher-student interaction and small-group interaction and concept mediation. Therefore, students who had a high level of teacher-student dialogue which utilized teacher led discussions with integrated scaffolding techniques where the same students who mediated the ideas within the small group discussions. Those students whose teacher-student interactions consisted of dialogue with little positive teacher feedback made no contributions within the small group regardless of their level of concept development.

Development of a quantitative diagnostic method of estrogen receptor expression levels by immunohistochemistry using organic fluorescent material-assembled nanoparticles

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

Gonda, Kohsuke, E-mail: gonda@med.tohoku.ac.jp; Miyashita, Minoru; Watanabe, Mika

2012-09-28

Highlights: Black-Right-Pointing-Pointer Organic fluorescent material-assembled nanoparticles for IHC were prepared. Black-Right-Pointing-Pointer New nanoparticle fluorescent intensity was 10.2-fold greater than Qdot655. Black-Right-Pointing-Pointer Nanoparticle staining analyzed a wide range of ER expression levels in tissue. Black-Right-Pointing-Pointer Nanoparticle staining enhanced the quantitative sensitivity for ER diagnosis. -- Abstract: The detection of estrogen receptors (ERs) by immunohistochemistry (IHC) using 3,3 Prime -diaminobenzidine (DAB) is slightly weak as a prognostic marker, but it is essential to the application of endocrine therapy, such as antiestrogen tamoxifen-based therapy. IHC using DAB is a poor quantitative method because horseradish peroxidase (HRP) activity depends on reaction time, temperature andmore » substrate concentration. However, IHC using fluorescent material provides an effective method to quantitatively use IHC because the signal intensity is proportional to the intensity of the photon excitation energy. However, the high level of autofluorescence has impeded the development of quantitative IHC using fluorescence. We developed organic fluorescent material (tetramethylrhodamine)-assembled nanoparticles for IHC. Tissue autofluorescence is comparable to the fluorescence intensity of quantum dots, which are the most representative fluorescent nanoparticles. The fluorescent intensity of our novel nanoparticles was 10.2-fold greater than quantum dots, and they did not bind non-specifically to breast cancer tissues due to the polyethylene glycol chain that coated their surfaces. Therefore, the fluorescent intensity of our nanoparticles significantly exceeded autofluorescence, which produced a significantly higher signal-to-noise ratio on IHC-imaged cancer tissues than previous methods. Moreover, immunostaining data from our nanoparticle fluorescent IHC and IHC with DAB were compared in the same region of adjacent tissues sections to quantitatively examine the two methods. The results demonstrated that our nanoparticle staining analyzed a wide range of ER expression levels with higher accuracy and quantitative sensitivity than DAB staining. This enhancement in the diagnostic accuracy and sensitivity for ERs using our immunostaining method will improve the prediction of responses to therapies that target ERs and progesterone receptors that are induced by a downstream ER signal.« less

Quantitative Reasoning in Environmental Science: A Learning Progression

ERIC Educational Resources Information Center

Mayes, Robert Lee; Forrester, Jennifer Harris; Christus, Jennifer Schuttlefield; Peterson, Franziska Isabel; Bonilla, Rachel; Yestness, Nissa

2014-01-01

The ability of middle and high school students to reason quantitatively within the context of environmental science was investigated. A quantitative reasoning (QR) learning progression was created with three progress variables: quantification act, quantitative interpretation, and quantitative modeling. An iterative research design was used as it…

An assessment of the reliability of quantitative genetics estimates in study systems with high rate of extra-pair reproduction and low recruitment.

PubMed

Bourret, A; Garant, D

2017-03-01

Quantitative genetics approaches, and particularly animal models, are widely used to assess the genetic (co)variance of key fitness related traits and infer adaptive potential of wild populations. Despite the importance of precision and accuracy of genetic variance estimates and their potential sensitivity to various ecological and population specific factors, their reliability is rarely tested explicitly. Here, we used simulations and empirical data collected from an 11-year study on tree swallow (Tachycineta bicolor), a species showing a high rate of extra-pair paternity and a low recruitment rate, to assess the importance of identity errors, structure and size of the pedigree on quantitative genetic estimates in our dataset. Our simulations revealed an important lack of precision in heritability and genetic-correlation estimates for most traits, a low power to detect significant effects and important identifiability problems. We also observed a large bias in heritability estimates when using the social pedigree instead of the genetic one (deflated heritabilities) or when not accounting for an important cause of resemblance among individuals (for example, permanent environment or brood effect) in model parameterizations for some traits (inflated heritabilities). We discuss the causes underlying the low reliability observed here and why they are also likely to occur in other study systems. Altogether, our results re-emphasize the difficulties of generalizing quantitative genetic estimates reliably from one study system to another and the importance of reporting simulation analyses to evaluate these important issues.

Monitoring the dynamics of syntrophic β-oxidizing bacteria during anaerobic degradation of oleic acid by quantitative PCR.

PubMed

Ziels, Ryan M; Beck, David A C; Martí, Magalí; Gough, Heidi L; Stensel, H David; Svensson, Bo H

2015-04-01

The ecophysiology of long-chain fatty acid-degrading syntrophic β-oxidizing bacteria has been poorly understood due to a lack of quantitative abundance data. Here, TaqMan quantitative PCR (qPCR) assays targeting the 16S rRNA gene of the known mesophilic syntrophic β-oxidizing bacterial genera Syntrophomonas and Syntrophus were developed and validated. Microbial community dynamics were followed using qPCR and Illumina-based high-throughput amplicon sequencing in triplicate methanogenic bioreactors subjected to five consecutive batch feedings of oleic acid. With repeated oleic acid feeding, the initial specific methane production rate significantly increased along with the relative abundances of Syntrophomonas and methanogenic archaea in the bioreactor communities. The novel qPCR assays showed that Syntrophomonas increased from 7 to 31% of the bacterial community 16S rRNA gene concentration, whereas that of Syntrophus decreased from 0.02 to less than 0.005%. High-throughput amplicon sequencing also revealed that Syntrophomonas became the dominant genus within the bioreactor microbiomes. These results suggest that increased specific mineralization rates of oleic acid were attributed to quantitative shifts within the microbial communities toward higher abundances of syntrophic β-oxidizing bacteria and methanogenic archaea. The novel qPCR assays targeting syntrophic β-oxidizing bacteria may thus serve as monitoring tools to indicate the fatty acid β-oxidization potential of anaerobic digester communities. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Seasonal development of cambial activity in relation to xylem formation in Chinese fir.

PubMed

Wu, Hongyang; Xu, Huimin; Li, Hanyin; Wei, Dongmei; Lin, Jinxing; Li, Xiaojuan

2016-05-20

The vascular cambium is a lateral meristem which can differentiate into secondary phloem and xylem. The secondary growth of woody plants resulting from vascular cambium activity has been a focus of considerable attention, but the quantitative relationships between cambial activity and secondary xylem formation have been little studied. Our analysis of cytological changes in the cambium of Chinese fir (Cunninghamia lanceolata), revealed a significant positive correlation between vascular cambium cell numbers and cambium zone width through the seasonal cycle. Cambium cell numbers and the cambium cell radial diameter were closely related to xylem formation. Immuno-labeling showed that de-esterified homogalacturonan and (1-4)-β-d-galactan epitopes were highly abundant in cell walls of dormant-stage cambium, whereas high methylesterified homogalacturonan was strongly labeled in the active stage. Raman spectroscopy detected significant changes in the chemical composition of cell walls during the active-dormant stage transition. More pectin and less monolignols occurred in radial cell walls than in tangential walls during the dormant stage, but no significant changes were found in other stages, indicating that pectin accumulation facilitates cell wall expansion, with cambium activity transition. Our quantitative analysis of the relationship between cambial activity and xylem formation, as well as the cell wall modification during the active stage provides useful information about cambial characteristics and xylogenesis. Copyright © 2016. Published by Elsevier GmbH.

Chromosomal mapping of quantitative trait loci controlling elastin content in rat aorta.

PubMed

Gauguier, Dominique; Behmoaras, Jacques; Argoud, Karène; Wilder, Steven P; Pradines, Christelle; Bihoreau, Marie Thérèse; Osborne-Pellegrin, Mary; Jacob, Marie Paule

2005-03-01

Extracellular matrix molecules such as elastin and collagens provide mechanical support to the vessel wall. In addition to its structural role, elastin is a regulator that maintains homeostasis through biologic signaling. Genetically determined minor modifications in elastin and collagen in the aorta could influence the onset and evolution of arterial pathology, such as hypertension and its complications. We previously demonstrated that the inbred Brown Norway (BN) rat shows an aortic elastin deficit in both abdominal and thoracic segments, partly because of a decrease in tropoelastin synthesis when compared with the LOU rat, that elastin gene polymorphisms in these strains do not significantly account for. After a genome-wide search for quantitative trait loci (QTL) influencing the aortic elastin, collagen, and cell protein contents in an F2 population derived from BN and LOU rats, we identified on chromosomes 2 and 14, 3 QTL specifically controlling elastin levels, and a further highly significant QTL on chromosome 17 linked to the level of cell proteins. We also mapped 3 highly significant QTL linked to body weight (on chromosomes 1 and 3) and heart weight (on chromosome 1) in the cross. This study demonstrates the polygenic control of the content of key components of the arterial wall. Such information represents a first step in understanding possible mechanisms involved in dysregulation of these parameters in arterial pathology.

Label-Free Imaging of Female Genital Tract Melanocytic Lesions With Pump-Probe Microscopy: A Promising Diagnostic Tool.

PubMed

Robles, Francisco E; Deb, Sanghamitra; Fischer, Martin C; Warren, Warren S; Selim, Maria Angelica

2017-04-01

Melanomas of the female genital tract present a unique clinical challenge. Not only are these lesions in an anatomically sensitive area, but also they tend to be multifocal and have high recurrence rates. Furthermore, several benign melanocytic proliferations resemble early-stage melanoma clinically and/or histopathologically. Thus, there is a significant need for additional tools that can help correctly diagnose and stage these lesions. Here, we quantitatively and nondestructively analyze the chemical composition of melanin in excised pigmented lesions of the female genital tract using pump-probe microscopy, a high-resolution optical imaging technique that is sensitive to many biochemical properties of melanin. Thirty-one thin (~5 μm) tissue sections previously excised from female genital tract melanocytic lesions were imaged with pump-probe microscopy and analyzed. We find significant quantitative differences in melanin type and structure between melanoma and nonmalignant melanocytic proliferations. Our analysis also suggests a link between the molecular signatures of melanins and lesion-specific genetic mutations. Finally, significant differences are found between metastatic and nonmetastatic melanomas. The limitations of this work include the fact that molecular information is restricted to melanin pigment and the sample size is relatively small. Pump-probe microscopy provides unique information regarding the biochemical composition of genital tract melanocytic lesions, which can be used to improve the diagnosis and staging of vulvar melanomas.

Resected Brain Tissue, Seizure Onset Zone and Quantitative EEG Measures: Towards Prediction of Post-Surgical Seizure Control

PubMed Central

Andrzejak, Ralph G.; Hauf, Martinus; Pollo, Claudio; Müller, Markus; Weisstanner, Christian; Wiest, Roland; Schindler, Kaspar

2015-01-01

Background Epilepsy surgery is a potentially curative treatment option for pharmacoresistent patients. If non-invasive methods alone do not allow to delineate the epileptogenic brain areas the surgical candidates undergo long-term monitoring with intracranial EEG. Visual EEG analysis is then used to identify the seizure onset zone for targeted resection as a standard procedure. Methods Despite of its great potential to assess the epileptogenicty of brain tissue, quantitative EEG analysis has not yet found its way into routine clinical practice. To demonstrate that quantitative EEG may yield clinically highly relevant information we retrospectively investigated how post-operative seizure control is associated with four selected EEG measures evaluated in the resected brain tissue and the seizure onset zone. Importantly, the exact spatial location of the intracranial electrodes was determined by coregistration of pre-operative MRI and post-implantation CT and coregistration with post-resection MRI was used to delineate the extent of tissue resection. Using data-driven thresholding, quantitative EEG results were separated into normally contributing and salient channels. Results In patients with favorable post-surgical seizure control a significantly larger fraction of salient channels in three of the four quantitative EEG measures was resected than in patients with unfavorable outcome in terms of seizure control (median over the whole peri-ictal recordings). The same statistics revealed no association with post-operative seizure control when EEG channels contributing to the seizure onset zone were studied. Conclusions We conclude that quantitative EEG measures provide clinically relevant and objective markers of target tissue, which may be used to optimize epilepsy surgery. The finding that differentiation between favorable and unfavorable outcome was better for the fraction of salient values in the resected brain tissue than in the seizure onset zone is consistent with growing evidence that spatially extended networks might be more relevant for seizure generation, evolution and termination than a single highly localized brain region (i.e. a “focus”) where seizures start. PMID:26513359

Quantitative and Qualitative Assessment of Pulmonary Emphysema with T2-Weighted PROPELLER MRI in a High-Risk Population Compared to Low-Dose CT.

PubMed

Meier-Schroers, Michael; Sprinkart, Alois Martin; Becker, Manuel; Homsi, Rami; Thomas, Daniel

2018-03-07

 To determine the suitability of T2-weighted PROPELLER MRI for the assessment of pulmonary emphysema.  60 participants in a lung cancer screening program (30 subjects with pulmonary emphysema, and 30 control subjects without emphysema) were included for this retrospective study. All subjects were examined with low-dose CT (LDCT) and MRI within the screening program. The use of a T2-weighted PROPELLER sequence for the assessment of emphysema was analyzed and correlated with the results of LDCT. The presence and the extent of pulmonary emphysema were first assessed qualitatively using a three-point score, and then quantitatively with a semi-automated software program to obtain emphysema indices.  All 30 cases with pulmonary emphysema were accurately detected by MRI. There were 3 cases with emphysema according to MRI without emphysematous changes on LDCT (false-positive results). The qualitative scores as well as the emphysema indices were significantly higher in the emphysema group compared to the control group for MRI and LDCT (p < 0.001). Both the scores and the indices correlated significantly between MRI and LDCT (qualitative score of severity: r = 0.912/p < 0.001 in the emphysema group and r = 0.668/p < 0.001 in the control group; emphysema index: r = 0.960/p < 0.001 in the emphysema group and r = 0.746/p < 0.001 in the control group).  The presence and the extent of pulmonary emphysema may be assessed qualitatively and quantitatively by T2-weighted PROPELLER MRI with very good correlation to LDCT.   · T2-weighted PROPELLER MRI may be suitable for the assessment of pulmonary emphysema.. · There was significant correlation between MRI and LDCT regarding qualitative scores and quantitative emphysema indices in our study with correlation coefficients for different subgroups ranging from r = 0.668 to r = 0.960.. · T2-weighted PROPELLER MRI may have the potential to be used for follow-up examinations in patients with severe emphysema to avoid radiation exposure of repeated CTs.. · Meier-Schroers M, Sprinkart AM, Becker M et al. Quantitative and Qualitative Assessment of Pulmonary Emphysema with T2-Weighted PROPELLER MRI in a High-Risk Population Compared to Low-Dose CT. Fortschr Röntgenstr 2018; DOI: 10.1055/a-0577-5619. © Georg Thieme Verlag KG Stuttgart · New York.

Adaptational changes in the lipids and fatty acid profile of the cell and thylakoid membrane of rice plants exposed to sunlight.

PubMed

Vaz, Janet F; Sharma, Prabhat Kumar

2010-07-01

Adaptational changes occurring in the lipids and fatty acids of the cell and the thylakoid membrane in response to high light treatment, was studied in 30 days old rice (Oryza sativa L. cv. Jyothi) plants grown under low (150-200 μmol m(-2) s(-1)) or moderate (600-800 μmol m(-2) s(-1)) light conditions. Results were compared with rice plants grown in high (1200-2200 μmol m(-2) s(-1)) light conditions. Exposure of rice plants and isolated chloroplast to high light, resulted in an increase in the amount of malonaldehyde, indicating oxidation of membrane lipids. Qualitative and quantitative changes in the phosphoglycolipids and quantitative changes in neutral lipids were observed in rice plants grown under the different growth conditions. A few of the phosphoglycolipids and neutral lipids were present exclusively in plants grown at low or moderate or high light, indicating requirement of different type of lipid composition of rice plants in response to their different growth irradiances. However, no significant quantitative changes were observed in the different saturated and unsaturated fatty acid groups of total lipids in low, moderate and high light grown rice plants, as a result of exposure to high light. No qualitative changes in the fatty acid composition due to difference in growth irradiance or high light treatment were seen. The changes observed in the phosphoglycolipids and neutral lipid composition of cell and thylakoid membrane of low, moderate and high light grown rice plants in response to high light, are probably the result of physiological changes in the rice plants, to sustain optimum structure and function of the cell and thylakoid membrane to maintain active physiological functions to endure high light conditions.

Phenotypic characterization of glioblastoma identified through shape descriptors

NASA Astrophysics Data System (ADS)

Chaddad, Ahmad; Desrosiers, Christian; Toews, Matthew

2016-03-01

This paper proposes quantitatively describing the shape of glioblastoma (GBM) tissue phenotypes as a set of shape features derived from segmentations, for the purposes of discriminating between GBM phenotypes and monitoring tumor progression. GBM patients were identified from the Cancer Genome Atlas, and quantitative MR imaging data were obtained from the Cancer Imaging Archive. Three GBM tissue phenotypes are considered including necrosis, active tumor and edema/invasion. Volumetric tissue segmentations are obtained from registered T1˗weighted (T1˗WI) postcontrast and fluid-attenuated inversion recovery (FLAIR) MRI modalities. Shape features are computed from respective tissue phenotype segmentations, and a Kruskal-Wallis test was employed to select features capable of classification with a significance level of p < 0.05. Several classifier models are employed to distinguish phenotypes, where a leave-one-out cross-validation was performed. Eight features were found statistically significant for classifying GBM phenotypes with p <0.05, orientation is uninformative. Quantitative evaluations show the SVM results in the highest classification accuracy of 87.50%, sensitivity of 94.59% and specificity of 92.77%. In summary, the shape descriptors proposed in this work show high performance in predicting GBM tissue phenotypes. They are thus closely linked to morphological characteristics of GBM phenotypes and could potentially be used in a computer assisted labeling system.

Quantitative contrast-enhanced ultrasound for monitoring vedolizumab therapy in inflammatory bowel disease patients: a pilot study.

PubMed

Goertz, Ruediger S; Klett, Daniel; Wildner, Dane; Atreya, Raja; Neurath, Markus F; Strobel, Deike

2018-01-01

Background Microvascularization of the bowel wall can be visualized and quantified non-invasively by software-assisted analysis of derived time-intensity curves. Purpose To perform software-based quantification of bowel wall perfusion using quantitative contrast-enhanced ultrasound (CEUS) according to clinical response in patients with inflammatory bowel disease treated with vedolizumab. Material and Methods In a prospective study, in 18 out of 34 patients, high-frequency ultrasound of bowel wall thickness using color Doppler flow combined with CEUS was performed at baseline and after 14 weeks of treatment with vedolizumab. Clinical activity scores at week 14 were used to differentiate between responders and non-responders. CEUS parameters were calculated by software analysis of the video loops. Results Nine of 18 patients (11 with Crohn's disease and seven with ulcerative colitis) showed response to treatment with vedolizumab. Overall, the responder group showed a significant decrease in the semi-quantitative color Doppler vascularization score. Amplitude-derived CEUS parameters of mural microvascularization such as peak enhancement or wash-in rate decreased in responders, in contrast with non-responders. Time-derived parameters remained stable or increased during treatment in all patients. Conclusion Analysis of bowel microvascularization by CEUS shows statistically significant changes in the wash-in-rate related to response of vedolizumab therapy.

Statistical correction of the Winner’s Curse explains replication variability in quantitative trait genome-wide association studies

PubMed Central

Pe’er, Itsik

2017-01-01

Genome-wide association studies (GWAS) have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10−14), even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner’s Curse (p < 10−16). We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94). In contrast, ancestry differences between replication and discovery (13 studies, 385 loci) cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium. PMID:28715421

Influence of wastewater treatment plant discharges on microplastic concentrations in surface water.

PubMed

Estahbanati, Shirin; Fahrenfeld, N L

2016-11-01

The abundance of microplastic particles in the marine environment is well documented, but less is known about microplastics in the freshwater environment. Wastewater treatment plants (WWTPs) may not effectively remove microplastics allowing for their release to the freshwater environment. To investigate concentration of microplastic in fresh water and the impact of WWTP effluent, samples were collected upstream and downstream of four major municipal WWTPs on the Raritan River, NJ. Microplastics were categorized into three quantitative categories (500-2000 μm, 250-500 μm, 125-250 μm), and one semi-quantitative category (63-125 μm). Then, microplastics were classified as primary (manufactured in small size) or secondary (derived from larger plastics) based on morphology. The concentration of microplastics in the 125-250 and 250-500 μm size categories significantly increased downstream of WWTP. The smaller size classes, often not quantified in microplastic studies, were in high relative abundance across sampling sites. While primary microplastics significantly increased downstream of WWTP, secondary microplastic was the dominant type in the quantitative size categories (66-88%). A moderate correlation between microplastic and distance downstream was observed. These results have implications for understanding the fate and transport of microplastics in the freshwater environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Harm Done to Reproducibility by the Culture of Null Hypothesis Significance Testing.

PubMed

Lash, Timothy L

2017-09-15

In the last few years, stakeholders in the scientific community have raised alarms about a perceived lack of reproducibility of scientific results. In reaction, guidelines for journals have been promulgated and grant applicants have been asked to address the rigor and reproducibility of their proposed projects. Neither solution addresses a primary culprit, which is the culture of null hypothesis significance testing that dominates statistical analysis and inference. In an innovative research enterprise, selection of results for further evaluation based on null hypothesis significance testing is doomed to yield a low proportion of reproducible results and a high proportion of effects that are initially overestimated. In addition, the culture of null hypothesis significance testing discourages quantitative adjustments to account for systematic errors and quantitative incorporation of prior information. These strategies would otherwise improve reproducibility and have not been previously proposed in the widely cited literature on this topic. Without discarding the culture of null hypothesis significance testing and implementing these alternative methods for statistical analysis and inference, all other strategies for improving reproducibility will yield marginal gains at best. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Quantitative trait loci for a neurocranium deformity, lack of operculum, in gilthead seabream (Sparus aurata L.).

PubMed

Negrín-Báez, D; Navarro, A; Afonso, J M; Toro, M A; Zamorano, M J

2016-04-01

Lack of operculum, a neurocranial deformity, is the most common external abnormality to be found among industrially produced gilthead seabream (Sparus aurata L.), and this entails significant financial losses. This study conducts, for the first time in this species, a quantitative trait loci (QTL) analysis of the lack of operculum. A total of 142 individuals from a paternal half-sibling family (six full-sibling families) were selected for QTL mapping. They had previously shown a highly significant association with the prevalence of lack of operculum in a segregation analysis. All the fish were genotyped for 106 microsatellite markers using a set of multiplex PCRs (ReMsa1-ReMsa13). A linear regression methodology was used for the QTL analysis. Four QTL were detected for this deformity, two of which (QTLOP1 and QTLOP2) were significant. They were located at LG (linkage group) nine and LG10 respectively. Both QTL showed a large effect (about 27%), and furthermore, the association between lack of operculum and sire allelic segregation observed was statistically significant in the QTLOP1 analysis. These results represent a significant step towards including marker-assisted selection for this deformity in genetic breeding programmes to reduce the incidence of the deformity in the species. © 2016 Stichting International Foundation for Animal Genetics.

Geographic and demographic variabilities of quantitative parameters in stress myocardial computed tomography perfusion.

PubMed

Park, Jinoh; Kim, Hyun-Sook; Hwang, Hye Jeon; Yang, Dong Hyun; Koo, Hyun Jung; Kang, Joon-Won; Kim, Young-Hak

2017-09-01

To evaluate the geographic and demographic variabilities of the quantitative parameters of computed tomography perfusion (CTP) of the left ventricular (LV) myocardium in patients with normal coronary artery on computed tomography angiography (CTA). From a multicenter CTP registry of stress and static computed tomography, we retrospectively recruited 113 patients (mean age, 60 years; 57 men) without perfusion defect on visual assessment and minimal (< 20% of diameter stenosis) or no coronary artery disease on CTA. Using semiautomatic analysis software, quantitative parameters of the LV myocardium, including the myocardial attenuation in stress and rest phases, transmural perfusion ratio (TPR), and myocardial perfusion reserve index (MPRI), were evaluated in 16 myocardial segments. In the lateral wall of the LV myocardium, all quantitative parameters except for MPRI were significantly higher compared with those in the other walls. The MPRI showed consistent values in all myocardial walls (anterior to lateral wall: range, 25% to 27%; p = 0.401). At the basal level of the myocardium, all quantitative parameters were significantly lower than those at the mid- and apical levels. Compared with men, women had significantly higher values of myocardial attenuation and TPR. Age, body mass index, and Framingham risk score were significantly associated with the difference in myocardial attenuation. Geographic and demographic variabilities of quantitative parameters in stress myocardial CTP exist in healthy subjects without significant coronary artery disease. This information may be helpful when assessing myocardial perfusion defects in CTP.

Statistical analysis of electroconvection near an ion-selective membrane in the highly chaotic regime

NASA Astrophysics Data System (ADS)

Druzgalski, Clara; Mani, Ali

2016-11-01

We investigate electroconvection and its impact on ion transport in a model system comprised of an ion-selective membrane, an aqueous electrolyte, and an external electric field applied normal to the membrane. We develop a direct numerical simulation code to solve the governing Poisson-Nernst-Planck and Navier-Stokes equations in three dimensions using a specialized parallel numerical algorithm and sufficient resolution to capture the high frequency and high wavenumber physics. We show a comprehensive statistical analysis of the transport phenomena in the highly chaotic regime. Qualitative and quantitative comparisons of two-dimensional (2D) and 3D simulations include prediction of the mean concentration fields as well as the spectra of concentration, charge density, and velocity signals. Our analyses reveal a significant quantitative difference between 2D and 3D electroconvection. Furthermore, we show that high-intensity yet short-lived current density hot spots appear randomly on the membrane surface, contributing significantly to the mean current density. By examining cross correlations between current density on the membrane and other field quantities we explore the physical mechanisms leading to current hot spots. We also present analysis of transport fluxes in the context of ensemble-averaged equations. Our analysis reveals that in the highly chaotic regime the mixing layer (ML), which spans the majority of the domain extent, is governed by advective fluctuations. Furthermore, we show that in the ML the mean electromigration fluxes cancel out for positive and negative ions, indicating that the mean transport of total salt content within the ML can be represented via the electroneutral approximation. Finally, we present an assessment of the importance of different length scales in enhancing transport by computing the cross covariance of concentration and velocity fluctuations in the wavenumber space. Our analysis indicates that in the majority of the domain the large scales contribute most significantly to transport, while the effects of small scales become more appreciable in regions very near the membrane.

Portable low-coherence interferometry for quantitatively imaging fast dynamics with extended field of view

NASA Astrophysics Data System (ADS)

Shaked, Natan T.; Girshovitz, Pinhas; Frenklach, Irena

2014-06-01

We present our recent advances in the development of compact, highly portable and inexpensive wide-field interferometric modules. By a smart design of the interferometric system, including the usage of low-coherence illumination sources and common-path off-axis geometry of the interferometers, spatial and temporal noise levels of the resulting quantitative thickness profile can be sub-nanometric, while processing the phase profile in real time. In addition, due to novel experimentally-implemented multiplexing methods, we can capture low-coherence off-axis interferograms with significantly extended field of view and in faster acquisition rates. Using these techniques, we quantitatively imaged rapid dynamics of live biological cells including sperm cells and unicellular microorganisms. Then, we demonstrated dynamic profiling during lithography processes of microscopic elements, with thicknesses that may vary from several nanometers to hundreds of microns. Finally, we present new algorithms for fast reconstruction (including digital phase unwrapping) of off-axis interferograms, which allow real-time processing in more than video rate on regular single-core computers.

Alpha-A crystallin: quantitation of C-terminal modification during lens aging

NASA Technical Reports Server (NTRS)

Takemoto, L.; Gopalakrishnan, S.; Spooner, B. S. (Principal Investigator)

1994-01-01

Previous studies have demonstrated that the C-terminal region of alpha-A crystallin is susceptible to age-dependent, posttranslational modification. To quantitate the amount of modification, alpha-A crystallin was purified from total proteins of the aging bovine lens, then digested with lys-C endoproteinase. Reverse phase, high pressure liquid chromatography was used to resolve and quantitate the resulting peptides, to determine the amount of C-terminal peptide relative to peptides from other regions of the protein that have not been reported to undergo modification. The results indicate that relative to alpha-A crystallin from newborn lens, posttranslational modification has occurred in approximately 45-55% of the C-terminal region from mature lens. These results demonstrate extensive modification of the C-terminal region of alpha-A crystallin from the mature lens, indicating that during the aging process, posttranslational modifications in this region may make significant contributions to the aggregated state and/or molecular chaperone properties of the molecule.

Dynamic inundation mapping of Hurricane Harvey flooding in the Houston metro area using hyper-resolution modeling and quantitative image reanalysis

NASA Astrophysics Data System (ADS)

Noh, S. J.; Lee, J. H.; Lee, S.; Zhang, Y.; Seo, D. J.

2017-12-01

Hurricane Harvey was one of the most extreme weather events in Texas history and left significant damages in the Houston and adjoining coastal areas. To understand better the relative impact to urban flooding of extreme amount and spatial extent of rainfall, unique geography, land use and storm surge, high-resolution water modeling is necessary such that natural and man-made components are fully resolved. In this presentation, we reconstruct spatiotemporal evolution of inundation during Hurricane Harvey using hyper-resolution modeling and quantitative image reanalysis. The two-dimensional urban flood model used is based on dynamic wave approximation and 10 m-resolution terrain data, and is forced by the radar-based multisensor quantitative precipitation estimates. The model domain includes Buffalo, Brays, Greens and White Oak Bayous in Houston. The model is simulated using hybrid parallel computing. To evaluate dynamic inundation mapping, we combine various qualitative crowdsourced images and video footages with LiDAR-based terrain data.

Ultrasensitive Sample Quantitation via Selected Reaction Monitoring Using CITP/CZE-ESI-Triple Quadrupole MS

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

Wang, Chenchen; Lee, Cheng S.; Smith, Richard D.

2012-11-10

We demonstrate the direct coupling of transient capillary isotachophoresis/ capillary zone electrophoresis (CITP/CZE) with a high sensitivity triple quadrupole mass spectrometer operating in selected reaction monitoring (SRM) mode for sample quantitation. The capability of CITP/CZE for in situ sample enrichment and separation has been shown to significantly improve the analytical figures of merit. A linear dynamic range spanning more than 4 orders of magnitude was observed. An average signal-to-noise ratio (S/N) of 49.6 was observed for 50 attomoles of targeted peptide in the presence of a complex and much more abundant bovine serum albumin (BSA) digest products. A correlation ofmore » variation (CV) less than 10 % for peak area was measured from triplicate sample analyses at 50 pM peptide concentration, showing good reproducibility of this online CITP/CZE-SRM mass spectrometry (MS) platform, and with limit of quantitation (LOQ) demonstrated to be well below 50 pM.« less

Pansharpening on the Narrow Vnir and SWIR Spectral Bands of SENTINEL-2

NASA Astrophysics Data System (ADS)

Vaiopoulos, A. D.; Karantzalos, K.

2016-06-01

In this paper results from the evaluation of several state-of-the-art pansharpening techniques are presented for the VNIR and SWIR bands of Sentinel-2. A procedure for the pansharpening is also proposed which aims at respecting the closest spectral similarities between the higher and lower resolution bands. The evaluation included 21 different fusion algorithms and three evaluation frameworks based both on standard quantitative image similarity indexes and qualitative evaluation from remote sensing experts. The overall analysis of the evaluation results indicated that remote sensing experts disagreed with the outcomes and method ranking from the quantitative assessment. The employed image quality similarity indexes and quantitative evaluation framework based on both high and reduced resolution data from the literature didn't manage to highlight/evaluate mainly the spatial information that was injected to the lower resolution images. Regarding the SWIR bands none of the methods managed to deliver significantly better results than a standard bicubic interpolation on the original low resolution bands.

Comparison of quantitative and qualitative tests for glucose-6-phosphate dehydrogenase deficiency.

PubMed

LaRue, Nicole; Kahn, Maria; Murray, Marjorie; Leader, Brandon T; Bansil, Pooja; McGray, Sarah; Kalnoky, Michael; Zhang, Hao; Huang, Huiqiang; Jiang, Hui; Domingo, Gonzalo J

2014-10-01

A barrier to eliminating Plasmodium vivax malaria is inadequate treatment of infected patients. 8-Aminoquinoline-based drugs clear the parasite; however, people with glucose-6-phosphate dehydrogenase (G6PD) deficiency are at risk for hemolysis from these drugs. Understanding the performance of G6PD deficiency tests is critical for patient safety. Two quantitative assays and two qualitative tests were evaluated. The comparison of quantitative assays gave a Pearson correlation coefficient of 0.7585 with significant difference in mean G6PD activity, highlighting the need to adhere to a single reference assay. Both qualitative tests had high sensitivity and negative predictive value at a cutoff G6PD value of 40% of normal activity if interpreted conservatively and performed under laboratory conditions. The performance of both tests dropped at a cutoff level of 45%. Cytochemical staining of specimens confirmed that heterozygous females with > 50% G6PD-deficient cells can seem normal by phenotypic tests. © The American Society of Tropical Medicine and Hygiene.

Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation.

PubMed

Yegnasubramanian, Srinivasan; Lin, Xiaohui; Haffner, Michael C; DeMarzo, Angelo M; Nelson, William G

2006-02-09

Hypermethylation of CpG island (CGI) sequences is a nearly universal somatic genome alteration in cancer. Rapid and sensitive detection of DNA hypermethylation would aid in cancer diagnosis and risk stratification. We present a novel technique, called COMPARE-MS, that can rapidly and quantitatively detect CGI hypermethylation with high sensitivity and specificity in hundreds of samples simultaneously. To quantitate CGI hypermethylation, COMPARE-MS uses real-time PCR of DNA that was first digested by methylation-sensitive restriction enzymes and then precipitated by methyl-binding domain polypeptides immobilized on a magnetic solid matrix. We show that COMPARE-MS could detect five genome equivalents of methylated CGIs in a 1000- to 10,000-fold excess of unmethylated DNA. COMPARE-MS was used to rapidly quantitate hypermethylation at multiple CGIs in >155 prostate tissues, including benign and malignant prostate specimens, and prostate cell lines. This analysis showed that GSTP1, MDR1 and PTGS2 CGI hypermethylation as determined by COMPARE-MS could differentiate between malignant and benign prostate with sensitivities >95% and specificities approaching 100%. This novel technology could significantly improve our ability to detect CGI hypermethylation.

Quantitative characterization of mechanically indented in vivo human skin in adults and infants using optical coherence tomography

NASA Astrophysics Data System (ADS)

Huang, Pin-Chieh; Pande, Paritosh; Shelton, Ryan L.; Joa, Frank; Moore, Dave; Gillman, Elisa; Kidd, Kimberly; Nolan, Ryan M.; Odio, Mauricio; Carr, Andrew; Boppart, Stephen A.

2017-03-01

Influenced by both the intrinsic viscoelasticity of the tissue constituents and the time-evolved redistribution of fluid within the tissue, the biomechanical response of skin can reflect not only localized pathology but also systemic physiology of an individual. While clinical diagnosis of skin pathologies typically relies on visual inspection and manual palpation, a more objective and quantitative approach for tissue characterization is highly desirable. Optical coherence tomography (OCT) is an interferometry-based imaging modality that enables in vivo assessment of cross-sectional tissue morphology with micron-scale resolution, which surpasses those of most standard clinical imaging tools, such as ultrasound imaging and magnetic resonance imaging. This pilot study investigates the feasibility of characterizing the biomechanical response of in vivo human skin using OCT. OCT-based quantitative metrics were developed and demonstrated on the human subject data, where a significant difference between deformed and nondeformed skin was revealed. Additionally, the quantified postindentation recovery results revealed differences between aged (adult) and young (infant) skin. These suggest that OCT has the potential to quantitatively assess the mechanically perturbed skin as well as distinguish different physiological conditions of the skin, such as changes with age or disease.

Customized Molecular Phenotyping by Quantitative Gene Expression and Pattern Recognition Analysis

PubMed Central

Akilesh, Shreeram; Shaffer, Daniel J.; Roopenian, Derry

2003-01-01

Description of the molecular phenotypes of pathobiological processes in vivo is a pressing need in genomic biology. We have implemented a high-throughput real-time PCR strategy to establish quantitative expression profiles of a customized set of target genes. It enables rapid, reproducible data acquisition from limited quantities of RNA, permitting serial sampling of mouse blood during disease progression. We developed an easy to use statistical algorithm—Global Pattern Recognition—to readily identify genes whose expression has changed significantly from healthy baseline profiles. This approach provides unique molecular signatures for rheumatoid arthritis, systemic lupus erythematosus, and graft versus host disease, and can also be applied to defining the molecular phenotype of a variety of other normal and pathological processes. PMID:12840047

Quantitative differential phase contrast imaging at high resolution with radially asymmetric illumination.

PubMed

Lin, Yu-Zi; Huang, Kuang-Yuh; Luo, Yuan

2018-06-15

Half-circle illumination-based differential phase contrast (DPC) microscopy has been utilized to recover phase images through a pair of images along multiple axes. Recently, the half-circle based DPC using 12-axis measurements significantly provides a circularly symmetric phase transfer function to improve accuracy for more stable phase recovery. Instead of using half-circle-based DPC, we propose a new scheme of DPC under radially asymmetric illumination to achieve circularly symmetric phase transfer function and enhance the accuracy of phase recovery in a more stable and efficient fashion. We present the design, implementation, and experimental image data demonstrating the ability of our method to obtain quantitative phase images of microspheres, as well as live fibroblast cell samples.

Quality evaluation of moluodan concentrated pill using high-performance liquid chromatography fingerprinting coupled with chemometrics.

PubMed

Tao, Lingyan; Zhang, Qing; Wu, Yongjiang; Liu, Xuesong

2016-12-01

In this study, a fast and effective high-performance liquid chromatography method was developed to obtain a fingerprint chromatogram and quantitative analysis simultaneously of four indexes including gallic acid, chlorogenic acid, albiflorin and paeoniflorin of the traditional Chinese medicine Moluodan Concentrated Pill. The method was performed by using a Waters X-bridge C 18 reversed phase column on an Agilent 1200S high-performance liquid chromatography system coupled with diode array detection. The mobile phase of the high-performance liquid chromatography method was composed of 20 mmol/L phosphate solution and acetonitrile with a 1 mL/min eluent velocity, under a detection temperature of 30°C and a UV detection wavelength of 254 nm. After the methodology validation, 16 batches of Moluodan Concentrated Pill were analyzed by this high-performance liquid chromatography method and both qualitative and quantitative evaluation results were achieved by similarity analysis, principal component analysis and hierarchical cluster analysis. The results of these three chemometrics were in good agreement and all indicated that batch 10 and batch 16 showed significant differences with the other 14 batches. This suggested that the developed high-performance liquid chromatography method could be applied in the quality evaluation of Moluodan Concentrated Pill. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative computed tomography and aerosol morphometry in COPD and alpha1-antitrypsin deficiency.

PubMed

Shaker, S B; Maltbaek, N; Brand, P; Haeussermann, S; Dirksen, A

2005-01-01

Relative area of emphysema below -910 Hounsfield units (RA-910) and 15th percentile density (PD15) are quantitative computed tomography (CT) parameters used in the diagnosis of emphysema. New concepts for noninvasive diagnosis of emphysema are aerosol-derived airway morphometry, which measures effective airspace dimensions (EAD) and aerosol bolus dispersion (ABD). Quantitative CT, ABD and EAD were compared in 20 smokers with chronic obstructive pulmonary disease (COPD) and 22 patients with alpha1-antitrypsin deficiency (AAD) with a similar degree of airway obstruction and reduced diffusion capacity. In both groups, there was a significant correlation between RA-910 and PD15 and pulmonary function tests (PFTs). A significant correlation was also found between EAD, RA-910 and PD15 in the study population as a whole. Upon separation into two groups, the significance disappeared for the smokers with COPD and strengthened for those with AAD, where EAD correlated significantly with RA-910 and PD15. ABD was similar in the two groups and did not correlate with PFT and quantitative CT in either group. In conclusion, based on quantitative computed tomography and aerosol-derived airway morphometry, emphysema was significantly more severe in patients with alpha1-antitrypsin deficiency compared with patients with usual emphysema, despite similar measures of pulmonary function tests.

Quantitative evaluation of palatal bone thickness for the placement of orthodontic miniscrews in adults with different facial types

PubMed Central

Wang, Yunji; Qiu, Ye; Liu, Henglang; He, Jinlong; Fan, Xiaoping

2017-01-01

Objectives: To quantitatively evaluate palatal bone thickness in adults with different facial types using cone beam computed tomography (CBCT). Methods: The CBCT volumetric data of 123 adults (mean age, 26.8 years) collected between August 2014 and August 2016 was retrospectively studied. The subjects were divided into a low-angle group (39 subjects), a normal-angle group (48 subjects) and a high-angle group (36 subjects) based on facial types assigned by cephalometric radiography. The thickness of the palatal bone was assessed at designated points. A repeated-measure analysis of variance (rm-ANOVA) test was used to test the relationship between facial types and palatal bone thickness. Results: Compared to the low-angle group, the high-angle group had significantly thinner palatal bones (p<0.05), except for the anterior-midline, anterior-medial and middle-midline areas. Conclusion: The safest zone for the placement of microimplants is the anterior part of the paramedian palate. Clinicians should pay special attention to the probability of thinner bone plates and the risk of perforation in high-angle patients. PMID:28917071

Highly sensitive image-derived indices of water-stressed plants using hyperspectral imaging in SWIR and histogram analysis

PubMed Central

Kim, David M.; Zhang, Hairong; Zhou, Haiying; Du, Tommy; Wu, Qian; Mockler, Todd C.; Berezin, Mikhail Y.

2015-01-01

The optical signature of leaves is an important monitoring and predictive parameter for a variety of biotic and abiotic stresses, including drought. Such signatures derived from spectroscopic measurements provide vegetation indices – a quantitative method for assessing plant health. However, the commonly used metrics suffer from low sensitivity. Relatively small changes in water content in moderately stressed plants demand high-contrast imaging to distinguish affected plants. We present a new approach in deriving sensitive indices using hyperspectral imaging in a short-wave infrared range from 800 nm to 1600 nm. Our method, based on high spectral resolution (1.56 nm) instrumentation and image processing algorithms (quantitative histogram analysis), enables us to distinguish a moderate water stress equivalent of 20% relative water content (RWC). The identified image-derived indices 15XX nm/14XX nm (i.e. 1529 nm/1416 nm) were superior to common vegetation indices, such as WBI, MSI, and NDWI, with significantly better sensitivity, enabling early diagnostics of plant health. PMID:26531782

Usefulness of quantitative susceptibility mapping for the diagnosis of Parkinson disease.

PubMed

Murakami, Y; Kakeda, S; Watanabe, K; Ueda, I; Ogasawara, A; Moriya, J; Ide, S; Futatsuya, K; Sato, T; Okada, K; Uozumi, T; Tsuji, S; Liu, T; Wang, Y; Korogi, Y

2015-06-01

Quantitative susceptibility mapping allows overcoming several nonlocal restrictions of susceptibility-weighted and phase imaging and enables quantification of magnetic susceptibility. We compared the diagnostic accuracy of quantitative susceptibility mapping and R2* (1/T2*) mapping to discriminate between patients with Parkinson disease and controls. For 21 patients with Parkinson disease and 21 age- and sex-matched controls, 2 radiologists measured the quantitative susceptibility mapping values and R2* values in 6 brain structures (the thalamus, putamen, caudate nucleus, pallidum, substantia nigra, and red nucleus). The quantitative susceptibility mapping values and R2* values of the substantia nigra were significantly higher in patients with Parkinson disease (P < .01); measurements in other brain regions did not differ significantly between patients and controls. For the discrimination of patients with Parkinson disease from controls, receiver operating characteristic analysis suggested that the optimal cutoff values for the substantia nigra, based on the Youden Index, were >0.210 for quantitative susceptibility mapping and >28.8 for R2*. The sensitivity, specificity, and accuracy of quantitative susceptibility mapping were 90% (19 of 21), 86% (18 of 21), and 88% (37 of 42), respectively; for R2* mapping, they were 81% (17 of 21), 52% (11 of 21), and 67% (28 of 42). Pair-wise comparisons showed that the areas under the receiver operating characteristic curves were significantly larger for quantitative susceptibility mapping than for R2* mapping (0.91 versus 0.69, P < .05). Quantitative susceptibility mapping showed higher diagnostic performance than R2* mapping for the discrimination between patients with Parkinson disease and controls. © 2015 by American Journal of Neuroradiology.

Primary TKA Patients with Quantifiably Balanced Soft-Tissue Achieve Significant Clinical Gains Sooner than Unbalanced Patients

PubMed Central

Gustke, Kenneth A.; Golladay, Gregory J.; Roche, Martin W.; Elson, Leah C.; Anderson, Christopher R.

2014-01-01

Although total knee arthroplasty has a high success rate, poor outcomes and early revision are associated with ligament imbalance. This multicenter evaluation was performed in order to provide 1-year followup of a previously reported group of patients who had sensor-assisted TKA, comparing the clinical outcomes of quantitatively balanced versus unbalanced patients. At 1 year, the balanced cohort scored 179.3 and 10.4 in KSS and WOMAC, respectively; the unbalanced cohort scored 156.1 and 17.9 in KSS and WOMAC (P < 0.001; P = 0.085). The average activity level scores of quantitatively balanced patients were 68.6 (corresponding to tennis, light jogging, and heavy yard work), while the average activity level of unbalanced patients was 46.7 (corresponding to light housework, and limited walking distances) (P = 0.015). Out of all confounding variables, a balanced articulation was the most significant contributing factor to improved postoperative outcomes (P < 0.001). PMID:25210632

Contribution entrepreneurial knowledge, skills competence, and self-efficacy to student entrepreneurship readiness of multimedia expertise at vocational high school in Malang

NASA Astrophysics Data System (ADS)

Islami, Pio Arfianova Ftirizky; Elmunsyah, Hakkun; Muladi

2017-09-01

This study aims to determine the contribution of entrepreneurship knowledge, skills competence, and self-efficacy to entrepreneurship readiness. The design used in this research using a quantitative approach and knowledge test techniques using regression analysis. The number of samples in this study as many as 181 students. The results showed that there was a significant contribution between entrepreneurship knowledge to entrepreneurship readiness. There is also a significant contribution between the skills competence to entrepreneurship readiness and there is a significant contribution between self-efficacy to entrepreneurship readiness. Futhermore, there is a significant contribution simultaneously between entrepreneurship knowledge, skill competence; self-efficacy to entrepreneurship readiness.

Quantitative measurement of HER2 expression in breast cancers: comparison with 'real-world' routine HER2 testing in a multicenter Collaborative Biomarker Study and correlation with overall survival.

PubMed

Yardley, Denise A; Kaufman, Peter A; Huang, Weidong; Krekow, Lea; Savin, Michael; Lawler, William E; Zrada, Stephen; Starr, Alexander; Einhorn, Harvey; Schwartzberg, Lee S; Adams, John W; Lie, Yolanda; Paquet, Agnes C; Sperinde, Jeff; Haddad, Mojgan; Anderson, Steve; Brigino, Marlon; Pesano, Rick; Bates, Michael P; Weidler, Jodi; Bosserman, Linda

2015-03-18

Accurate assessment of HER2 status is critical in determining appropriate therapy for breast cancer patients but the best HER2 testing methodology has yet to be defined. In this study, we compared quantitative HER2 expression by the HERmark™ Breast Cancer Assay (HERmark) with routine HER2 testing by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), and correlated HER2 results with overall survival (OS) of breast cancer patients in a multicenter Collaborative Biomarker Study (CBS). Two hundred and thirty-two formalin-fixed, paraffin-embedded breast cancer tissues and local laboratory HER2 testing results were provided by 11 CBS sites. HERmark assay and central laboratory HER2 IHC retesting were retrospectively performed in a blinded fashion. HER2 results by all testing methods were obtained in 192 cases. HERmark yielded a continuum of total HER2 expression (H2T) ranging from 0.3 to 403 RF/mm2 (approximately 3 logs). The distribution of H2T levels correlated significantly (P<0.0001) with all routine HER2 testing results. The concordance of positive and negative values (equivocal cases excluded) between HERmark and routine HER2 testing was 84% for local IHC, 96% for central IHC, 85% for local FISH, and 84% for local HER2 status. OS analysis revealed a significant correlation of shorter OS with HER2 positivity by local IHC (HR=2.6, P=0.016), central IHC (HR=3.2, P=0.015), and HERmark (HR=5.1, P<0.0001) in this cohort of patients most of whom received no HER2-targeted therapy. The OS curve of discordant low (HER2 positive but H2T low, 10% of all cases) was aligned with concordant negative (HER2 negative and H2T low, HR=1.9, P=0.444), but showed a significantly longer OS than concordant positive (HER2 positive and H2T high, HR=0.31, P=0.024). Conversely, the OS curve of discordant high (HER2 negative but H2T high, 9% of all cases) was aligned with concordant positive (HR=0.41, P=0.105), but showed a significantly shorter OS than concordant negative (HR=41, P<0.0001). Quantitative HER2 measurement by HERmark is highly sensitive, accurately quantifies HER2 protein expression and correlates well with routine HER2 testing. When HERmark and local HER2 results were discordant, HERmark more accurately predicted overall survival.

Measurement of /sup 125/I-low density lipoprotein uptake in selected tissues of the squirrel monkey by quantitative autoradiography

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

Tompkins, R.G.; Schnitzer, J.J.; Yarmush, M.L.

1988-09-01

A recently developed technique of absolute quantitative light microscopic autoradiography of /sup 125/I-labeled proteins in biologic specimens was used to measure /sup 125/I-low density lipoprotein (/sup 125/I-LDL) concentration levels in various tissues of the squirrel monkey after 30 minutes of in vivo LDL circulation. Liver and adrenal cortex exhibited high /sup 125/I-LDL concentrations, presumably because of binding to specific cell surface receptors and/or internalization in vascular beds with high permeability to LDL. High tissue concentrations of LDL were associated with the zona fasciculata and reticularis of the adrenal cortex and the interstitial cells of Leydig in the testis; significantly lowermore » levels of /sup 125/I-LDL were observed in the adrenal medulla, the zona glomerulosa, and germinal centers of the testis. Contrary to previous reports, low /sup 125/I-LDL concentrations were observed throughout the gastrointestinal tract and in lymph nodes. In addition, multiple arterial intramural focal areas of high /sup 125/I-LDL concentrations were identified in arteries supplying the adrenal gland, lymph node, small bowel, and liver.« less

Functionalized vertical GaN micro pillar arrays with high signal-to-background ratio for detection and analysis of proteins secreted from breast tumor cells.

PubMed

Choi, Mun-Ki; Kim, Gil-Sung; Jeong, Jin-Tak; Lim, Jung-Taek; Lee, Won-Yong; Umar, Ahmad; Lee, Sang-Kwon

2017-11-02

The detection of cancer biomarkers has recently attracted significant attention as a means of determining the correct course of treatment with targeted therapeutics. However, because the concentration of these biomarkers in blood is usually relatively low, highly sensitive biosensors for fluorescence imaging and precise detection are needed. In this study, we have successfully developed vertical GaN micropillar (MP) based biosensors for fluorescence sensing and quantitative measurement of CA15-3 antigens. The highly ordered vertical GaN MP arrays result in the successful immobilization of CA15-3 antigens on each feature of the arrays, thereby allowing the detection of an individual fluorescence signal from the top surface of the arrays owing to the high regularity of fluorophore-tagged MP spots and relatively low background signal. Therefore, our fluorescence-labeled and CA15-3 functionalized vertical GaN-MP-based biosensor is suitable for the selective quantitative analysis of secreted CA15-3 antigens from MCF-7 cell lines, and helps in the early diagnosis and prognosis of serious diseases as well as the monitoring of the therapeutic response of breast cancer patients.

Quantitative Comparison of Minimum Inductance and Minimum Power Algorithms for the Design of Shim Coils for Small Animal Imaging

PubMed Central

HUDSON, PARISA; HUDSON, STEPHEN D.; HANDLER, WILLIAM B.; SCHOLL, TIMOTHY J.; CHRONIK, BLAINE A.

2010-01-01

High-performance shim coils are required for high-field magnetic resonance imaging and spectroscopy. Complete sets of high-power and high-performance shim coils were designed using two different methods: the minimum inductance and the minimum power target field methods. A quantitative comparison of shim performance in terms of merit of inductance (ML) and merit of resistance (MR) was made for shim coils designed using the minimum inductance and the minimum power design algorithms. In each design case, the difference in ML and the difference in MR given by the two design methods was <15%. Comparison of wire patterns obtained using the two design algorithms show that minimum inductance designs tend to feature oscillations within the current density; while minimum power designs tend to feature less rapidly varying current densities and lower power dissipation. Overall, the differences in coil performance obtained by the two methods are relatively small. For the specific case of shim systems customized for small animal imaging, the reduced power dissipation obtained when using the minimum power method is judged to be more significant than the improvements in switching speed obtained from the minimum inductance method. PMID:20411157

Post-translational quantitation by SRM/MRM: applications in cardiology.

PubMed

Gianazza, Erica; Banfi, Cristina

2018-06-04

Post-translational modifications (PTMs) have an important role in the regulation of protein function, localization and interaction with other molecules. PTMs apply a dynamic control of proteins both in physiological and pathological conditions. The study of disease-specific PTMs allows identifying potential biomarkers and developing effective drugs. Enrichment techniques combined with high-resolution MS/MS analysis provide attractive results on PTMs characterization. Selected reaction monitoring/multiple reaction monitoring (SRM/MRM) is a powerful targeted assay for the quantitation and validation of PTMs in complex biological samples. Areas covered: The most frequent PTMs are described in terms of biological role and analytical methods commonly used to detect them. The applications of SRM/MRM for the absolute quantitation of PTMs are reported and a specific section is focused on PTMs detection in proteins that are involved in cardiovascular system and heart diseases. Expert commentary: PTMs characterization in relation to disease pathology is still in progress, but targeted proteomics by LC-MS/MS has significantly upgraded the knowledge in the last years. Advances in enrichment strategies and software tools will facilitate the interpretation of high PTMs complexity. Promising studies confirm the great potentiality of SRM/MRM to study PTMs in cardiovascular field and PTMomics could be very useful in a clinical perspective.

Tuning plasmons layer-by-layer for quantitative colloidal sensing with surface-enhanced Raman spectroscopy.

PubMed

Anderson, William J; Nowinska, Kamila; Hutter, Tanya; Mahajan, Sumeet; Fischlechner, Martin

2018-04-19

Surface-enhanced Raman spectroscopy (SERS) is well known for its high sensitivity that emerges due to the plasmonic enhancement of electric fields typically on gold and silver nanostructures. However, difficulties associated with the preparation of nanostructured substrates with uniform and reproducible features limit reliability and quantitation using SERS measurements. In this work we use layer-by-layer (LbL) self-assembly to incorporate multiple functional building blocks of collaborative assemblies of nanoparticles on colloidal spheres to fabricate SERS sensors. Gold nanoparticles (AuNPs) are packaged in discrete layers, effectively 'freezing nano-gaps', on spherical colloidal cores to achieve multifunctionality and reproducible sensing. Coupling between layers tunes the plasmon resonance for optimum SERS signal generation to achieve a 10 nM limit of detection. Significantly, using the layer-by-layer construction, SERS-active AuNP layers are spaced out and thus optically isolated. This uniquely allows the creation of an internal standard within each colloidal sensor to enable highly reproducible self-calibrated sensing. By using 4-mercaptobenzoic acid (4-MBA) as the internal standard adenine concentrations are quantified to an accuracy of 92.6-99.5%. Our versatile approach paves the way for rationally designed yet quantitative colloidal SERS sensors and their use in a variety of sensing applications.

Development of cell-based quantitative evaluation method for cell cycle-arrest type cancer drugs for apoptosis by high precision surface plasmon resonance sensor

NASA Astrophysics Data System (ADS)

Ona, Toshihiro; Nishijima, Hiroshi; Kosaihira, Atsushi; Shibata, Junko

2008-04-01

In vitro rapid and quantitative cell-based assay is demanded to verify the efficacy prediction of cancer drugs since a cancer patient may have unconventional aspects of tumor development. Here, we show the rapid and non-label quantitative verifying method and instrumentation of apoptosis for cell cycle-arrest type cancer drugs (Roscovitine and D-allose) by reaction analysis of living liver cancer cells cultured on a sensor chip with a newly developed high precision (50 ndeg s -1 average fluctuation) surface plasmon resonance (SPR) sensor. The time-course cell reaction as the SPR angle change rate for 10 min from 30 min cell culture with a drug was significantly related to cell viability. By the simultaneous detection of differential SPR angle change and fluorescence by specific probes using the new instrument, the SPR angle was related to the nano-order potential decrease in inner mitochondrial membrane potential. The results obtained are universally valid for the cell cycle-arrest type cancer drugs, which mediate apoptosis through different cell-signaling pathways, by a liver cancer cell line of Hep G2 (P<0.001). This system towards the application to evaluate personal therapeutic potentials of drugs using cancer cells from patients in clinical use.

Preoperative Cerebral Oxygen Extraction Fraction Imaging Generated from 7T MR Quantitative Susceptibility Mapping Predicts Development of Cerebral Hyperperfusion following Carotid Endarterectomy.

PubMed

Nomura, J-I; Uwano, I; Sasaki, M; Kudo, K; Yamashita, F; Ito, K; Fujiwara, S; Kobayashi, M; Ogasawara, K

2017-12-01

Preoperative hemodynamic impairment in the affected cerebral hemisphere is associated with the development of cerebral hyperperfusion following carotid endarterectomy. Cerebral oxygen extraction fraction images generated from 7T MR quantitative susceptibility mapping correlate with oxygen extraction fraction images on positron-emission tomography. The present study aimed to determine whether preoperative oxygen extraction fraction imaging generated from 7T MR quantitative susceptibility mapping could identify patients at risk for cerebral hyperperfusion following carotid endarterectomy. Seventy-seven patients with unilateral internal carotid artery stenosis (≥70%) underwent preoperative 3D T2*-weighted imaging using a multiple dipole-inversion algorithm with a 7T MR imager. Quantitative susceptibility mapping images were then obtained, and oxygen extraction fraction maps were generated. Quantitative brain perfusion single-photon emission CT was also performed before and immediately after carotid endarterectomy. ROIs were automatically placed in the bilateral middle cerebral artery territories in all images using a 3D stereotactic ROI template, and affected-to-contralateral ratios in the ROIs were calculated on quantitative susceptibility mapping-oxygen extraction fraction images. Ten patients (13%) showed post-carotid endarterectomy hyperperfusion (cerebral blood flow increases of ≥100% compared with preoperative values in the ROIs on brain perfusion SPECT). Multivariate analysis showed that a high quantitative susceptibility mapping-oxygen extraction fraction ratio was significantly associated with the development of post-carotid endarterectomy hyperperfusion (95% confidence interval, 33.5-249.7; P = .002). Sensitivity, specificity, and positive- and negative-predictive values of the quantitative susceptibility mapping-oxygen extraction fraction ratio for the prediction of the development of post-carotid endarterectomy hyperperfusion were 90%, 84%, 45%, and 98%, respectively. Preoperative oxygen extraction fraction imaging generated from 7T MR quantitative susceptibility mapping identifies patients at risk for cerebral hyperperfusion following carotid endarterectomy. © 2017 by American Journal of Neuroradiology.

Quasi-experimental nonequivalent (pretest and posttest) control-group study of the effects of microcomputer-based laboratory systems on academic achievement in high school chemistry students at two South Carolina high schools

NASA Astrophysics Data System (ADS)

Venables, Jeffrey M.

The literature on microcomputer-based laboratories (MBL) lacks quantitative studies that measure the effect of MBL on student achievement. The purpose of this study was to investigate the effect of MBL systems on the achievement of high school chemistry students. The first research question examined the effect of MBL systems on student achievement in high school chemistry laboratories. The second question analyzed the effect of MBL systems on the academic achievement of students of different genders, ethnicities, and socioeconomic backgrounds. This quasi-experimental quantitative research study evaluated the effects of MBL on student achievement in high school chemistry. The sample consisted of 124 college preparatory chemistry students at two high schools in a South Carolina school district. There were 42 participants in the experimental group and 82 participants in the control group. Both experimental and groups completed a pre- and post-test with MBL being the independent variable. The mean difference score for the experimental group was compared to that of the control group using an independent-measures t test and an analysis of variance. For the second research question, results were analyzed using a two-factor analysis of variance. Participant scores were broken down by gender, ethnicity, and socioeconomic status in order to identify potential differences. The results revealed no significant differences between the experimental and control groups, and no significant differences in effects of MBL on different segments of the population. Future studies should examine students using MBL for longer durations than one unit of study. As society continues to make technological advances, the effective assessment and implementation of technology resources for the classroom are becoming increasingly important.

3.0T MR imaging of the ankle: Axial traction for morphological cartilage evaluation, quantitative T2 mapping and cartilage diffusion imaging-A preliminary study.

PubMed

Jungmann, Pia M; Baum, Thomas; Schaeffeler, Christoph; Sauerschnig, Martin; Brucker, Peter U; Mann, Alexander; Ganter, Carl; Bieri, Oliver; Rummeny, Ernst J; Woertler, Klaus; Bauer, Jan S

2015-08-01

To determine the impact of axial traction during high resolution 3.0T MR imaging of the ankle on morphological assessment of articular cartilage and quantitative cartilage imaging parameters. MR images of n=25 asymptomatic ankles were acquired with and without axial traction (6kg). Coronal and sagittal T1-weighted (w) turbo spin echo (TSE) sequences with a driven equilibrium pulse and sagittal fat-saturated intermediate-w (IMfs) TSE sequences were acquired for morphological evaluation on a four-point scale (1=best, 4=worst). For quantitative assessment of cartilage degradation segmentation was performed on 2D multislice-multiecho (MSME) SE T2, steady-state free-precession (SSFP; n=8) T2 and SSFP diffusion-weighted imaging (DWI; n=8) images. Wilcoxon-tests and paired t-tests were used for statistical analysis. With axial traction, joint space width increased significantly and delineation of cartilage surfaces was rated superior (P<0.05). Cartilage surfaces were best visualized on coronal T1-w images (P<0.05). Differences for cartilage matrix evaluation were smaller. Subchondral bone evaluation, motion artifacts and image quality were not significantly different between the acquisition methods (P>0.05). T2 values were lower at the tibia than at the talus (P<0.001). Reproducibility was better for images with axial traction. Axial traction increased the joint space width, allowed for better visualization of cartilage surfaces and improved compartment discrimination and reproducibility of quantitative cartilage parameters. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Quantitative Methylation Profiles for Multiple Tumor Suppressor Gene Promoters in Salivary Gland Tumors

PubMed Central

Durr, Megan L.; Mydlarz, Wojciech K.; Shao, Chunbo; Zahurak, Marianna L.; Chuang, Alice Y.; Hoque, Mohammad O.; Westra, William H.; Liegeois, Nanette J.; Califano, Joseph A.; Sidransky, David; Ha, Patrick K.

2010-01-01

Background Methylation profiling of tumor suppressor gene (TSGs) promoters is quickly becoming a powerful diagnostic tool for the early detection, prognosis, and even prediction of clinical response to treatment. Few studies address this in salivary gland tumors (SGTs); hence the promoter methylation profile of various TSGs was quantitatively assessed in primary SGT tissue to determine if tumor-specific alterations could be detected. Methodology DNA isolated from 78 tumor and 17 normal parotid gland specimens was assayed for promoter methylation status of 19 TSGs by fluorescence-based, quantitative methylation-specific PCR (qMSP). The data were utilized in a binary fashion as well as quantitatively (using a methylation quotient) allowing for better profiling and interpretation of results. Principal Findings The average number of methylation events across the studied genes was highest in salivary duct carcinoma (SDC), with a methylation value of 9.6, compared to the normal 4.5 (p<0.0003). There was a variable frequency and individual methylation quotient detected, depending on the TSG and the tumor type. When comparing normal, benign, and malignant SGTs, there was a statistically significant trend for increasing methylation in APC, Mint 1, PGP9.5, RAR-β, and Timp3. Conclusions/Significance Screening promoter methylation profiles in SGTs showed considerable heterogeneity. The methylation status of certain markers was surprisingly high in even normal salivary tissue, confirming the need for such controls. Several TSGs were found to be associated with malignant SGTs, especially SDC. Further study is needed to evaluate the potential use of these associations in the detection, prognosis, and therapeutic outcome of these rare tumors. PMID:20520817

Automated Quantitative Analysis of Retinal Microvasculature in Normal Eyes on Optical Coherence Tomography Angiography.

PubMed

Lupidi, Marco; Coscas, Florence; Cagini, Carlo; Fiore, Tito; Spaccini, Elisa; Fruttini, Daniela; Coscas, Gabriel

2016-09-01

To describe a new automated quantitative technique for displaying and analyzing macular vascular perfusion using optical coherence tomography angiography (OCT-A) and to determine a normative data set, which might be used as reference in identifying progressive changes due to different retinal vascular diseases. Reliability study. A retrospective review of 47 eyes of 47 consecutive healthy subjects imaged with a spectral-domain OCT-A device was performed in a single institution. Full-spectrum amplitude-decorrelation angiography generated OCT angiograms of the retinal superficial and deep capillary plexuses. A fully automated custom-built software was used to provide quantitative data on the foveal avascular zone (FAZ) features and the total vascular and avascular surfaces. A comparative analysis between central macular thickness (and volume) and FAZ metrics was performed. Repeatability and reproducibility were also assessed in order to establish the feasibility and reliability of the method. The comparative analysis between the superficial capillary plexus and the deep capillary plexus revealed a statistically significant difference (P < .05) in terms of FAZ perimeter, surface, and major axis and a not statistically significant difference (P > .05) when considering total vascular and avascular surfaces. A linear correlation was demonstrated between central macular thickness (and volume) and the FAZ surface. Coefficients of repeatability and reproducibility were less than 0.4, thus demonstrating high intraobserver repeatability and interobserver reproducibility for all the examined data. A quantitative approach on retinal vascular perfusion, which is visible on Spectralis OCT angiography, may offer an objective and reliable method for monitoring disease progression in several retinal vascular diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

Roton Minimum as a Fingerprint of Magnon-Higgs Scattering in Ordered Quantum Antiferromagnets.

PubMed

Powalski, M; Uhrig, G S; Schmidt, K P

2015-11-13

A quantitative description of magnons in long-range ordered quantum antiferromagnets is presented which is consistent from low to high energies. It is illustrated for the generic S=1/2 Heisenberg model on the square lattice. The approach is based on a continuous similarity transformation in momentum space using the scaling dimension as the truncation criterion. Evidence is found for significant magnon-magnon attraction inducing a Higgs resonance. The high-energy roton minimum in the magnon dispersion appears to be induced by strong magnon-Higgs scattering.

Recent applications of gas chromatography with high-resolution mass spectrometry.

PubMed

Špánik, Ivan; Machyňáková, Andrea

2018-01-01

Gas chromatography coupled to high-resolution mass spectrometry is a powerful analytical method that combines excellent separation power of gas chromatography with improved identification based on an accurate mass measurement. These features designate gas chromatography with high-resolution mass spectrometry as the first choice for identification and structure elucidation of unknown volatile and semi-volatile organic compounds. Gas chromatography with high-resolution mass spectrometry quantitative analyses was previously focused on the determination of dioxins and related compounds using magnetic sector type analyzers, a standing requirement of many international standards. The introduction of a quadrupole high-resolution time-of-flight mass analyzer broadened interest in this method and novel applications were developed, especially for multi-target screening purposes. This review is focused on the development and the most interesting applications of gas chromatography coupled to high-resolution mass spectrometry towards analysis of environmental matrices, biological fluids, and food safety since 2010. The main attention is paid to various approaches and applications of gas chromatography coupled to high-resolution mass spectrometry for non-target screening to identify contaminants and to characterize the chemical composition of environmental, food, and biological samples. The most interesting quantitative applications, where a significant contribution of gas chromatography with high-resolution mass spectrometry over the currently used methods is expected, will be discussed as well. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of prognostic and predictive value of microtubule associated protein tau in two independent cohorts.

PubMed

Baquero, Maria T; Lostritto, Karen; Gustavson, Mark D; Bassi, Kimberly A; Appia, Franck; Camp, Robert L; Molinaro, Annette M; Harris, Lyndsay N; Rimm, David L

2011-11-02

Microtubule associated proteins (MAPs) endogenously regulate microtubule stabilization and have been reported as prognostic and predictive markers for taxane response. The microtubule stabilizer, MAP-tau, has shown conflicting results. We quantitatively assessed MAP-tau expression in two independent breast cancer cohorts to determine prognostic and predictive value of this biomarker. MAP-tau expression was evaluated in the retrospective Yale University breast cancer cohort (n = 651) using tissue microarrays and also in the TAX 307 cohort, a clinical trial randomized for TAC versus FAC chemotherapy (n = 140), using conventional whole tissue sections. Expression was measured using the AQUA method for quantitative immunofluorescence. Scores were correlated with clinicopathologic variables, survival, and response to therapy. Assessment of the Yale cohort using Cox univariate analysis indicated an improved overall survival (OS) in tumors with a positive correlation between high MAP-tau expression and overall survival (OS) (HR = 0.691, 95% CI = 0.489-0.974; P = 0.004). Kaplan Meier analysis showed 10-year survival for 65% of patients with high MAP-tau expression compared to 52% with low expression (P = .006). In TAX 307, high expression was associated with significantly longer median time to tumor progression (TTP) regardless of treatment arm (33.0 versus 23.4 months, P = 0.010) with mean TTP of 31.2 months. Response rates did not differ by MAP-tau expression (P = 0.518) or by treatment arm (P = 0.584). Quantitative measurement of MAP-tau expression has prognostic value in both cohorts, with high expression associated with longer TTP and OS. Differences by treatment arm or response rate in low versus high MAP-tau groups were not observed, indicating that MAP-tau is not associated with response to taxanes and is not a useful predictive marker for taxane-based chemotherapy.

Quantitative assessment of hTERT mRNA expression in dysplastic nodules of HBV-related hepatocarcinogenesis.

PubMed

Oh, Bong-Kyeong; Kim, Young-Joo; Park, Young Nyun; Choi, Jinsub; Kim, Kyung Sik; Park, Chanil

2006-04-01

Telomerase reverse transcriptase (hTERT) is the rate-limiting determinant of telomerase, which is critical for carcinogenesis. Dysplastic nodules (DNs) appear to be preneoplastic lesions of hepatocellular carcinomas (HCCs). In this study, in order to characterize DNs, hTERT mRNA, hTERT gene dosage, and mRNA for c-myc, a transcriptional activator of hTERT were studied in human multi-step hepatocarcinogenesis. Fifty four hepatic nodules including 5 large regenerative nodules, 14 low-grade DNs, 7 high-grade DNs, 11 DNs with HCC foci and 17 HCCs, 23 livers with chronic hepatitis/cirrhosis, and 6 normal livers were examined. Transcript levels were measured by real-time quantitative RT-PCR and gene dosages by real-time PCR and Southern blotting. The hTERT mRNA levels increased with the progression of hepatocarcinogenesis, and a significant induction in the transition between low- and high-grade DNs was seen. Most high-grade DNs strongly expressed hTERT mRNA at levels similar to those of HCCs. Twenty-one percent of low-grade DNs had high levels of hTERT mRNA, up to those of high-grade DNs and there was no difference in the pathological features between low-grade DNs with and without increased hTERT mRNA levels. No correlation was found between hTERT mRNA levels, hTERT gene dosage, and c-myc mRNA levels. These results suggest that the induction of hTERT mRNA is an important early event and that its measurement by real-time quantitative RT-PCR is a useful tool to detect premalignant/malignant tendencies in hepatic nodules. However, hTERT gene dosage and c-myc expression are not the main mechanisms regulating hTERT expression in hepatocarcinogenesis.

Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.

PubMed

Tu, Chengjian; Li, Jun; Sheng, Quanhu; Zhang, Ming; Qu, Jun

2014-04-04

Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.

Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data

PubMed Central

2015-01-01

Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R2 > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery. PMID:24635752

High-brightness laser imaging with tunable speckle reduction enabled by electroactive micro-optic diffusers.

PubMed

Farrokhi, Hamid; Rohith, Thazhe Madam; Boonruangkan, Jeeranan; Han, Seunghwoi; Kim, Hyunwoong; Kim, Seung-Woo; Kim, Young-Jin

2017-11-10

High coherence of lasers is desirable in high-speed, high-resolution, and wide-field imaging. However, it also causes unavoidable background speckle noise thus degrades the image quality in traditional microscopy and more significantly in interferometric quantitative phase imaging (QPI). QPI utilizes optical interference for high-precision measurement of the optical properties where the speckle can severely distort the information. To overcome this, we demonstrated a light source system having a wide tunability in the spatial coherence over 43% by controlling the illumination angle, scatterer's size, and the rotational speed of an electroactive-polymer rotational micro-optic diffuser. Spatially random phase modulation was implemented for the lower speckle imaging with over a 50% speckle reduction without a significant degradation in the temporal coherence. Our coherence control technique will provide a unique solution for a low-speckle, full-field, and coherent imaging in optically scattering media in the fields of healthcare sciences, material sciences and high-precision engineering.

MGMT promoter methylation determined by HRM in comparison to MSP and pyrosequencing for predicting high-grade glioma response.

PubMed

Switzeny, Olivier J; Christmann, Markus; Renovanz, Mirjam; Giese, Alf; Sommer, Clemens; Kaina, Bernd

2016-01-01

The DNA repair protein O(6)-methylguanine-DNA methyltransferase (MGMT) causes resistance of cancer cells to alkylating agents and, therefore, is a well-established predictive marker for high-grade gliomas that are routinely treated with alkylating drugs. Since MGMT is highly epigenetically regulated, the MGMT promoter methylation status is taken as an indicator of MGMT silencing, predicting the outcome of glioma therapy. MGMT promoter methylation is usually determined by methylation specific PCR (MSP), which is a labor intensive and error-prone method often used semi-quantitatively. Searching for alternatives, we used closed-tube high resolution melt (HRM) analysis, which is a quantitative method, and compared it with MSP and pyrosequencing regarding its predictive value. We analyzed glioblastoma cell lines with known MGMT activity and formalin-fixed samples from IDH1 wild-type high-grade glioma patients (WHO grade III/IV) treated with radiation and temozolomide by HRM, MSP, and pyrosequencing. The data were compared as to progression-free survival (PFS) and overall survival (OS) of patients exhibiting the methylated and unmethylated MGMT status. A promoter methylation cut-off level relevant for PFS and OS was determined. In a multivariate Cox regression model, methylation of MGMT promoter of high-grade gliomas analyzed by HRM, but not MSP, was found to be an independent predictive marker for OS. Univariate Kaplan-Meier analyses revealed for PFS and OS a significant and better discrimination between methylated and unmethylated tumors when quantitative HRM was used instead of MSP. Compared to MSP and pyrosequencing, the HRM method is simple, cost effective, highly accurate and fast. HRM is at least equivalent to pyrosequencing in quantifying the methylation level. It is superior in predicting PFS and OS of high-grade glioma patients compared to MSP and, therefore, can be recommended being used routinely for determination of the MGMT status of gliomas.

Hydrologic applications of weather radar

NASA Astrophysics Data System (ADS)

Seo, Dong-Jun; Habib, Emad; Andrieu, Hervé; Morin, Efrat

2015-12-01

By providing high-resolution quantitative precipitation information (QPI), weather radars have revolutionized hydrology in the last two decades. With the aid of GIS technology, radar-based quantitative precipitation estimates (QPE) have enabled routine high-resolution hydrologic modeling in many parts of the world. Given the ever-increasing need for higher-resolution hydrologic and water resources information for a wide range of applications, one may expect that the use of weather radar will only grow. Despite the tremendous progress, a number of significant scientific, technological and engineering challenges remain to realize its potential. New challenges are also emerging as new areas of applications are discovered, explored and pursued. The purpose of this special issue is to provide the readership with some of the latest advances, lessons learned, experiences gained, and science issues and challenges related to hydrologic applications of weather radar. The special issue features 20 contributions on various topics which reflect the increasing diversity as well as the areas of focus in radar hydrology today. The contributions may be grouped as follows:

Morphological characterization of coral reefs by combining lidar and MBES data: A case study from Yuanzhi Island, South China Sea

NASA Astrophysics Data System (ADS)

Zhang, Kai; Yang, Fanlin; Zhang, Hande; Su, Dianpeng; Li, QianQian

2017-06-01

The correlation between seafloor morphological features and biological complexity has been identified in numerous recent studies. This research focused on the potential for accurate characterization of coral reefs based on high-resolution bathymetry from multiple sources. A standard deviation (STD) based method for quantitatively characterizing terrain complexity was developed that includes robust estimation to correct for irregular bathymetry and a calibration for the depth-dependent variablity of measurement noise. Airborne lidar and shipborne sonar bathymetry measurements from Yuanzhi Island, South China Sea, were merged to generate seamless high-resolution coverage of coral bathymetry from the shoreline to deep water. The new algorithm was applied to the Yuanzhi Island surveys to generate maps of quantitive terrain complexity, which were then compared to in situ video observations of coral abundance. The terrain complexity parameter is significantly correlated with seafloor coral abundance, demonstrating the potential for accurately and efficiently mapping coral abundance through seafloor surveys, including combinations of surveys using different sensors.

Dependence of Liquid Supercooling on Liquid Overheating Levels of Al Small Particles

PubMed Central

Mei, Qingsong; Li, Juying

2015-01-01

The liquid thermal history effect on liquid supercooling behavior has been found in various metals and alloys; typically the degree of liquid supercooling (ΔT−) increases with the increase of liquid overheating (ΔT+) up to several to tens of degrees above the equilibrium melting point (T0). Here we report quantitative experimental measurements on the ΔT−-ΔT+ relationship of Al small particles encapsulated in Al2O3 shells by using a differential scanning calorimeter. We find a remarkable dependence of ΔT− on ΔT+ of Al small particles, extending to at least 340 °C above T0 of Al (~1.36T0), which indicates the existence of temperature-dependent crystallization centers in liquid Al up to very high liquid overheating levels. Our results demonstrate quantitatively the significant effect of liquid thermal history on the supercooling behavior of Al and its alloys, and raise new considerations about the dependence of ΔT− on ΔT+ at very high ΔT+ levels. PMID:28787806

Rapid Determination of Lymphogranuloma Venereum Serovars of Chlamydia trachomatis by Quantitative High-Resolution Melt Analysis (HRMA)

PubMed Central

Stevens, Matthew P.; Garland, Suzanne M.; Zaia, Angelo M.; Tabrizi, Sepehr N.

2012-01-01

A quantitative high-resolution melt analysis assay was developed to differentiate lymphogranuloma venereum-causing serovars of Chlamydia trachomatis (L1 to L3) from other C. trachomatis serovars (D to K). The detection limit of this assay is approximately 10 copies per reaction, comparable to the limits of other quantitative-PCR-based methods. PMID:22933594

The Relationship between Student's Quantitative Skills, Application of Math, Science Courses, and Science Marks at Single-Sex Independent High Schools

ERIC Educational Resources Information Center

Cambridge, David

2012-01-01

For independent secondary schools who offer rigorous curriculum to attract students, integration of quantitative skills in the science courses has become an important definition of rigor. However, there is little research examining students' quantitative skills in relation to high school science performance within the single-sex independent school…

Low angle light scattering analysis: a novel quantitative method for functional characterization of human and murine platelet receptors.

PubMed

Mindukshev, Igor; Gambaryan, Stepan; Kehrer, Linda; Schuetz, Claudia; Kobsar, Anna; Rukoyatkina, Natalia; Nikolaev, Viacheslav O; Krivchenko, Alexander; Watson, Steve P; Walter, Ulrich; Geiger, Joerg

2012-07-01

Determinations of platelet receptor functions are indispensable diagnostic indicators of cardiovascular and hemostatic diseases including hereditary and acquired receptor defects and receptor responses to drugs. However, presently available techniques for assessing platelet function have some disadvantages, such as low sensitivity and the requirement of large sample sizes and unphysiologically high agonist concentrations. Our goal was to develop and initially characterize a new technique designed to quantitatively analyze platelet receptor activation and platelet function on the basis of measuring changes in low angle light scattering. We developed a novel technique based on low angle light scattering registering changes in light scattering at a range of different angles in platelet suspensions during activation. The method proved to be highly sensitive for simultaneous real time detection of changes in size and shape of platelets during activation. Unlike commonly-used methods, the light scattering method could detect platelet shape change and aggregation in response to nanomolar concentrations of extracellular nucleotides. Furthermore, our results demonstrate that the advantages of the light scattering method make it a choice method for platelet receptor monitoring and for investigation of both murine and human platelets in disease models. Our data demonstrate the suitability and superiority of this new low angle light scattering method for comprehensive analyses of platelet receptors and functions. This highly sensitive, quantitative, and online detection of essential physiological, pathophysiological and pharmacological-response properties of human and mouse platelets is a significant improvement over conventional techniques.

Technical note: quantitative measures of iris color using high resolution photographs.

PubMed

Edwards, Melissa; Gozdzik, Agnes; Ross, Kendra; Miles, Jon; Parra, Esteban J

2012-01-01

Our understanding of the genetic architecture of iris color is still limited. This is partly related to difficulties associated with obtaining quantitative measurements of eye color. Here we introduce a new automated method for measuring iris color using high resolution photographs. This method extracts color measurements in the CIE 1976 L*a*b* (CIELAB) color space from a 256 by 256 pixel square sampled from the 9:00 meridian of the iris. Color is defined across three dimensions: L* (the lightness coordinate), a* (the red-green coordinate), and b* (the blue-yellow coordinate). We applied this method to a sample of individuals of diverse ancestry (East Asian, European and South Asian) that was genotyped for the HERC2 rs12913832 polymorphism, which is strongly associated with blue eye color. We identified substantial variation in the CIELAB color space, not only in the European sample, but also in the East Asian and South Asian samples. As expected, rs12913832 was significantly associated with quantitative iris color measurements in subjects of European ancestry. However, this SNP was also strongly associated with iris color in the South Asian sample, although there were no participants with blue irides in this sample. The usefulness of this method is not restricted only to the study of iris pigmentation. High-resolution pictures of the iris will also make it possible to study the genetic variation involved in iris textural patterns, which show substantial heritability in human populations. Copyright © 2011 Wiley Periodicals, Inc.

Magnetic Resonance Fingerprinting - a promising new approach to obtain standardized imaging biomarkers from MRI.

PubMed

2015-04-01

Current routine MRI examinations rely on the acquisition of qualitative images that have a contrast "weighted" for a mixture of (magnetic) tissue properties. Recently, a novel approach was introduced, namely MR Fingerprinting (MRF) with a completely different approach to data acquisition, post-processing and visualization. Instead of using a repeated, serial acquisition of data for the characterization of individual parameters of interest, MRF uses a pseudo randomized acquisition that causes the signals from different tissues to have a unique signal evolution or 'fingerprint' that is simultaneously a function of the multiple material properties under investigation. The processing after acquisition involves a pattern recognition algorithm to match the fingerprints to a predefined dictionary of predicted signal evolutions. These can then be translated into quantitative maps of the magnetic parameters of interest. MR Fingerprinting (MRF) is a technique that could theoretically be applied to most traditional qualitative MRI methods and replaces them with acquisition of truly quantitative tissue measures. MRF is, thereby, expected to be much more accurate and reproducible than traditional MRI and should improve multi-center studies and significantly reduce reader bias when diagnostic imaging is performed. Key Points • MR fingerprinting (MRF) is a new approach to data acquisition, post-processing and visualization.• MRF provides highly accurate quantitative maps of T1, T2, proton density, diffusion.• MRF may offer multiparametric imaging with high reproducibility, and high potential for multicenter/ multivendor studies.

Design, Validation, and Testing of a Hot-Film Anemometer for Hypersonic Flow

NASA Astrophysics Data System (ADS)

Sheplak, Mark

The application of constant-temperature hot-film anemometry to hypersonic flow has been reviewed and extended in this thesis. The objective of this investigation was to develop a measurement tool capable of yielding continuous, high-bandwidth, quantitative, normal mass-flux and total -temperature measurements in moderate-enthalpy environments. This research has produced a probe design that represents a significant advancement over existing designs, offering the following improvements: (1) a five-fold increase in bandwidth; (2) true stagnation-line sensor placement; (3) a two order-of-magnitude decrease in sensor volume; and (4) over a 70% increase in maximum film temperature. These improvements were achieved through substrate design, sensor placement, the use of high-temperature materials, and state -of-the-art microphotolithographic fabrication techniques. The experimental study to characterize the probe was performed in four different hypersonic wind tunnels at NASA-Langley Research Center. The initial test consisted of traversing the hot film through a Mach 6, flat-plate, turbulent boundary layer in air. The detailed static-calibration measurements that followed were performed in two different hypersonic flows: a Mach 11 helium flow and Mach 6 air flow. The final test of this thesis consisted of traversing the probe through the Mach 6 wake of a 70^ circ blunt body. The goal of this test was to determine the state (i.e., laminar or turbulent) of the wake. These studies indicate that substrate conduction effects result in instrumentation characteristics that prevent the hot-film anemometer from being used as a quantitative tool. The extension of this technique to providing quantitative information is dependent upon the development of lower thermal-conductivity substrate materials. However, the probe durability, absence of strain gauging, and high bandwidth represent significant improvements over the hot-wire technique for making qualitative measurements. Potential uses for this probe are: frequency identification for resonant flows, transition studies, turbulence detection for quiet-tunnel development and reattaching turbulent shear flows, and qualitative turbulence studies of shock-wave/turbulent boundary layer interactions.

[Effect of algorithms for calibration set selection on quantitatively determining asiaticoside content in Centella total glucosides by near infrared spectroscopy].

PubMed

Zhan, Xue-yan; Zhao, Na; Lin, Zhao-zhou; Wu, Zhi-sheng; Yuan, Rui-juan; Qiao, Yan-jiang

2014-12-01

The appropriate algorithm for calibration set selection was one of the key technologies for a good NIR quantitative model. There are different algorithms for calibration set selection, such as Random Sampling (RS) algorithm, Conventional Selection (CS) algorithm, Kennard-Stone(KS) algorithm and Sample set Portioning based on joint x-y distance (SPXY) algorithm, et al. However, there lack systematic comparisons between two algorithms of the above algorithms. The NIR quantitative models to determine the asiaticoside content in Centella total glucosides were established in the present paper, of which 7 indexes were classified and selected, and the effects of CS algorithm, KS algorithm and SPXY algorithm for calibration set selection on the accuracy and robustness of NIR quantitative models were investigated. The accuracy indexes of NIR quantitative models with calibration set selected by SPXY algorithm were significantly different from that with calibration set selected by CS algorithm or KS algorithm, while the robustness indexes, such as RMSECV and |RMSEP-RMSEC|, were not significantly different. Therefore, SPXY algorithm for calibration set selection could improve the predicative accuracy of NIR quantitative models to determine asiaticoside content in Centella total glucosides, and have no significant effect on the robustness of the models, which provides a reference to determine the appropriate algorithm for calibration set selection when NIR quantitative models are established for the solid system of traditional Chinese medcine.

Clinical significance of quantitative analysis of facial nerve enhancement on MRI in Bell's palsy.

PubMed

Song, Mee Hyun; Kim, Jinna; Jeon, Ju Hyun; Cho, Chang Il; Yoo, Eun Hye; Lee, Won-Sang; Lee, Ho-Ki

2008-11-01

Quantitative analysis of the facial nerve on the lesion side as well as the normal side, which allowed for more accurate measurement of facial nerve enhancement in patients with facial palsy, showed statistically significant correlation with the initial severity of facial nerve inflammation, although little prognostic significance was shown. This study investigated the clinical significance of quantitative measurement of facial nerve enhancement in patients with Bell's palsy by analyzing the enhancement pattern and correlating MRI findings with initial severity of facial palsy and clinical outcome. Facial nerve enhancement was measured quantitatively by using the region of interest on pre- and postcontrast T1-weighted images in 44 patients diagnosed with Bell's palsy. The signal intensity increase on the lesion side was first compared with that of the contralateral side and then correlated with the initial degree of facial palsy and prognosis. The lesion side showed significantly higher signal intensity increase compared with the normal side in all of the segments except for the mastoid segment. Signal intensity increase at the internal auditory canal and labyrinthine segments showed correlation with the initial degree of facial palsy but no significant difference was found between different prognostic groups.

Genetics of Variation in Serum Uric Acid and Cardiovascular Risk Factors in Mexican Americans

PubMed Central

Voruganti, V. Saroja; Nath, Subrata D.; Cole, Shelley A.; Thameem, Farook; Jowett, Jeremy B.; Bauer, Richard; MacCluer, Jean W.; Blangero, John; Comuzzie, Anthony G.; Abboud, Hanna E.; Arar, Nedal H.

2009-01-01

Background: Elevated serum uric acid is associated with several cardiovascular disease (CVD) risk factors such as hypertension, inflammation, endothelial dysfunction, insulin resistance, dyslipidemia, and obesity. However, the role of uric acid as an independent risk factor for CVD is not yet clear. Objective: The aim of the study was to localize quantitative trait loci regulating variation in serum uric acid and also establish the relationship between serum uric acid and other CVD risk factors in Mexican Americans (n = 848; men = 310, women = 538) participating in the San Antonio Family Heart Study. Methods: Quantitative genetic analysis was conducted using variance components decomposition method, implemented in the software program SOLAR. Results: Mean ± sd of serum uric acid was 5.35 ± 1.38 mg/dl. Univariate genetic analysis showed serum uric acid and other CVD risk markers to be significantly heritable (P < 0.005). Bivariate analysis showed significant correlation of serum uric acid with body mass index, waist circumference, waist/hip ratio, total body fat, plasma insulin, serum triglycerides, high-density lipoprotein cholesterol, C-reactive protein, and granulocyte macrophage-colony stimulating factor (P < 0.05). A genome-wide scan for detecting quantitative trait loci regulating serum uric acid variation showed a significant logarithm of odds (LOD) score of 4.72 (empirical LOD score = 4.62; P < 0.00001) on chromosome 3p26. One LOD support interval contains 25 genes, of which an interesting candidate gene is chemokine receptor 2. Summary: There is a significant genetic component in the variation in serum uric acid and evidence of pleiotropy between serum uric acid and other cardiovascular risk factors. PMID:19001525

Clinical antibacterial effectiveness of the self-adjusting file system.

PubMed

Neves, M A S; Rôças, I N; Siqueira, J F

2014-04-01

To evaluate in vivo the antibacterial effectiveness of the self-adjusting file (SAF) using molecular methods. Root canals from single-rooted teeth with apical periodontitis were instrumented using the SAF system under continuous irrigation with 2.5% NaOCl. DNA extracts from samples taken before and after instrumentation were subjected to quantitative analysis of total bacteria counts and levels of streptococci by quantitative real-time polymerase chain reaction (qPCR). The reverse-capture checkerboard assay was also used to identify 28 bacterial taxa before (S1) and after (S2) SAF instrumentation. SAF was also compared with a conventional hand nickel-titanium instrumentation technique for total bacterial reduction. Data from qPCR were analysed statistically within groups using the Wilcoxon matched pairs test and between groups using the Mann-Whitney U-test and the Fisher's exact test, with significance level set at P < 0.05. Self-adjusting file significantly reduced the total bacterial counts from a mean number of 1.96 × 10(7) cells to 1.34 × 10(4) cells (P < 0.001). Quantitatively, the 99.9% reduction in total bacterial counts associated with the SAF system was significantly superior to the 95.1% reduction obtained by hand instrumentation (P < 0.001). Qualitatively, SAF resulted in significantly more cases with negative PCR results for bacteria (54.5%) than hand instrumentation (4.5%) (P < 0.001). The SAF system succeeded in significantly reducing the streptococcal levels, but four cases still harboured these bacteria in S2. Checkerboard analysis revealed that not only streptococci but also some anaerobic and even as-yet-uncultivated bacteria may resist the effects of chemomechanical procedures. The SAF instrumentation system was highly effective in reducing bacterial populations from infected root canals and performed significantly better than hand instrumentation. However, because half of the samples still had detectable bacteria after preparation with SAF, supplementary disinfection is still required to maximize bacterial elimination. © 2013 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Dosimetric variations due to interfraction organ deformation in cervical cancer brachytherapy.

PubMed

Kobayashi, Kazuma; Murakami, Naoya; Wakita, Akihisa; Nakamura, Satoshi; Okamoto, Hiroyuki; Umezawa, Rei; Takahashi, Kana; Inaba, Koji; Igaki, Hiroshi; Ito, Yoshinori; Shigematsu, Naoyuki; Itami, Jun

2015-12-01

We quantitatively estimated dosimetric variations due to interfraction organ deformation in multi-fractionated high-dose-rate brachytherapy (HDRBT) for cervical cancer using a novel surface-based non-rigid deformable registration. As the number of consecutive HDRBT fractions increased, simple addition of dose-volume histogram parameters significantly overestimated the dose, compared with distribution-based dose addition. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

System and process for pulsed multiple reaction monitoring

DOEpatents

Belov, Mikhail E

2013-05-17

A new pulsed multiple reaction monitoring process and system are disclosed that uses a pulsed ion injection mode for use in conjunction with triple-quadrupole instruments. The pulsed injection mode approach reduces background ion noise at the detector, increases amplitude of the ion signal, and includes a unity duty cycle that provides a significant sensitivity increase for reliable quantitation of proteins/peptides present at attomole levels in highly complex biological mixtures.

A non-radioisotopic quantitative competitive polymerase chain reaction method: application in measurement of human herpesvirus 7 load.

PubMed

Kidd, I M; Clark, D A; Emery, V C

2000-06-01

Quantitative-competitive polymerase chain reaction (QCPCR) is a well-optimised and objective methodology for the determination of viral load in clinical specimens. A major advantage of QCPCR is the ability to control for the differential modulation of the PCR process in the presence of potentially inhibitory material. QCPCR protocols were developed previously for CMV, HHV-6, HHV-7 and HHV-8 and relied upon radioactively labelled primers, followed by autoradiography of the separated and digested PCR products to quantify viral load. Whilst this approach offers high accuracy and dynamic range, non-radioactive approaches would be attractive. Here, an alternative detection system is reported, based on simple ethidium bromide staining and computer analysis of the separated reaction products, which enables its adoption in the analysis of a large number of samples. In calibration experiments using cloned HHV-7 DNA, the ethidium bromide detection method showed an improved correlation with known copy number over that obtained with the isotopic method. In addition, 67 HHV-7 PCR positive blood samples, derived from immunocompromised patients, were quantified using both detection techniques. The results showed a highly significant correlation with no significant difference between the two methods. The applicability of the computerised densitometry method in the routine laboratory is discussed.

Quantitative, high-resolution epigenetic profiling of CpG loci identifies associations with cord blood plasma homocysteine and birth weight in humans

PubMed Central

Ismail, Khaled MK; Haworth, Kim E; Mein, Charles; Carroll, William D

2011-01-01

Supplementation with folic acid during pregnancy is known to reduce the risk of neural tube defects and low birth weight. It is thought that folate and other one-carbon intermediates might secure these clinical effects via DNA methylation. We examined the effects of folate on the human methylome using quantitative interrogation of 27,578 CpG loci associated with 14,496 genes at single-nucleotide resolution across 12 fetal cord blood samples. Consistent with previous studies, the majority of CpG dinucleotides located within CpG islands exhibited hypomethylation while those outside CpG islands showed mid-high methylation. However, for the first time in human samples, unbiased analysis of methylation across samples revealed a significant correlation of methylation patterns with plasma homocysteine, LINE-1 methylation and birth weight centile. Additionally, CpG methylation significantly correlated with either birth weight or LINE-1 methylation were predominantly located in CpG islands. These data indicate that levels of folate-associated intermediates in cord blood reflect their influence and consequences for the fetal epigenome and potentially on pregnancy outcome. In these cases, their influence might be exerted during late gestation or reflect those present during the peri-conceptual period. PMID:20864804

Esophagus cancer and occupational exposure to asbestos: results from a meta-analysis of epidemiology studies.

PubMed

Li, B; Tang, S P; Wang, K Z

2016-07-01

The relationship between occupational asbestos exposure and esophagus cancer (EC) is not fully understood. We performed a meta-analysis to quantitatively assess the association. We systematically searched databases of PubMed, EMBASE, and Web of Science for studies with quantitative estimates of asbestos exposure and EC mortality. Pooled standardized mortality ratios (SMRs) and their corresponding 95% confidence intervals (CIs) were calculated. Twenty cohort studies on EC and asbestos exposure were included in this meta-analysis. Overall, occupational exposure to asbestos was associated with an excess risk of EC (SMR = 1.24, 95% CI: 1.13-1.38, P < 0.001), with little evidence of heterogeneity among studies (I(2) = 0.0%, P = 0.682). Being male, exposure to chrysotile or mixed asbestos, working at textile industry, long study follow-up (≥20 years), Asia, Europe and America cohorts with larger cohort size (>500), and high-exposure group all contribute to significantly higher SMR. Publication bias was not detected (Egger's test P-value = 0.374). This meta-analysis suggested that occupational asbestos exposure might be associated with an increased risk of EC in male. High-exposure level of asbestos could contribute to significantly higher risk of EC mortality. © 2015 International Society for Diseases of the Esophagus.

Design, synthesis, antiviral bioactivity and three-dimensional quantitative structure-activity relationship study of novel ferulic acid ester derivatives containing quinazoline moiety.

PubMed

Wu, Zengxue; Zhang, Jian; Chen, Jixiang; Pan, Jianke; Zhao, Lei; Liu, Dengyue; Zhang, Awei; Chen, Jin; Hu, Deyu; Song, Baoan

2017-10-01

Ferulic acid and quinazoline derivatives possess good antiviral activities. In order to develop novel compounds with high antiviral activities, a series of ferulic acid ester derivatives containing quinazoline were synthesized and evaluated for their antiviral activities. Bioassays indicated that some of the compounds exhibited good antiviral activities in vivo against tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV). One of the compounds demonstrated significant curative and protective activities against TMV and CMV, with EC 50 values of 162.14, 114.61 and 255.49, 138.81 mg L -1 , respectively, better than those of ningnanmycin (324.51, 168.84 and 373.88, 272.70 mg L -1 ). The values of q 2 and r 2 for comparative molecular field analysis and comparative molecular similarity index analysis in the TMV (0.508, 0.663 and 0.992, 0.930) and CMV (0.530, 0.626 and 0.997, 0.981) models presented good predictive abilities. Some of the title compounds demonstrated good antiviral activities. Three-dimensional quantitative structure-activity relationship models revealed that the antiviral activities depend on steric and electrostatic properties. These results could provide significant structural insights for the design of highly active ferulic acid derivatives. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis

PubMed Central

Sulyok, Michael; Liu, Xingzhong; Rao, Mingyong

2016-01-01

Pu-erh is a tea produced in Yunnan, China by microbial fermentation of fresh Camellia sinensis leaves by two processes, the traditional raw fermentation and the faster, ripened fermentation. We characterized fungal and bacterial communities in leaves and both Pu-erhs by high-throughput, rDNA-amplicon sequencing and we characterized the profile of bioactive extrolite mycotoxins in Pu-erh teas by quantitative liquid chromatography-tandem mass spectrometry. We identified 390 fungal and 629 bacterial OTUs from leaves and both Pu-erhs. Major findings are: 1) fungal diversity drops and bacterial diversity rises due to raw or ripened fermentation, 2) fungal and bacterial community composition changes significantly between fresh leaves and both raw and ripened Pu-erh, 3) aging causes significant changes in the microbial community of raw, but not ripened, Pu-erh, and, 4) ripened and well-aged raw Pu-erh have similar microbial communities that are distinct from those of young, raw Ph-erh tea. Twenty-five toxic metabolites, mainly of fungal origin, were detected, with patulin and asperglaucide dominating and at levels supporting the Chinese custom of discarding the first preparation of Pu-erh and using the wet tea to then brew a pot for consumption. PMID:27337135

Plant leaf chlorophyll content retrieval based on a field imaging spectroscopy system.

PubMed

Liu, Bo; Yue, Yue-Min; Li, Ru; Shen, Wen-Jing; Wang, Ke-Lin

2014-10-23

A field imaging spectrometer system (FISS; 380-870 nm and 344 bands) was designed for agriculture applications. In this study, FISS was used to gather spectral information from soybean leaves. The chlorophyll content was retrieved using a multiple linear regression (MLR), partial least squares (PLS) regression and support vector machine (SVM) regression. Our objective was to verify the performance of FISS in a quantitative spectral analysis through the estimation of chlorophyll content and to determine a proper quantitative spectral analysis method for processing FISS data. The results revealed that the derivative reflectance was a more sensitive indicator of chlorophyll content and could extract content information more efficiently than the spectral reflectance, which is more significant for FISS data compared to ASD (analytical spectral devices) data, reducing the corresponding RMSE (root mean squared error) by 3.3%-35.6%. Compared with the spectral features, the regression methods had smaller effects on the retrieval accuracy. A multivariate linear model could be the ideal model to retrieve chlorophyll information with a small number of significant wavelengths used. The smallest RMSE of the chlorophyll content retrieved using FISS data was 0.201 mg/g, a relative reduction of more than 30% compared with the RMSE based on a non-imaging ASD spectrometer, which represents a high estimation accuracy compared with the mean chlorophyll content of the sampled leaves (4.05 mg/g). Our study indicates that FISS could obtain both spectral and spatial detailed information of high quality. Its image-spectrum-in-one merit promotes the good performance of FISS in quantitative spectral analyses, and it can potentially be widely used in the agricultural sector.

Plant Leaf Chlorophyll Content Retrieval Based on a Field Imaging Spectroscopy System

PubMed Central

Liu, Bo; Yue, Yue-Min; Li, Ru; Shen, Wen-Jing; Wang, Ke-Lin

2014-01-01

A field imaging spectrometer system (FISS; 380–870 nm and 344 bands) was designed for agriculture applications. In this study, FISS was used to gather spectral information from soybean leaves. The chlorophyll content was retrieved using a multiple linear regression (MLR), partial least squares (PLS) regression and support vector machine (SVM) regression. Our objective was to verify the performance of FISS in a quantitative spectral analysis through the estimation of chlorophyll content and to determine a proper quantitative spectral analysis method for processing FISS data. The results revealed that the derivative reflectance was a more sensitive indicator of chlorophyll content and could extract content information more efficiently than the spectral reflectance, which is more significant for FISS data compared to ASD (analytical spectral devices) data, reducing the corresponding RMSE (root mean squared error) by 3.3%–35.6%. Compared with the spectral features, the regression methods had smaller effects on the retrieval accuracy. A multivariate linear model could be the ideal model to retrieve chlorophyll information with a small number of significant wavelengths used. The smallest RMSE of the chlorophyll content retrieved using FISS data was 0.201 mg/g, a relative reduction of more than 30% compared with the RMSE based on a non-imaging ASD spectrometer, which represents a high estimation accuracy compared with the mean chlorophyll content of the sampled leaves (4.05 mg/g). Our study indicates that FISS could obtain both spectral and spatial detailed information of high quality. Its image-spectrum-in-one merit promotes the good performance of FISS in quantitative spectral analyses, and it can potentially be widely used in the agricultural sector. PMID:25341439

A Quantitative Analysis of Pulsed Signals Emitted by Wild Bottlenose Dolphins.

PubMed

Luís, Ana Rita; Couchinho, Miguel N; Dos Santos, Manuel E

2016-01-01

Common bottlenose dolphins (Tursiops truncatus), produce a wide variety of vocal emissions for communication and echolocation, of which the pulsed repertoire has been the most difficult to categorize. Packets of high repetition, broadband pulses are still largely reported under a general designation of burst-pulses, and traditional attempts to classify these emissions rely mainly in their aural characteristics and in graphical aspects of spectrograms. Here, we present a quantitative analysis of pulsed signals emitted by wild bottlenose dolphins, in the Sado estuary, Portugal (2011-2014), and test the reliability of a traditional classification approach. Acoustic parameters (minimum frequency, maximum frequency, peak frequency, duration, repetition rate and inter-click-interval) were extracted from 930 pulsed signals, previously categorized using a traditional approach. Discriminant function analysis revealed a high reliability of the traditional classification approach (93.5% of pulsed signals were consistently assigned to their aurally based categories). According to the discriminant function analysis (Wilk's Λ = 0.11, F3, 2.41 = 282.75, P < 0.001), repetition rate is the feature that best enables the discrimination of different pulsed signals (structure coefficient = 0.98). Classification using hierarchical cluster analysis led to a similar categorization pattern: two main signal types with distinct magnitudes of repetition rate were clustered into five groups. The pulsed signals, here described, present significant differences in their time-frequency features, especially repetition rate (P < 0.001), inter-click-interval (P < 0.001) and duration (P < 0.001). We document the occurrence of a distinct signal type-short burst-pulses, and highlight the existence of a diverse repertoire of pulsed vocalizations emitted in graded sequences. The use of quantitative analysis of pulsed signals is essential to improve classifications and to better assess the contexts of emission, geographic variation and the functional significance of pulsed signals.

Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

PubMed Central

Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

2011-01-01

Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

The FAQUIRE Approach: FAst, QUantitative, hIghly Resolved and sEnsitivity Enhanced 1H, 13C Data.

PubMed

Farjon, Jonathan; Milande, Clément; Martineau, Estelle; Akoka, Serge; Giraudeau, Patrick

2018-02-06

The targeted analysis of metabolites in complex mixtures is a challenging issue. NMR is one of the major tools in this field, but there is a strong need for more sensitive, better-resolved, and faster quantitative methods. In this framework, we introduce the concept of FAst, QUantitative, hIghly Resolved and sEnsitivity enhanced (FAQUIRE) NMR to push forward the limits of metabolite NMR analysis. 2D 1 H, 13 C 2D quantitative maps are promising alternatives for enhancing the spectral resolution but are highly time-consuming because of (i) the intrinsic nature of 2D, (ii) the longer recycling times required for quantitative conditions, and (iii) the higher number of scans needed to reduce the level of detection/quantification to access low concentrated metabolites. To reach this aim, speeding up the recently developed QUantItative Perfected and pUre shifted HSQC (QUIPU HSQC) is an interesting attempt to develop the FAQUIRE concept. Thanks to the combination of spectral aliasing, nonuniform sampling, and variable repetition time, the acquisition time of 2D quantitative maps is reduced by a factor 6 to 9, while conserving a high spectral resolution thanks to a pure shift approach. The analytical potential of the new Quick QUIPU HSQC (Q QUIPU HSQC) is evaluated on a model metabolite sample, and its potential is shown on breast-cell extracts embedding metabolites at millimolar to submillimolar concentrations.

Quantitative diffusion MRI using reduced field-of-view and multi-shot acquisition techniques: Validation in phantoms and prostate imaging.

PubMed

Zhang, Yuxin; Holmes, James; Rabanillo, Iñaki; Guidon, Arnaud; Wells, Shane; Hernando, Diego

2018-09-01

To evaluate the reproducibility of quantitative diffusion measurements obtained with reduced Field of View (rFOV) and Multi-shot EPI (msEPI) acquisitions, using single-shot EPI (ssEPI) as a reference. Diffusion phantom experiments, and prostate diffusion-weighted imaging in healthy volunteers and patients with known or suspected prostate cancer were performed across the three different sequences. Quantitative diffusion measurements of apparent diffusion coefficient, and diffusion kurtosis parameters (healthy volunteers), were obtained and compared across diffusion sequences (rFOV, msEPI, and ssEPI). Other possible confounding factors like b-value combinations and acquisition parameters were also investigated. Both msEPI and rFOV have shown reproducible quantitative diffusion measurements relative to ssEPI; no significant difference in ADC was observed across pulse sequences in the standard diffusion phantom (p = 0.156), healthy volunteers (p ≥ 0.12) or patients (p ≥ 0.26). The ADC values within the non-cancerous central gland and peripheral zone of patients were 1.29 ± 0.17 × 10 -3  mm 2 /s and 1.74 ± 0.23 × 10 -3  mm 2 /s respectively. However, differences in quantitative diffusion parameters were observed across different number of averages for rFOV, and across b-value groups and diffusion models for all the three sequences. Both rFOV and msEPI have the potential to provide high image quality with reproducible quantitative diffusion measurements in prostate diffusion MRI. Copyright © 2018 Elsevier Inc. All rights reserved.

Hematocrit Measurement with R2* and Quantitative Susceptibility Mapping in Postmortem Brain.

PubMed

Walsh, A J; Sun, H; Emery, D J; Wilman, A H

2018-05-24

Noninvasive venous oxygenation quantification with MR imaging will improve the neurophysiologic investigation and the understanding of the pathophysiology in neurologic diseases. Available MR imaging methods are limited by sensitivity to flow and often require assumptions of the hematocrit level. In situ postmortem imaging enables evaluation of methods in a fully deoxygenated environment without flow artifacts, allowing direct calculation of hematocrit. This study compares 2 venous oxygenation quantification methods in in situ postmortem subjects. Transverse relaxation (R2*) mapping and quantitative susceptibility mapping were performed on a whole-body 4.7T MR imaging system. Intravenous measurements in major draining intracranial veins were compared between the 2 methods in 3 postmortem subjects. The quantitative susceptibility mapping technique was also applied in 10 healthy control subjects and compared with reference venous oxygenation values. In 2 early postmortem subjects, R2* mapping and quantitative susceptibility mapping measurements within intracranial veins had a significant and strong correlation ( R 2 = 0.805, P = .004 and R 2 = 0.836, P = .02). Higher R2* and susceptibility values were consistently demonstrated within gravitationally dependent venous segments during the early postmortem period. Hematocrit ranged from 0.102 to 0.580 in postmortem subjects, with R2* and susceptibility as large as 291 seconds -1 and 1.75 ppm, respectively. Measurements of R2* and quantitative susceptibility mapping within large intracranial draining veins have a high correlation in early postmortem subjects. This study supports the use of quantitative susceptibility mapping for evaluation of in vivo venous oxygenation and postmortem hematocrit concentrations. © 2018 by American Journal of Neuroradiology.

A Review: Some biological effects of high LET radiations

NASA Technical Reports Server (NTRS)

Wiley, A., Jr.

1972-01-01

There are qualitative and quantitative differences in the biological damage observed after exposure to high LET radiation as compared to that caused by low LET radiations. This review is concerned with these differences, which are ultimately reflected at the biochemical, cellular and even whole animal levels. In general, high LET radiations seem to produce biochemical damage which is more severe and possibly less repairable. Experimental data for those effects are presented in terms of biochemical RBE's with consideration of both early and late manifestations. An LET independent process by which significant biochemical damage may result from protons, neutrons and negative pion mesons is discussed.

Analytical Glycobiology at High Sensitivity: Current Approaches and Directions

PubMed Central

Novotny, Milos V.; Alley, William R.; Mann, Benjamin F.

2013-01-01

This review summarizes the analytical advances made during the last several years in the structural and quantitative determinations of glycoproteins in complex biological mixtures. The main analytical techniques used in the fields of glycomics and glycoproteomics involve different modes of mass spectrometry and their combinations with capillary separation methods such as microcolumn liquid chromatography and capillary electrophoresis. The needs for high-sensitivity measurements have been emphasized in the oligosaccharide profiling used in the field of biomarker discovery through MALDI mass spectrometry. High-sensitivity profiling of both glycans and glycopeptides from biological fluids and tissue extracts has been aided significantly through lectin preconcentration and the uses of affinity chromatography. PMID:22945852

Association of the gut microbiota mobilome with hospital location and birth weight in preterm infants.

PubMed

Ravi, Anuradha; Estensmo, Eva Lena F; Abée-Lund, Trine M L'; Foley, Steven L; Allgaier, Bernhard; Martin, Camilia R; Claud, Erika C; Rudi, Knut

2017-11-01

BackgroundThe preterm infant gut microbiota is vulnerable to different biotic and abiotic factors. Although the development of this microbiota has been extensively studied, the mobilome-i.e. the mobile genetic elements (MGEs) in the gut microbiota-has not been considered. Therefore, the aim of this study was to investigate the association of the mobilome with birth weight and hospital location in the preterm infant gut microbiota.MethodsThe data set consists of fecal samples from 62 preterm infants with and without necrotizing enterocolitis (NEC) from three different hospitals. We analyzed the gut microbiome by using 16S rRNA amplicon sequencing, shot-gun metagenome sequencing, and quantitative PCR. Predictive models and other data analyses were performed using MATLAB and QIIME.ResultSThe microbiota composition was significantly different between NEC-positive and NEC-negative infants and significantly different between hospitals. An operational taxanomic unit (OTU) showed strong positive and negative correlation with NEC and birth weight, respectively, whereas none showed significance for mode of delivery. Metagenome analyses revealed high levels of conjugative plasmids with MGEs and virulence genes. Results from quantitative PCR showed that the plasmid signature genes were significantly different between hospitals and in NEC-positive infants.ConclusionOur results point toward an association of the mobilome with hospital location in preterm infants.

Assessment of Occupational Health and Safety for a Gas Meter Manufacturing Plant

NASA Astrophysics Data System (ADS)

Korkmaz, Ece; Iskender, Gulen; Germirli Babuna, Fatos

2016-10-01

This study investigates the occupational health and safety for a gas meter manufacturing plant. The risk assessment and management study is applied to plastic injection and mounting departments of the factory through quantitative Fine Kinney method and the effect of adopting 5S workplace organization procedure on risk assessment is examined. The risk assessment reveals that there are 17 risks involved; 14 grouped in high risk class (immediate improvement as required action); 2 in significant (measures to be taken as required action) and one in possible risk class (monitoring as required action). Among 14 high risks, 4 can be reduced by 83 % to be grouped under possible class when 5S is applied. One significant risk is observed to be lowered by 78 % and considered as possible risk due to the application of 5S. As a result of either 67 or 50 % reductions in 7 high risks, these risks are converted to be members of significant risk group after 5S implications.

Blood Pyrrole-Protein Adducts--A Biomarker of Pyrrolizidine Alkaloid-Induced Liver Injury in Humans.

PubMed

Ruan, Jianqing; Gao, Hong; Li, Na; Xue, Junyi; Chen, Jie; Ke, Changqiang; Ye, Yang; Fu, Peter Pi-Cheng; Zheng, Jiang; Wang, Jiyao; Lin, Ge

2015-01-01

Pyrrolizidine alkaloids (PAs) induce liver injury (PA-ILI) and is very likely to contribute significantly to drug-induced liver injury (DILI). In this study we used a newly developed ultra-high performance liquid chromatography-triple quadrupole-mass spectrometry (UHPLC-MS)-based method to detect and quantitate blood pyrrole-protein adducts in DILI patients. Among the 46 suspected DILI patients, 15 were identified as PA-ILI by the identification of PA-containing herbs exposed. Blood pyrrole-protein adducts were detected in all PA-ILI patients (100%). These results confirm that PA-ILI is one of the major causes of DILI and that blood pyrrole-protein adducts quantitated by the newly developed UHPLC-MS method can serve as a specific biomarker of PA-ILI.

Assessing signal-to-noise in quantitative proteomics: multivariate statistical analysis in DIGE experiments.

PubMed

Friedman, David B

2012-01-01

All quantitative proteomics experiments measure variation between samples. When performing large-scale experiments that involve multiple conditions or treatments, the experimental design should include the appropriate number of individual biological replicates from each condition to enable the distinction between a relevant biological signal from technical noise. Multivariate statistical analyses, such as principal component analysis (PCA), provide a global perspective on experimental variation, thereby enabling the assessment of whether the variation describes the expected biological signal or the unanticipated technical/biological noise inherent in the system. Examples will be shown from high-resolution multivariable DIGE experiments where PCA was instrumental in demonstrating biologically significant variation as well as sample outliers, fouled samples, and overriding technical variation that would not be readily observed using standard univariate tests.

A facile one-step fluorescence method for the quantitation of low-content single base deamination impurity in synthetic oligonucleotides.

PubMed

Su, Xiaoye; Liang, Ruiting; Stolee, Jessica A

2018-06-05

Oligonucleotides are being researched and developed as potential drug candidates for the treatment of a broad spectrum of diseases. The characterization of antisense oligonucleotide (ASO) impurities caused by base mutations (e.g. deamination) which are closely related to the target ASO is a significant analytical challenge. Herein, we describe a novel one-step method, utilizing a strategy that combines fluorescence-ON detection with competitive hybridization, to achieve single base mutation quantitation in extensively modified synthetic ASOs. Given that this method is highly specific and sensitive (LoQ = 4 nM), we envision that it will find utility for screening other impurities as well as sequencing modified oligonucleotides. Copyright © 2018 Elsevier B.V. All rights reserved.

Correlation and path coefficient analysis of quantitative characters in spine gourd (Momordica dioica Roxb.).

PubMed

Aliya, F; Begum, H; Reddy, M T; Sivaraj, N; Pandravada, S R; Narshimulu, G

2014-05-01

Fifty genotypes of spine gourd (Momordica dioica Roxb.) were evaluated in a randomized block design with two replications at the Vegetable Research Station, Rajendranagar, Hyderabad, Andhra Pradesh, India during kharif, 2012. Correlation and path coefficient analysis were carried out to study the character association and contribution, respectively for twelve quantitative characters namely vine length (m), number of stems per plant, days to first female flower appearance, first female flowering node, days to first fruit harvest, days to last fruit harvest, fruiting period (days), fruit length (cm), fruit width (cm), fruit weight (g), number of fruits per plant and fruit yield per plant (kg) for identification of the potential selection indices. Correlation and path coefficient analyses revealed that fruiting period and number of fruits per plant not only had positively significant correlation with fruit yield but also had positively high direct effect on it and are regarded as the main determinants of fruit yield. Days to first fruit harvest had positively moderate direct effect on fruit yield and its association was negatively significant, days to last fruit harvest had negatively high direct effect on fruit yield and its association was significant positively, hence restricted simultaneous selection can be made for days to first fruit harvest and days to last fruit harvest. The improvement in fruit yield can be effective if selection is based on days to first fruit harvest, days to last fruit harvest, fruiting period and number of fruits per plant.

Assessment of the Diversity of Pseudomonas spp. and Fusarium spp. in Radix pseudostellariae Rhizosphere under Monoculture by Combining DGGE and Quantitative PCR

PubMed Central

Chen, Jun; Wu, Linkun; Xiao, Zhigang; Wu, Yanhong; Wu, Hongmiao; Qin, Xianjin; Wang, Juanying; Wei, Xiaoya; Khan, Muhammad U.; Lin, Sheng; Lin, Wenxiong

2017-01-01

Radix pseudostellariae is a perennial tonic medicinal plant, with high medicinal value. However, consecutive monoculture of this plant in the same field results in serious decrease in both yield and quality. In this study, a 3-year field experiment was performed to identify the inhibitory effect of growth caused by prolonged monoculture of R. pseudostellariae. DGGE analysis was used to explore the shifts in the structure and diversity of soil Fusarium and Pseudomonas communities along a 3-year gradient of monoculture. The results demonstrated that extended monoculture significantly boosted the diversity of Fusarium spp., but declined Pseudomonas spp. diversity. Quantitative PCR analysis showed a significant increase in Fusarium oxysporum, but a decline in Pseudomonas spp. Furthermore, abundance of antagonistic Pseudomonas spp. possessing antagonistic ability toward F. oxysporum significantly decreased in consecutively monocultured soils. Phenolic acid mixture at the same ratio as detected in soil could boost mycelial and sporular growth of pathogenic F. oxysporum while inhibit the growth of antagonistic Pseudomonas sp. CJ313. Moreover, plant bioassays showed that Pseudomonas sp. CJ313 had a good performance that protected R. pseudostellariae from infection by F. oxysporum. In conclusion, this study demonstrated that extended monoculture of R. pseudostellariae could alter the Fusarium and Pseudomonas communities in the plant rhizosphere, leading to relatively low level of antagonistic microorganisms, but with relatively high level of pathogenic microorganisms. PMID:28966607

Altered Expression of Ganglioside Metabolizing Enzymes Results in GM3 Ganglioside Accumulation in Cerebellar Cells of a Mouse Model of Juvenile Neuronal Ceroid Lipofuscinosis.

PubMed

Somogyi, Aleksandra; Petcherski, Anton; Beckert, Benedikt; Huebecker, Mylene; Priestman, David A; Banning, Antje; Cotman, Susan L; Platt, Frances M; Ruonala, Mika O; Tikkanen, Ritva

2018-02-22

Juvenile neuronal ceroid lipofuscinosis (JNCL) is caused by mutations in the CLN3 gene. Most JNCL patients exhibit a 1.02 kb genomic deletion removing exons 7 and 8 of this gene, which results in a truncated CLN3 protein carrying an aberrant C-terminus. A genetically accurate mouse model ( Cln3 Δex7/8 mice) for this deletion has been generated. Using cerebellar precursor cell lines generated from wildtype and Cln3 Δex7/8 mice, we have here analyzed the consequences of the CLN3 deletion on levels of cellular gangliosides, particularly GM3, GM2, GM1a and GD1a. The levels of GM1a and GD1a were found to be significantly reduced by both biochemical and cytochemical methods. However, quantitative high-performance liquid chromatography analysis revealed a highly significant increase in GM3, suggesting a metabolic blockade in the conversion of GM3 to more complex gangliosides. Quantitative real-time PCR analysis revealed a significant reduction in the transcripts of the interconverting enzymes, especially of β-1,4- N -acetyl-galactosaminyl transferase 1 (GM2 synthase), which is the enzyme converting GM3 to GM2. Thus, our data suggest that the complex a-series gangliosides are reduced in Cln3 Δex7/8 mouse cerebellar precursor cells due to impaired transcription of the genes responsible for their synthesis.

Altered Expression of Ganglioside Metabolizing Enzymes Results in GM3 Ganglioside Accumulation in Cerebellar Cells of a Mouse Model of Juvenile Neuronal Ceroid Lipofuscinosis

PubMed Central

Somogyi, Aleksandra; Petcherski, Anton; Beckert, Benedikt; Huebecker, Mylene; Priestman, David A.; Banning, Antje; Cotman, Susan L.; Platt, Frances M.; Ruonala, Mika O.

2018-01-01

Juvenile neuronal ceroid lipofuscinosis (JNCL) is caused by mutations in the CLN3 gene. Most JNCL patients exhibit a 1.02 kb genomic deletion removing exons 7 and 8 of this gene, which results in a truncated CLN3 protein carrying an aberrant C-terminus. A genetically accurate mouse model (Cln3Δex7/8 mice) for this deletion has been generated. Using cerebellar precursor cell lines generated from wildtype and Cln3Δex7/8 mice, we have here analyzed the consequences of the CLN3 deletion on levels of cellular gangliosides, particularly GM3, GM2, GM1a and GD1a. The levels of GM1a and GD1a were found to be significantly reduced by both biochemical and cytochemical methods. However, quantitative high-performance liquid chromatography analysis revealed a highly significant increase in GM3, suggesting a metabolic blockade in the conversion of GM3 to more complex gangliosides. Quantitative real-time PCR analysis revealed a significant reduction in the transcripts of the interconverting enzymes, especially of β-1,4-N-acetyl-galactosaminyl transferase 1 (GM2 synthase), which is the enzyme converting GM3 to GM2. Thus, our data suggest that the complex a-series gangliosides are reduced in Cln3Δex7/8 mouse cerebellar precursor cells due to impaired transcription of the genes responsible for their synthesis. PMID:29470438

Radiation-Induced Damage to Microstructure of Parotid Gland: Evaluation Using High-Resolution Magnetic Resonance Imaging

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

Kan, Tomoko, E-mail: tkan@grape.med.tottori-u.ac.j; Kodani, Kazuhiko; Michimoto, Koichi

Purpose: To elucidate the radiation-induced damage to the microstructure of the parotid gland using high-resolution magnetic resonance imaging. Methods and Materials: High-resolution magnetic resonance imaging of the parotid gland was performed before radiotherapy (RT) and during the RT period or {<=}3 weeks after RT completion for 12 head-and-neck cancer patients using a 1.5-T scanner with a microscopy coil. The maximal cross-sectional area of the gland was evaluated, and changes in the internal architecture of the gland were assessed both visually and quantitatively. Results: Magnetic resonance images were obtained at a median parotid gland dose of 36 Gy (range, 11-64). Accordingmore » to the quantitative analysis, the maximal cross-sectional area of the gland was reduced, the width of the main duct was narrowed, and the intensity ratio of the main duct lumen to background was significantly decreased after RT (p <.0001). According to the visual assessment, the width of the main duct tended to narrow and the contrast of the duct lumen tended to be decreased, but no significant differences were noted. The visibility of the duct branches was unclear in 10 patients (p = .039), and the septum became dense in 11 patients (p = .006) after RT. Conclusion: High-resolution magnetic resonance imaging is a noninvasive method of evaluating radiation-induced changes to the internal architecture of the parotid gland. Morphologic changes in the irradiated parotid gland were demonstrated during the RT course even when a relatively small dose was delivered to the gland.« less

Radiochromium (chromium-51) evaluation of gastrointestinal blood loss associated with placebo, aspirin, and nabumetone

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

Lussier, A.; LeBel, E.

Gastrointestinal blood loss is one of the most serious clinical events induced by drugs. To date, almost no nonsteroidal anti-inflammatory drug has been shown to be devoid of that side effect in a strictly controlled study. The objective of this study was to assess quantitatively, by use of radioactive chromium (chromium-51)-labeled red blood cells, gastrointestinal blood loss associated with nabumetone (1000 mg daily), aspirin (3.6 g daily), and placebo. A total of 37 normal subjects, divided among the three treatment groups and a fourth group that received no treatment, were assessed clinically and quantitatively for gastrointestinal blood loss over amore » period of 28 days of active treatment. The results with chromium-51, analyzed on a logarithmic scale, revealed no statistically significant differences between the nabumetone, placebo, and control groups. Gastrointestinal blood loss in the aspirin group, however, was elevated when compared with all other groups at a high level of statistical significance (p less than 0.001). It is concluded that, under conditions in which aspirin causes substantial gastrointestinal microbleeding, nabumetone is not significantly different from placebo.« less

Coatomer subunit beta 2 (COPB2), identified by label-free quantitative proteomics, regulates cell proliferation and apoptosis in human prostate carcinoma cells.

PubMed

Mi, Yuanyuan; Sun, Chuanyu; Wei, Bingbing; Sun, Feiyu; Guo, Yijun; Hu, Qingfeng; Ding, Weihong; Zhu, Lijie; Xia, Guowei

2018-01-01

Label-free quantitative proteomics has broad applications in the identification of differentially expressed proteins. Here, we applied this method to identify differentially expressed proteins (such as coatomer subunit beta 2 [COPB2]) and evaluated the functions and molecular mechanisms of these proteins in prostate cancer (PCA) cell proliferation. Proteins extracted from surgically resected PCA tissues and adjacent tissues of 3 patients were analyzed by label-free quantitative proteomics. The target protein was confirmed by bioinformatics and GEO dataset analyses. To investigate the role of the target protein in PCA, we used lentivirus-mediated small-interfering RNA (siRNA) to knockdown protein expression in the prostate carcinoma cell line, CWR22RV1 cells and assessed gene and protein expression by reverse transcription quantitative polymerase chain reaction and western blotting. CCK8 and colony formation assays were conducted to evaluate cell proliferation. Cell cycle distributions and apoptosis were assayed by flow cytometry. We selected the differentiation-related protein COPB2 as our target protein based on the results of label-free quantitative proteomics. High expression of COPB2 was found in PCA tissue and was related to poor overall survival based on a public dataset. Cell proliferation was significantly inhibited in COPB2-knockdown CWR22RV1 cells, as demonstrated by CCK8 and colony formation assays. Additionally, the apoptosis rate and percentage of cells in the G 1 phase were increased in COPB2-knockdown cells compared with those in control cells. CDK2, CDK4, and cyclin D1 were downregulated, whereas p21 Waf1/Cip1 and p27 Kip1 were upregulated, affecting the cell cycle signaling pathway. COPB2 significantly promoted CWR22RV1 cell proliferation through the cell cycle signaling pathway. Thus, silencing of COPB2 may have therapeutic applications in PCA. Copyright © 2017 Elsevier Inc. All rights reserved.

iTRAQ Quantitative Proteomic Comparison of Metastatic and Non-Metastatic Uveal Melanoma Tumors

PubMed Central

Crabb, John W.; Hu, Bo; Crabb, John S.; Triozzi, Pierre; Saunthararajah, Yogen; Singh, Arun D.

2015-01-01

Background Uveal melanoma is the most common malignancy of the adult eye. The overall mortality rate is high because this aggressive cancer often metastasizes before ophthalmic diagnosis. Quantitative proteomic analysis of primary metastasizing and non-metastasizing tumors was pursued for insights into mechanisms and biomarkers of uveal melanoma metastasis. Methods Eight metastatic and 7 non-metastatic human primary uveal melanoma tumors were analyzed by LC MS/MS iTRAQ technology with Bruch’s membrane/choroid complex from normal postmortem eyes as control tissue. Tryptic peptides from tumor and control proteins were labeled with iTRAQ tags, fractionated by cation exchange chromatography, and analyzed by LC MS/MS. Protein identification utilized the Mascot search engine and the human Uni-Prot/Swiss-Protein database with false discovery ≤ 1%; protein quantitation utilized the Mascot weighted average method. Proteins designated differentially expressed exhibited quantitative differences (p ≤ 0.05, t-test) in a training set of five metastatic and five non-metastatic tumors. Logistic regression models developed from the training set were used to classify the metastatic status of five independent tumors. Results Of 1644 proteins identified and quantified in 5 metastatic and 5 non-metastatic tumors, 12 proteins were found uniquely in ≥ 3 metastatic tumors, 28 were found significantly elevated and 30 significantly decreased only in metastatic tumors, and 31 were designated differentially expressed between metastatic and non-metastatic tumors. Logistic regression modeling of differentially expressed collagen alpha-3(VI) and heat shock protein beta-1 allowed correct prediction of metastasis status for each of five independent tumor specimens. Conclusions The present data provide new clues to molecular differences in metastatic and non-metastatic uveal melanoma tumors. While sample size is limited and validation required, the results support collagen alpha-3(VI) and heat shock protein beta-1 as candidate biomarkers of uveal melanoma metastasis and establish a quantitative proteomic database for uveal melanoma primary tumors. PMID:26305875

Quantitative imaging of protein targets in the human brain with PET

NASA Astrophysics Data System (ADS)

Gunn, Roger N.; Slifstein, Mark; Searle, Graham E.; Price, Julie C.

2015-11-01

PET imaging of proteins in the human brain with high affinity radiolabelled molecules has a history stretching back over 30 years. During this period the portfolio of protein targets that can be imaged has increased significantly through successes in radioligand discovery and development. This portfolio now spans six major categories of proteins; G-protein coupled receptors, membrane transporters, ligand gated ion channels, enzymes, misfolded proteins and tryptophan-rich sensory proteins. In parallel to these achievements in radiochemical sciences there have also been significant advances in the quantitative analysis and interpretation of the imaging data including the development of methods for image registration, image segmentation, tracer compartmental modeling, reference tissue kinetic analysis and partial volume correction. In this review, we analyze the activity of the field around each of the protein targets in order to give a perspective on the historical focus and the possible future trajectory of the field. The important neurobiology and pharmacology is introduced for each of the six protein classes and we present established radioligands for each that have successfully transitioned to quantitative imaging in humans. We present a standard quantitative analysis workflow for these radioligands which takes the dynamic PET data, associated blood and anatomical MRI data as the inputs to a series of image processing and bio-mathematical modeling steps before outputting the outcome measure of interest on either a regional or parametric image basis. The quantitative outcome measures are then used in a range of different imaging studies including tracer discovery and development studies, cross sectional studies, classification studies, intervention studies and longitudinal studies. Finally we consider some of the confounds, challenges and subtleties that arise in practice when trying to quantify and interpret PET neuroimaging data including motion artifacts, partial volume effects, age effects, image registration and normalization, input functions and metabolites, parametric imaging, receptor internalization and genetic factors.

A comparison study of image features between FFDM and film mammogram images

PubMed Central

Jing, Hao; Yang, Yongyi; Wernick, Miles N.; Yarusso, Laura M.; Nishikawa, Robert M.

2012-01-01

Purpose: This work is to provide a direct, quantitative comparison of image features measured by film and full-field digital mammography (FFDM). The purpose is to investigate whether there is any systematic difference between film and FFDM in terms of quantitative image features and their influence on the performance of a computer-aided diagnosis (CAD) system. Methods: The authors make use of a set of matched film-FFDM image pairs acquired from cadaver breast specimens with simulated microcalcifications consisting of bone and teeth fragments using both a GE digital mammography system and a screen-film system. To quantify the image features, the authors consider a set of 12 textural features of lesion regions and six image features of individual microcalcifications (MCs). The authors first conduct a direct comparison on these quantitative features extracted from film and FFDM images. The authors then study the performance of a CAD classifier for discriminating between MCs and false positives (FPs) when the classifier is trained on images of different types (film, FFDM, or both). Results: For all the features considered, the quantitative results show a high degree of correlation between features extracted from film and FFDM, with the correlation coefficients ranging from 0.7326 to 0.9602 for the different features. Based on a Fisher sign rank test, there was no significant difference observed between the features extracted from film and those from FFDM. For both MC detection and discrimination of FPs from MCs, FFDM had a slight but statistically significant advantage in performance; however, when the classifiers were trained on different types of images (acquired with FFDM or SFM) for discriminating MCs from FPs, there was little difference. Conclusions: The results indicate good agreement between film and FFDM in quantitative image features. While FFDM images provide better detection performance in MCs, FFDM and film images may be interchangeable for the purposes of training CAD algorithms, and a single CAD algorithm may be applied to either type of images. PMID:22830771

ICan: An Optimized Ion-Current-Based Quantification Procedure with Enhanced Quantitative Accuracy and Sensitivity in Biomarker Discovery

PubMed Central

2015-01-01

The rapidly expanding availability of high-resolution mass spectrometry has substantially enhanced the ion-current-based relative quantification techniques. Despite the increasing interest in ion-current-based methods, quantitative sensitivity, accuracy, and false discovery rate remain the major concerns; consequently, comprehensive evaluation and development in these regards are urgently needed. Here we describe an integrated, new procedure for data normalization and protein ratio estimation, termed ICan, for improved ion-current-based analysis of data generated by high-resolution mass spectrometry (MS). ICan achieved significantly better accuracy and precision, and lower false-positive rate for discovering altered proteins, over current popular pipelines. A spiked-in experiment was used to evaluate the performance of ICan to detect small changes. In this study E. coli extracts were spiked with moderate-abundance proteins from human plasma (MAP, enriched by IgY14-SuperMix procedure) at two different levels to set a small change of 1.5-fold. Forty-five (92%, with an average ratio of 1.71 ± 0.13) of 49 identified MAP protein (i.e., the true positives) and none of the reference proteins (1.0-fold) were determined as significantly altered proteins, with cutoff thresholds of ≥1.3-fold change and p ≤ 0.05. This is the first study to evaluate and prove competitive performance of the ion-current-based approach for assigning significance to proteins with small changes. By comparison, other methods showed remarkably inferior performance. ICan can be broadly applicable to reliable and sensitive proteomic survey of multiple biological samples with the use of high-resolution MS. Moreover, many key features evaluated and optimized here such as normalization, protein ratio determination, and statistical analyses are also valuable for data analysis by isotope-labeling methods. PMID:25285707

4D MEMRI atlas of neonatal FVB/N mouse brain development.

PubMed

Szulc, Kamila U; Lerch, Jason P; Nieman, Brian J; Bartelle, Benjamin B; Friedel, Miriam; Suero-Abreu, Giselle A; Watson, Charles; Joyner, Alexandra L; Turnbull, Daniel H

2015-09-01

The widespread use of the mouse as a model system to study brain development has created the need for noninvasive neuroimaging methods that can be applied to early postnatal mice. The goal of this study was to optimize in vivo three- (3D) and four-dimensional (4D) manganese (Mn)-enhanced MRI (MEMRI) approaches for acquiring and analyzing data from the developing mouse brain. The combination of custom, stage-dependent holders and self-gated (motion-correcting) 3D MRI sequences enabled the acquisition of high-resolution (100-μm isotropic), motion artifact-free brain images with a high level of contrast due to Mn-enhancement of numerous brain regions and nuclei. We acquired high-quality longitudinal brain images from two groups of FVB/N strain mice, six mice per group, each mouse imaged on alternate odd or even days (6 3D MEMRI images at each day) covering the developmental stages between postnatal days 1 to 11. The effects of Mn-exposure, anesthesia and MRI were assessed, showing small but significant transient effects on body weight and brain volume, which recovered with time and did not result in significant morphological differences when compared to controls. Metrics derived from deformation-based morphometry (DBM) were used for quantitative analysis of changes in volume and position of a number of brain regions. The cerebellum, a brain region undergoing significant changes in size and patterning at early postnatal stages, was analyzed in detail to demonstrate the spatiotemporal characterization made possible by this new atlas of mouse brain development. These results show that MEMRI is a powerful tool for quantitative analysis of mouse brain development, with great potential for in vivo phenotype analysis in mouse models of neurodevelopmental diseases. Copyright © 2015 Elsevier Inc. All rights reserved.

High-Resolution C-Arm CT and Metal Artifact Reduction Software: A Novel Imaging Modality for Analyzing Aneurysms Treated with Stent-Assisted Coil Embolization.

PubMed

Yuki, I; Kambayashi, Y; Ikemura, A; Abe, Y; Kan, I; Mohamed, A; Dahmani, C; Suzuki, T; Ishibashi, T; Takao, H; Urashima, M; Murayama, Y

2016-02-01

Combination of high-resolution C-arm CT and novel metal artifact reduction software may contribute to the assessment of aneurysms treated with stent-assisted coil embolization. This study aimed to evaluate the efficacy of a novel Metal Artifact Reduction prototype software combined with the currently available high spatial-resolution C-arm CT prototype implementation by using an experimental aneurysm model treated with stent-assisted coil embolization. Eight experimental aneurysms were created in 6 swine. Coil embolization of each aneurysm was performed by using a stent-assisted technique. High-resolution C-arm CT with intra-arterial contrast injection was performed immediately after the treatment. The obtained images were processed with Metal Artifact Reduction. Five neurointerventional specialists reviewed the image quality before and after Metal Artifact Reduction. Observational and quantitative analyses (via image analysis software) were performed. Every aneurysm was successfully created and treated with stent-assisted coil embolization. Before Metal Artifact Reduction, coil loops protruding through the stent lumen were not visualized due to the prominent metal artifacts produced by the coils. These became visible after Metal Artifact Reduction processing. Contrast filling in the residual aneurysm was also visualized after Metal Artifact Reduction in every aneurysm. Both the observational (P < .0001) and quantitative (P < .001) analyses showed significant reduction of the metal artifacts after application of the Metal Artifact Reduction prototype software. The combination of high-resolution C-arm CT and Metal Artifact Reduction enables differentiation of the coil mass, stent, and contrast material on the same image by significantly reducing the metal artifacts produced by the platinum coils. This novel image technique may improve the assessment of aneurysms treated with stent-assisted coil embolization. © 2016 by American Journal of Neuroradiology.

Analysis of phytochemical variations in dioecious Tinospora cordifolia stems using HPLC/QTOF MS/MS and UPLC/QqQLIT -MS/MS.

PubMed

Bajpai, Vikas; Singh, Awantika; Chandra, Preeti; Negi, M P S; Kumar, Nikhil; Kumar, Brijesh

2016-01-01

The stem of dioecious Tinospora cordifolia (Menispermaceae) is a commonly used traditional Ayurvedic medicine in India having several therapeutic properties. To develop and validate LC-MS methods for the identification and simultaneous quantitation of various secondary metabolites and to study metabolomic variations in the stem of male and female plants. Ethanolic extract of stems were analysed by HPLC/ESI-QTOF-MS/MS for rapid screening of bioactive phytochemicals. High resolution MS and MS/MS in positive ESI mode were used for structural investigation of secondary metabolites. An UPLC/ESI-QqQ(LIT) -MS/MS method in MRM mode was developed and validated for the simultaneous quantitation of five bioactive alkaloids. Identification and characterisation of 36 metabolites including alkaloids, sesquiterpenes and phytoecdysteroids were performed using LC-MS and MS/MS techniques. The bioactive alkaloids such as jatrorrhizine, magnoflorine, isocorydine, palmatine and tetrahydropalmatine were successfully quantified in male and female plants. The mean abundances of magnoflorine jatrorrhizine, and oblongine were significantly (P < 0.05) higher in male plants while mean abundances of tetrahydropalmatine, norcoclaurine, and reticuline were significantly (P < 0.05) higher in female plants. Phytochemicals in the stem of male and female Tinospora cordifolia showed significant qualitative and quantitative variations. LC-MS and MS/MS methods can be used to differentiate between male and female plants based on their chemical profiles and quantities of the marker bioactive alkaloids. This chemical composition difference was also evident during vegetative stage when there were no male and female flowers. Copyright © 2015 John Wiley & Sons, Ltd.

Acoustic radiation force impulse (ARFI) elastography for detection of renal damage in children.

PubMed

Göya, Cemil; Hamidi, Cihad; Ece, Aydın; Okur, Mehmet Hanifi; Taşdemir, Bekir; Çetinçakmak, Mehmet Güli; Hattapoğlu, Salih; Teke, Memik; Şahin, Cahit

2015-01-01

Acoustic radiation force impulse (ARFI) imaging is a promising method for noninvasive evaluation of the renal parenchyma. To investigate the contribution of ARFI quantitative US elastography for the detection of renal damage in kidneys with and without vesicoureteral reflux (VUR). One hundred seventy-six kidneys of 88 children (46 male, 42 female) who had been referred for voiding cystourethrography and 20 healthy controls were prospectively investigated. Patients were assessed according to severity of renal damage on dimercaptosuccinic acid (DMSA) scintigraphy. Ninety-eight age- and gender-matched healthy children constituted the control group. Quantitative shear wave velocity (SWV) measurements were performed in the upper and lower poles and in the interpolar region of each kidney. DMSA scintigraphy was performed in 62 children (124 kidneys). Comparisons of SWV values of kidneys with and without renal damage and/or VUR were done. Significantly higher SWV values were found in non-damaged kidneys. Severely damaged kidneys had the lowest SWV values (P < 0.001). High-grade (grade V-IV) refluxing kidneys had the lowest SWV values, while non-refluxing kidneys had the highest values (P < 0.05). Significant negative correlations were found between the mean quantitative US elastography values and DMSA scarring score (r = -0.788, P < 0.001) and VUR grade (r = -0.634, P < 0.001). SWV values of the control kidneys were significantly higher than those of damaged kidneys (P < 0.05). Our findings suggest decreasing SWV of renal units with increasing grades of vesicoureteric reflux, increasing DMSA-assessed renal damage and decreasing DMSA-assessed differential function.

Identifying symptoms of ovarian cancer: a qualitative and quantitative study.

PubMed

Bankhead, C R; Collins, C; Stokes-Lampard, H; Rose, P; Wilson, S; Clements, A; Mant, D; Kehoe, S T; Austoker, J

2008-07-01

Symptoms of ovarian cancer are often vague and consequently a high proportion of women with ovarian cancer are not referred to the appropriate clinic. To identify diagnostic factors for ovarian cancer. A qualitative and quantitative study. Four UK hospitals. One hundred and twenty-four women referred to hospital with suspected ovarian malignancy. Women were interviewed prior to diagnosis (n = 63), or soon after. A thematic analysis was conducted. Emergent symptoms were quantitatively analysed to identify distinguishing features of ovarian cancer. Symptoms in women with and without ovarian cancer. Diagnoses comprised 44 malignancies, 59 benign gynaecological pathologies and 21 normal findings. Of the malignancies, 25 women had stage III or more disease, with an average age of 59 years. The benign/normal cohort was significantly younger (48 years). Multivariate analysis revealed persistent abdominal distension (OR 5.2, 95% CI 1.3-20.5), postmenopausal bleeding (OR 9.2, 95% CI 1.1-76.1), appetite loss (OR 3.2, 95% CI 1.1-9.2), early satiety (OR 5.0, 95% CI 1.6-15.7) and progressive symptoms (OR 3.6, 95% CI 1.3-9.8) as independent, statistically significant variables associated with ovarian cancer. Fluctuating distension was not associated with ovarian cancer (OR 0.4, 95% CI 0-4.1). Women frequently used the term bloating, but this represented two distinct events: persistent abdominal distension and fluctuating distension/discomfort. Ovarian cancer is not a silent killer. Clinicians should distinguish between persistent and fluctuating distension. Recognition of the significance of symptoms described by women could lead to earlier and more appropriate referral.

Noninvasive Dry Eye Assessment Using High-Technology Ophthalmic Examination Devices.

PubMed

Yamaguchi, Masahiko; Sakane, Yuri; Kamao, Tomoyuki; Zheng, Xiaodong; Goto, Tomoko; Shiraishi, Atsushi; Ohashi, Yuichi

2016-11-01

Recently, the number of dry eye cases has dramatically increased. Thus, it is important that easy screening, exact diagnoses, and suitable treatments be available. We developed 3 original and noninvasive assessments for this disorder. First, a DR-1 dry eye monitor was used to determine the tear meniscus height quantitatively by capturing a tear meniscus digital image that was analyzed by Meniscus Processor software. The DR-1 meniscus height value significantly correlated with the fluorescein meniscus height (r = 0.06, Bland-Altman analysis). At a cutoff value of 0.22 mm, sensitivity of the dry eye diagnosis was 84.1% with 90.9% specificity. Second, the Tear Stability Analysis System was used to quantitatively measure tear film stability using a topographic modeling system corneal shape analysis device. Tear film stability was objectively and quantitatively evaluated every second during sustained eye openings. The Tear Stability Analysis System is currently installed in an RT-7000 autorefractometer and topographer to automate the diagnosis of dry eye. Third, the Ocular Surface Thermographer uses ophthalmic thermography for diagnosis. The decrease in ocular surface temperature in dry eyes was significantly greater than that in normal eyes (P < 0.001) at 10 seconds after eye opening. Decreased corneal temperature correlated significantly with the tear film breakup time (r = 0.572; P < 0.001). When changes in the ocular surface temperature of the cornea were used as indicators for dry eye, sensitivity was 0.83 and specificity was 0.80 after 10 seconds. This article describes the details and potential of these 3 noninvasive dry eye assessment systems.

A Second-Generation Device for Automated Training and Quantitative Behavior Analyses of Molecularly-Tractable Model Organisms

PubMed Central

Blackiston, Douglas; Shomrat, Tal; Nicolas, Cindy L.; Granata, Christopher; Levin, Michael

2010-01-01

A deep understanding of cognitive processes requires functional, quantitative analyses of the steps leading from genetics and the development of nervous system structure to behavior. Molecularly-tractable model systems such as Xenopus laevis and planaria offer an unprecedented opportunity to dissect the mechanisms determining the complex structure of the brain and CNS. A standardized platform that facilitated quantitative analysis of behavior would make a significant impact on evolutionary ethology, neuropharmacology, and cognitive science. While some animal tracking systems exist, the available systems do not allow automated training (feedback to individual subjects in real time, which is necessary for operant conditioning assays). The lack of standardization in the field, and the numerous technical challenges that face the development of a versatile system with the necessary capabilities, comprise a significant barrier keeping molecular developmental biology labs from integrating behavior analysis endpoints into their pharmacological and genetic perturbations. Here we report the development of a second-generation system that is a highly flexible, powerful machine vision and environmental control platform. In order to enable multidisciplinary studies aimed at understanding the roles of genes in brain function and behavior, and aid other laboratories that do not have the facilities to undergo complex engineering development, we describe the device and the problems that it overcomes. We also present sample data using frog tadpoles and flatworms to illustrate its use. Having solved significant engineering challenges in its construction, the resulting design is a relatively inexpensive instrument of wide relevance for several fields, and will accelerate interdisciplinary discovery in pharmacology, neurobiology, regenerative medicine, and cognitive science. PMID:21179424

Determination of Mycotoxin Production of Fusarium Species in Genetically Modified Maize Varieties by Quantitative Flow Immunocytometry.

PubMed

Bánáti, Hajnalka; Darvas, Béla; Fehér-Tóth, Szilvia; Czéh, Árpád; Székács, András

2017-02-22

Levels of mycotoxins produced by Fusarium species in genetically modified (GM) and near-isogenic maize, were determined using multi-analyte, microbead-based flow immunocytometry with fluorescence detection, for the parallel quantitative determination of fumonisin B1, deoxynivalenol, zearalenone, T-2, ochratoxin A, and aflatoxin B1. Maize varieties included the genetic events MON 810 and DAS-59122-7 , and their isogenic counterparts. Cobs were artificially infested by F. verticillioides and F. proliferatum conidia, and contained F. graminearum and F. sporotrichoides natural infestation. The production of fumonisin B1 and deoxynivalenol was substantially affected in GM maize lines: F. verticillioides , with the addition of F. graminearum and F. sporotrichoides , produced significantly lower levels of fumonisin B1 (~300 mg·kg -1 ) in DAS-59122-7 than in its isogenic line (~580 mg·kg -1 ), while F. proliferatum , in addition to F. graminearum and F. sporotrichoides , produced significantly higher levels of deoxynivalenol (~18 mg·kg -1 ) in MON 810 than in its isogenic line (~5 mg·kg -1 ). Fusarium verticillioides , with F. graminearum and F. sporotrichoides , produced lower amounts of deoxynivalenol and zearalenone than F. proliferatum , with F. graminearum and F. sporotrichoides . T-2 toxin production remained unchanged when considering the maize variety. The results demonstrate the utility of the Fungi-Plex™ quantitative flow immunocytometry method, applied for the high throughput parallel determination of the target mycotoxins.

Thermal Nondestructive Characterization of Corrosion in Boiler Tubes by Application fo a Moving Line Heat Source

NASA Technical Reports Server (NTRS)

Cramer, K. Elliott; Winfree, William P.

2000-01-01

Wall thinning in utility boiler waterwall tubing is a significant inspection concern for boiler operators. Historically, conventional ultrasonics has been used lor inspection of these tubes. This technique has proved to be very labor intensive and slow. This has resulted in a "spot check" approach to inspections, making thickness measurements over a relatively small percentage of the total boiler wall area. NASA Langley Research Center has developed a thermal NDE technique designed to image and quantitatively characterize the amount of material thinning present in steel tubing. The technique involves the movement of a thermal line source across the outer surface of the tubing followed by an infrared imager at a fixed distance behind the line source. Quantitative images of the material loss due to corrosion are reconstructed from measurements of the induced surface temperature variations. This paper will present a discussion of the development of the thermal imaging system as well as the techniques used to reconstruct images of flaws. The application of the thermal line source, coupled with this analysis technique, represents a significant improvement in the inspection speed for large structures such as boiler waterwalls while still providing high-resolution thickness measurements. A theoretical basis for the technique will be presented thus demonstrating the quantitative nature of the technique. Further, results of laboratory experiments on flat Panel specimens with fabricated material loss regions will be presented.

Development of a quantitative PCR assay for monitoring Streptococcus agalactiae colonization and tissue tropism in experimentally infected tilapia.

PubMed

Su, Y-L; Feng, J; Li, Y-W; Bai, J-S; Li, A-X

2016-02-01

Streptococcus agalactiae has become one of the most important emerging pathogens in the aquaculture industry and has resulted in large economic losses for tilapia farms in China. In this study, three pairs of specific primers were designed and tested for their specificities and sensitivities in quantitative real-time polymerase chain reactions (qPCRs) after optimization of the annealing temperature. The primer pair IGS-s/IGS-a, which targets the 16S-23S rRNA intergenic spacer region, was finally chosen, having a detection limit of 8.6 copies of S. agalactiae DNA in a 20 μL reaction mixture. Bacterial tissue tropism was demonstrated by qPCR in Oreochromis niloticus 5 days post-injection with a virulent S. agalactiae strain. Bacterial loads were detected at the highest level in brain, followed by moderately high levels in kidney, heart, spleen, intestines, and eye. Significantly lower bacterial loads were observed in muscle, gill and liver. In addition, significantly lower bacterial loads were observed in the brain of convalescent O. niloticus 14 days post-injection with several different S. agalactiae strains. The qPCR for the detection of S. agalactiae developed in this study provides a quantitative tool for investigating bacterial tissue tropism in infected fish, as well as for monitoring bacterial colonization in convalescent fish. © 2015 John Wiley & Sons Ltd.

Estimation of genetic parameters and detection of quantitative trait loci for metabolites in Danish Holstein milk.

PubMed

Buitenhuis, A J; Sundekilde, U K; Poulsen, N A; Bertram, H C; Larsen, L B; Sørensen, P

2013-05-01

Small components and metabolites in milk are significant for the utilization of milk, not only in dairy food production but also as disease predictors in dairy cattle. This study focused on estimation of genetic parameters and detection of quantitative trait loci for metabolites in bovine milk. For this purpose, milk samples were collected in mid lactation from 371 Danish Holstein cows in first to third parity. A total of 31 metabolites were detected and identified in bovine milk by using (1)H nuclear magnetic resonance (NMR) spectroscopy. Cows were genotyped using a bovine high-density single nucleotide polymorphism (SNP) chip. Based on the SNP data, a genomic relationship matrix was calculated and used as a random factor in a model together with 2 fixed factors (herd and lactation stage) to estimate the heritability and breeding value for individual metabolites in the milk. Heritability was in the range of 0 for lactic acid to >0.8 for orotic acid and β-hydroxybutyrate. A single SNP association analysis revealed 7 genome-wide significant quantitative trait loci [malonate: Bos taurus autosome (BTA)2 and BTA7; galactose-1-phosphate: BTA2; cis-aconitate: BTA11; urea: BTA12; carnitine: BTA25; and glycerophosphocholine: BTA25]. These results demonstrate that selection for metabolites in bovine milk may be possible. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Alloplastic total temporomandibular joint replacements: do they perform like natural joints? Prospective cohort study with a historical control.

PubMed

Wojczyńska, A; Leiggener, C S; Bredell, M; Ettlin, D A; Erni, S; Gallo, L M; Colombo, V

2016-10-01

The aim of this study was to qualitatively and quantitatively describe the biomechanics of existing total alloplastic reconstructions of temporomandibular joints (TMJ). Fifteen patients with unilateral or bilateral TMJ total joint replacements and 15 healthy controls were evaluated via dynamic stereometry technology. This non-invasive method combines three-dimensional imaging of the subject's anatomy with jaw tracking. It provides an insight into the patient's jaw joint movements in real time and provides a quantitative evaluation. The patients were also evaluated clinically for jaw opening, protrusive and laterotrusive movements, pain, interference with eating, and satisfaction with the joint replacements. The qualitative assessment revealed that condyles of bilateral total joint replacements displayed similar basic motion patterns to those of unilateral prostheses. Quantitatively, mandibular movements of artificial joints during opening, protrusion, and laterotrusion were all significantly shorter than those of controls. A significantly restricted mandibular range of motion in replaced joints was also observed clinically. Fifty-three percent of patients suffered from chronic pain at rest and 67% reported reduced chewing function. Nonetheless, patients declared a high level of satisfaction with the replacement. This study shows that in order to gain a comprehensive understanding of complex therapeutic measures, a multidisciplinary approach is needed. Copyright © 2016 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

A quantitative study on the mass elevation effect of the Rocky Mountains and its significance for treeline distribution

NASA Astrophysics Data System (ADS)

WANG, J.; Zhang, B.

2016-12-01

The Rocky Mountains are the highest and most extensive of all in the North America. To quantify mass elevation effect (MEE) of the Rocky Mountains, we applied meteorological station records, NCAR/NCEP free air temperature and DEM data to calculate temperature difference (ΔT) between the inner and outer Rocky Mountains, defined as the magnitude of MEE. Results show that the mean ΔT for all adopted stations was 1.8 °, with high ΔT occurring in the Southern Rocky Mountains in the Colorado State and in the basins of Southern Wyoming. The MEE of the Rocky Mountains can be modeled with three factors of mountain base elevation (MBE), latitude and hygric continentality as independent variables. The model has a high explanatory power of 68.9%, and the three factors contribute 45.65%, 36.05% and 18.03%, respectively. Especially, MBE contributed the most to MEE of both the whole and the Southern Rocky Mountains, i.e., 45.65%, and 55.21%, respectively. Moreover, we investigated the significance of MEE for treeline distribution. The treeline is always higher in the inner than in the outer mountains, with a difference of 600 m to 1300 m. This difference corresponds well to air temperature difference between the inner and outer mountain ranges. This study developed a quantitative model for the MEE of the Rocky Mountains and improves our understanding of the intra-mountain ecology and especially the high treelines in the Rocky Mountains.

Process evaluation of the Data-driven Quality Improvement in Primary Care (DQIP) trial: quantitative examination of variation between practices in recruitment, implementation and effectiveness.

PubMed

Dreischulte, Tobias; Grant, Aileen; Hapca, Adrian; Guthrie, Bruce

2018-01-05

The cluster randomised trial of the Data-driven Quality Improvement in Primary Care (DQIP) intervention showed that education, informatics and financial incentives for general medical practices to review patients with ongoing high-risk prescribing of non-steroidal anti-inflammatory drugs and antiplatelets reduced the primary end point of high-risk prescribing by 37%, where both ongoing and new high-risk prescribing were significantly reduced. This quantitative process evaluation examined practice factors associated with (1) participation in the DQIP trial, (2) review activity (extent and nature of documented reviews) and (3) practice level effectiveness (relative reductions in the primary end point). Invited practices recruited (n=33) and not recruited (n=32) to the DQIP trial in Scotland, UK. (1) Characteristics of recruited versus non-recruited practices. Associations of (2) practice characteristics and 'adoption' (self-reported implementation work done by practices) with documented review activity and (3) of practice characteristics, DQIP adoption and review activity with effectiveness. (1) Recruited practices had lower performance in the quality and outcomes framework than those declining participation. (2) Not being an approved general practitioner training practice and higher self-reported adoption were significantly associated with higher review activity. (3) Effectiveness ranged from a relative increase in high-risk prescribing of 24.1% to a relative reduction of 77.2%. High-risk prescribing and DQIP adoption (but not documented review activity) were significantly associated with greater effectiveness in the final multivariate model, explaining 64.0% of variation in effectiveness. Intervention implementation and effectiveness of the DQIP intervention varied substantially between practices. Although the DQIP intervention primarily targeted review of ongoing high-risk prescribing, the finding that self-reported DQIP adoption was a stronger predictor of effectiveness than documented review activity supports that reducing initiation and/or re-initiation of high-risk prescribing is key to its effectiveness. NCT01425502; Post-results. © 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.

Comparison of semi-quantitative and quantitative dynamic contrast-enhanced MRI evaluations of vertebral marrow perfusion in a rat osteoporosis model.

PubMed

Zhu, Jingqi; Xiong, Zuogang; Zhang, Jiulong; Qiu, Yuyou; Hua, Ting; Tang, Guangyu

2017-11-14

This study aims to investigate the technical feasibility of semi-quantitative and quantitative dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in the assessment of longitudinal changes of marrow perfusion in a rat osteoporosis model, using bone mineral density (BMD) measured by micro-computed tomography (micro-CT) and histopathology as the gold standards. Fifty rats were randomly assigned to the control group (n=25) and ovariectomy (OVX) group whose bilateral ovaries were excised (n=25). Semi-quantitative and quantitative DCE-MRI, micro-CT, and histopathological examinations were performed on lumbar vertebrae at baseline and 3, 6, 9, and 12 weeks after operation. The differences between the two groups in terms of semi-quantitative DCE-MRI parameter (maximum enhancement, E max ), quantitative DCE-MRI parameters (volume transfer constant, K trans ; interstitial volume, V e ; and efflux rate constant, K ep ), micro-CT parameter (BMD), and histopathological parameter (microvessel density, MVD) were compared at each of the time points using an independent-sample t test. The differences in these parameters between baseline and other time points in each group were assessed via Bonferroni's multiple comparison test. A Pearson correlation analysis was applied to assess the relationships between DCE-MRI, micro-CT, and histopathological parameters. In the OVX group, the E max values decreased significantly compared with those of the control group at weeks 6 and 9 (p=0.003 and 0.004, respectively). The K trans values decreased significantly compared with those of the control group from week 3 (p<0.05). However, the V e values decreased significantly only at week 9 (p=0.032), and no difference in the K ep was found between two groups. The BMD values of the OVX group decreased significantly compared with those of the control group from week 3 (p<0.05). Transmission electron microscopy showed tighter gaps between vascular endothelial cells with swollen mitochondria in the OVX group from week 3. The MVD values of the OVX group decreased significantly compared with those of the control group only at week 12 (p=0.023). A weak positive correlation of E max and a strong positive correlation of K trans with MVD were found. Compared with semi-quantitative DCE-MRI, the quantitative DCE-MRI parameter K trans is a more sensitive and accurate index for detecting early reduced perfusion in osteoporotic bone.

Quantitative analysis of naphthenic acids in water by liquid chromatography-accurate mass time-of-flight mass spectrometry.

PubMed

Hindle, Ralph; Noestheden, Matthew; Peru, Kerry; Headley, John

2013-04-19

This study details the development of a routine method for quantitative analysis of oil sands naphthenic acids, which are a complex class of compounds found naturally and as contaminants in oil sands process waters from Alberta's Athabasca region. Expanding beyond classical naphthenic acids (CnH2n-zO2), those compounds conforming to the formula CnH2n-zOx (where 2≥x≤4) were examined in commercial naphthenic acid and environmental water samples. HPLC facilitated a five-fold reduction in ion suppression when compared to the more commonly used flow injection analysis. A comparison of 39 model naphthenic acids revealed significant variability in response factors, demonstrating the necessity of using naphthenic acid mixtures for quantitation, rather than model compounds. It was also demonstrated that naphthenic acidic heterogeneity (commercial and environmental) necessitates establishing a single NA mix as the standard against which all quantitation is performed. The authors present the first ISO17025 accredited method for the analysis of naphthenic acids in water using HPLC high resolution accurate mass time-of-flight mass spectrometry. The method detection limit was 1mg/L total oxy-naphthenic acids (Sigma technical mix). Copyright © 2013 Elsevier B.V. All rights reserved.

Three-dimensional modeling and quantitative analysis of gap junction distributions in cardiac tissue.

PubMed

Lackey, Daniel P; Carruth, Eric D; Lasher, Richard A; Boenisch, Jan; Sachse, Frank B; Hitchcock, Robert W

2011-11-01

Gap junctions play a fundamental role in intercellular communication in cardiac tissue. Various types of heart disease including hypertrophy and ischemia are associated with alterations of the spatial arrangement of gap junctions. Previous studies applied two-dimensional optical and electron-microscopy to visualize gap junction arrangements. In normal cardiomyocytes, gap junctions were primarily found at cell ends, but can be found also in more central regions. In this study, we extended these approaches toward three-dimensional reconstruction of gap junction distributions based on high-resolution scanning confocal microscopy and image processing. We developed methods for quantitative characterization of gap junction distributions based on analysis of intensity profiles along the principal axes of myocytes. The analyses characterized gap junction polarization at cell ends and higher-order statistical image moments of intensity profiles. The methodology was tested in rat ventricular myocardium. Our analysis yielded novel quantitative data on gap junction distributions. In particular, the analysis demonstrated that the distributions exhibit significant variability with respect to polarization, skewness, and kurtosis. We suggest that this methodology provides a quantitative alternative to current approaches based on visual inspection, with applications in particular in characterization of engineered and diseased myocardium. Furthermore, we propose that these data provide improved input for computational modeling of cardiac conduction.

Experimental Assessment and Enhancement of Planar Laser-Induced Fluorescence Measurements of Nitric Oxide in an Inverse Diffusion Flame

NASA Technical Reports Server (NTRS)

Partridge, William P.; Laurendeau, Normand M.

1997-01-01

We have experimentally assessed the quantitative nature of planar laser-induced fluorescence (PLIF) measurements of NO concentration in a unique atmospheric pressure, laminar, axial inverse diffusion flame (IDF). The PLIF measurements were assessed relative to a two-dimensional array of separate laser saturated fluorescence (LSF) measurements. We demonstrated and evaluated several experimentally-based procedures for enhancing the quantitative nature of PLIF concentration images. Because these experimentally-based PLIF correction schemes require only the ability to make PLIF and LSF measurements, they produce a more broadly applicable PLIF diagnostic compared to numerically-based correction schemes. We experimentally assessed the influence of interferences on both narrow-band and broad-band fluorescence measurements at atmospheric and high pressures. Optimum excitation and detection schemes were determined for the LSF and PLIF measurements. Single-input and multiple-input, experimentally-based PLIF enhancement procedures were developed for application in test environments with both negligible and significant quench-dependent error gradients. Each experimentally-based procedure provides an enhancement of approximately 50% in the quantitative nature of the PLIF measurements, and results in concentration images nominally as quantitative as LSF point measurements. These correction procedures can be applied to other species, including radicals, for which no experimental data are available from which to implement numerically-based PLIF enhancement procedures.

An integrative strategy for quantitative analysis of the N-glycoproteome in complex biological samples.

PubMed

Wang, Ji; Zhou, Chuang; Zhang, Wei; Yao, Jun; Lu, Haojie; Dong, Qiongzhu; Zhou, Haijun; Qin, Lunxiu

2014-01-15

The complexity of protein glycosylation makes it difficult to characterize glycosylation patterns on a proteomic scale. In this study, we developed an integrated strategy for comparatively analyzing N-glycosylation/glycoproteins quantitatively from complex biological samples in a high-throughput manner. This strategy entailed separating and enriching glycopeptides/glycoproteins using lectin affinity chromatography, and then tandem labeling them with 18O/16O to generate a mass shift of 6 Da between the paired glycopeptides, and finally analyzing them with liquid chromatography-mass spectrometry (LC-MS) and the automatic quantitative method we developed based on Mascot Distiller. The accuracy and repeatability of this strategy were first verified using standard glycoproteins; linearity was maintained within a range of 1:10-10:1. The peptide concentration ratios obtained by the self-build quantitative method were similar to both the manually calculated and theoretical values, with a standard deviation (SD) of 0.023-0.186 for glycopeptides. The feasibility of the strategy was further confirmed with serum from hepatocellular carcinoma (HCC) patients and healthy individuals; the expression of 44 glycopeptides and 30 glycoproteins were significantly different between HCC patient and control serum. This strategy is accurate, repeatable, and efficient, and may be a useful tool for identification of disease-related N-glycosylation/glycoprotein changes.

The other half of the story: effect size analysis in quantitative research.

PubMed

Maher, Jessica Middlemis; Markey, Jonathan C; Ebert-May, Diane

2013-01-01

Statistical significance testing is the cornerstone of quantitative research, but studies that fail to report measures of effect size are potentially missing a robust part of the analysis. We provide a rationale for why effect size measures should be included in quantitative discipline-based education research. Examples from both biological and educational research demonstrate the utility of effect size for evaluating practical significance. We also provide details about some effect size indices that are paired with common statistical significance tests used in educational research and offer general suggestions for interpreting effect size measures. Finally, we discuss some inherent limitations of effect size measures and provide further recommendations about reporting confidence intervals.

Ptychography: use of quantitative phase information for high-contrast label free time-lapse imaging of living cells

NASA Astrophysics Data System (ADS)

Suman, Rakesh; O'Toole, Peter

2014-03-01

Here we report a novel label free, high contrast and quantitative method for imaging live cells. The technique reconstructs an image from overlapping diffraction patterns using a ptychographical algorithm. The algorithm utilises both amplitude and phase data from the sample to report on quantitative changes related to the refractive index (RI) and thickness of the specimen. We report the ability of this technique to generate high contrast images, to visualise neurite elongation in neuronal cells, and to provide measure of cell proliferation.

A NOVEL TECHNIQUE FOR QUANTITATIVE ESTIMATION OF UPTAKE OF DIESEL EXHAUST PARTICLES BY LUNG CELLS

EPA Science Inventory

While airborne particulates like diesel exhaust particulates (DEP) exert significant toxicological effects on lungs, quantitative estimation of accumulation of DEP inside lung cells has not been reported due to a lack of an accurate and quantitative technique for this purpose. I...

The relationship between quantitative measures of disc height and disc signal intensity with Pfirrmann score of disc degeneration.

PubMed

Salamat, Sara; Hutchings, John; Kwong, Clemens; Magnussen, John; Hancock, Mark J

2016-01-01

To assess the relationship between quantitative measures of disc height and signal intensity with the Pfirrmann disc degeneration scoring system and to test the inter-rater reliability of the quantitative measures. Participants were 76 people who had recently recovered from their last episode of acute low back pain and underwent MRI scan on a single 3T machine. At all 380 lumbar discs, quantitative measures of disc height and signal intensity were made by 2 independent raters and compared to Pfirrmann scores from a single radiologist. For quantitative measures of disc height and signal intensity a "raw" score and 2 adjusted ratios were calculated and the relationship with Pfirrmann scores was assessed. The inter-tester reliability of quantitative measures was also investigated. There was a strong linear relationship between quantitative disc signal intensity and Pfirrmann scores for grades 1-4, but not for grades 4 and 5. For disc height only, Pfirrmann grade 5 had significantly reduced disc height compared to all other grades. Results were similar regardless of whether raw or adjusted scores were used. Inter-rater reliability for the quantitative measures was excellent (ICC > 0.97). Quantitative measures of disc signal intensity were strongly related to Pfirrmann scores from grade 1 to 4; however disc height only differentiated between grade 4 and 5 Pfirrmann scores. Using adjusted ratios for quantitative measures of disc height or signal intensity did not significantly alter the relationship with Pfirrmann scores.

Proposal for a quantitative index of flood disasters.

PubMed

Feng, Lihua; Luo, Gaoyuan

2010-07-01

Drawing on calculations of wind scale and earthquake magnitude, this paper develops a new quantitative method for measuring flood magnitude and disaster intensity. Flood magnitude is the quantitative index that describes the scale of a flood; the flood's disaster intensity is the quantitative index describing the losses caused. Both indices have numerous theoretical and practical advantages with definable concepts and simple applications, which lend them key practical significance.

Quantitation of Fine Displacement in Echography

NASA Astrophysics Data System (ADS)

Masuda, Kohji; Ishihara, Ken; Yoshii, Ken; Furukawa, Toshiyuki; Kumagai, Sadatoshi; Maeda, Hajime; Kodama, Shinzo

1993-05-01

A High-speed Digital Subtraction Echography was developed to visualize the fine displacement of human internal organs. This method indicates differences in position through time series images of high-frame-rate echography. Fine displacement less than ultrasonic wavelength can be observed. This method, however, lacks the ability to quantitatively measure displacement length. The subtraction between two successive images was affected by displacement direction in spite of the displacement length being the same. To solve this problem, convolution of an echogram with Gaussian distribution was used. To express displacement length as brightness quantitatively, normalization using a brightness gradient was applied. The quantitation algorithm was applied to successive B-mode images. Compared to the simply subtracted images, quantitated images express more precisely the motion of organs. Expansion of the carotid artery and fine motion of ventricular walls can be visualized more easily. Displacement length can be quantitated with wavelength. Under more static conditions, this system quantitates displacement length that is much less than wavelength.

Resilience, rapid transitions and regime shifts: fingerprinting the responses of Lake Żabińskie (NE Poland) to climate variability and human disturbance since 1000 AD

NASA Astrophysics Data System (ADS)

Tylmann, Wojciech; Hernández-Almeida, Iván; Grosjean, Martin; José Gómez Navarro, Juan; Larocque-Tobler, Isabelle; Bonk, Alicja; Enters, Dirk; Ustrzycka, Alicja; Piotrowska, Natalia; Przybylak, Rajmund; Wacnik, Agnieszka; Witak, Małgorzata

2016-04-01

Rapid ecosystem transitions and adverse effects on ecosystem services as responses to combined climate and human impacts are of major concern. Yet few quantitative observational data exist, particularly for ecosystems that have a long history of human intervention. Here, we combine quantitative summer and winter climate reconstructions, climate model simulations and proxies for three major environmental pressures (land use, nutrients and erosion) to explore the system dynamics, resilience, and the role of disturbance regimes in varved eutrophic Lake Żabińskie since AD 1000. Comparison between regional and global climate simulations and quantitative climate reconstructions indicate that proxy data capture noticeably natural forced climate variability, while internal variability appears as the dominant source of climate variability in the climate model simulations during most parts of the last millennium. Using different multivariate analyses and change point detection techniques, we identify ecosystem changes through time and shifts between rather stable states and highly variable ones, as expressed by the proxies for land-use, erosion and productivity in the lake. Prior to AD 1600, the lake ecosystem was characterized by a high stability and resilience against considerable observed natural climate variability. In contrast, lake-ecosystem conditions started to fluctuate at high frequency across a broad range of states after AD 1600. The period AD 1748-1868 represents the phase with the strongest human disturbance of the ecosystem. Analyses of the frequency of change points in the multi-proxy dataset suggests that the last 400 years were highly variable and flickering with increasing vulnerability of the ecosystem to the combined effects of climate variability and anthropogenic disturbances. This led to significant rapid ecosystem transformations.

Development of a testing method for asbestos fibers in treated materials of asbestos containing wastes by transmission electron microscopy

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

Yamamoto, Takashi, E-mail: tyama@nies.go.jp; Kida, Akiko; Noma, Yukio

Highlights: • A high sensitive and selective testing method for asbestos in treated materials of asbestos containing wastes was developed. • Asbestos can be determined at a limits are a few million fibers per gram and a few μg g{sup −1}. • High temperature melting treatment samples were determined by this method. Asbestos fiber concentration were below the quantitation limit in all samples, and total fiber concentrations were determined as 47–170 × 10{sup 6} g{sup −1}. - Abstract: Appropriate treatment of asbestos-containing wastes is a significant problem. In Japan, the inertization of asbestos-containing wastes based on new treatment processes approvedmore » by the Minister of the Environment is promoted. A highly sensitive method for testing asbestos fibers in inertized materials is required so that these processes can be approved. We developed a method in which fibers from milled treated materials are extracted in water by shaking, and are counted and identified by transmission electron microscopy. Evaluation of this method by using asbestos standards and simulated slag samples confirmed that the quantitation limits are a few million fibers per gram and a few μg/g in a sample of 50 mg per filter. We used this method to assay asbestos fibers in slag samples produced by high-temperature melting of asbestos-containing wastes. Fiber concentrations were below the quantitation limit in all samples, and total fiber concentrations were determined as 47–170 × 10{sup −6} f/g. Because the evaluation of treated materials by TEM is difficult owing to the limited amount of sample observable, this testing method should be used in conjunction with bulk analytical methods for sure evaluation of treated materials.« less

Evaluating Rapid Models for High-Throughput Exposure Forecasting (SOT)

EPA Science Inventory

High throughput exposure screening models can provide quantitative predictions for thousands of chemicals; however these predictions must be systematically evaluated for predictive ability. Without the capability to make quantitative, albeit uncertain, forecasts of exposure, the ...

Characterization of Minerals of Geochronological Interest by EPMA and Atom Probe Tomography

NASA Astrophysics Data System (ADS)

Snoeyenbos, D.; Jercinovic, M. J.; Reinhard, D. A.; Hombourger, C.

2012-12-01

Isotopic and chemical dating techniques for zircon and monazite rely on several assumptions: that initial common Pb is low to nonexistent, that the analyzed domain is chronologically homogeneous, and that any relative migration of radiogenic Pb and its parent isotopes has not exceeded the analyzed domain. Yet, both zircon and monazite commonly contain significant submicron heterogeneities that may challenge these assumptions and can complicate the interpretation of chemical and isotopic data. Compositional mapping and submicron quantitative analysis by EPMA and FE-EPMA have been found to be useful techniques both for the characterization of these heterogeneities, and for quantitative geochronological determinations within the analytical limits of these techniques and the statistics of submicron sampling. Complementary to high-resolution EPMA techniques is Atom Probe Tomography (APT), wherein a specimen with dimensions of a few hundreds of nanometers is field evaporated atom by atom. The original position of each atom is identified, along with its atomic species and isotope. The result is a reconstruction allowing quantitative three-dimensional study of the specimen at the atomic scale, with low detection limits and high mass resolution. With the introduction of laser-induced thermal pulsing to achieve field evaporation, the technique is no longer limited to conductive specimens. There exists the capability to explore the compositional and isotopic structure of insulating materials at sub-nanometer resolution. Minerals of geochronological interest have been studied by an analytical method involving first compositional mapping and submicron quantitative analysis by EPMA and FE-EPMA, and subsequent use of these data to select specific sites for APT specimen extraction by FIB. Examples presented include 1) zircon from the Taconian of New England, USA, containing a fossil resorption front included between an unmodified igneous core, and a subsequent metamorphic overgrowth, with significant redistribution of U, Th, P and Y along microfracture arrays extending into the overgrowth, and 2) Paleoproterozoic monazite in thin bands <1μm wide along cleavage planes within much older (Neoarchean) monazite from the Boothia mainland of the Western Churchill Province, Canada.

[Effects of long time different negative pressures on osteogenic differentiation of rabbit bone mesenchymal stem cells].

PubMed

Zhao, Bowen; Zhang, Hongwei; Xu, Qiang; Ge, Quanhu; Li, Bolong; Peng, Xinyu; Wu, Xiangwei

2017-05-01

To investigate the effects of long time different negative pressures on osteogenic diffe-rentiation of rabbit bone mesenchymal stem cells (BMSCs). The rabbit BMSCs were isolated and cultured by density gradient centrifugation. Flow cytometry was used to analyze expression of surface markers. The third passage cells cultured under condition of osteogenic induction and under different negative pressure of 0 mm Hg (control group), 75 mm Hg (low negative pressure group), and 150 mm Hg (high negative pressure group) (1 mm Hg=0.133 kPa), and the negative pressure time was 30 min/h. Cell growth was observed under phase contrast microscopy, and the growth curve was drawn; alkaline phosphatase (ALP) activity was detected by ELISA after induced for 3, 7, and 14 days. The mRNA and protein expressions of collagen type I (COL-I) and osteocalcin (OC) in BMSCs were analyzed by real-time fluorescence quantitative PCR and Western blot. The cultured cells were identified as BMSCs by flow cytometry. The third passage BMSCs exhibited typical long shuttle and irregular shape. Cell proliferation was inhibited with the increase of negative pressure. After induced for 4 days, the cell number of high negative pressure group was significantly less than that in control group and low negative pressure group ( P <0.05), but there was no significant difference between the low negative pressure group and the control group ( P >0.05); at 5-7 days, the cell number showed significant difference between 3 groups ( P <0.05). The greater the negative pressure was, the greater the inhibition of cell proliferation was. There was no significant difference in ALP activity between groups at 3 days after induction ( P >0.05); the ALP activity showed significant difference ( P <0.05) between the high negative pressure group and the control group at 7 days after induction; and significant difference was found in the ALP activity between 3 groups at 14 days after induction ( P <0.05). The greater the negative pressure was, the higher the ALP activity was. Real-time fluorescence quantitative PCR and Western blot detection showed that the mRNA and protein expressions of COL-I and OC protein were significantly higher in low negative pressure group and high negative pressure group than control group ( P <0.05), and in the high negative pressure group than the low negative pressure group ( P <0.05). With the increase of the negative pressure, the osteogenic differentiation ability of BMSCs increases gradually, but the cell proliferation is inhibited.

[Quantitative real-time PCR for target periodontal bacteria in subgingival plaque before and after local delivery of periocline, scaling and root planning].

PubMed

Deng, Shu-li; Wang, Ying; He, Jia-yan; Chen, Zhuo; Chen, Hui

2013-06-01

To compare the copy number of Porphyromonas gingivalis (Pg) and Prevotella intermedia (Pi) in subgingival plaque before and after local delivery of periocline (2% minocycline hydrochloride ointment, MO), scaling and root planning (SRP) by quantitative real-time PCR (qRT-PCR) and evaluate the efficacy. Sixty-two adults with moderate to severe chronic periodontitis were selected in the study. Microbial samples were taken from pocket before and after MO and SRP(7d). The samples were evaluated by qRT-PCR for Pg and Pi. Microbiological effectiveness of treatments was assessed using Kruskal-Wallis and Wilcoxon rank-sum test. All tests were two-sided with a significance level of 0.05. All analyses were conducted with SAS 9.1.3 software package. The copy number of Pg and Pi in subgingival plaque was 10(3)-10(6) and 10(2)-10(6). Bacterial loads of Pg were reduced in SPR+ MO, SRP and MO site. The counts of Pi decreased in SRP+ MO sites compared with those in the MO or SRP alone sites significantly (P<0.05). Quantitative real-time PCR (qRT-PCR) is used as a powerful tool with high sensitivity and specificity to quantitatively assess target periodontal bacteria. The results show that subgingival administration of MO and SRP was effective for reducing pathogenic bacteria and improving clinical outcome. Supported by 2011 National Clinical Specialist Construction Project; Natural Science Foundation of Zhejiang Province(LY13H140002); Education Department Funds of Zhejiang Province(20061258) and Medical General Research Project of Zhejiang Province(2012KYB121).

Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs.

PubMed

Sonnaert, Maarten; Kerckhofs, Greet; Papantoniou, Ioannis; Van Vlierberghe, Sandra; Boterberg, Veerle; Dubruel, Peter; Luyten, Frank P; Schrooten, Jan; Geris, Liesbet

2015-01-01

To progress the fields of tissue engineering (TE) and regenerative medicine, development of quantitative methods for non-invasive three dimensional characterization of engineered constructs (i.e. cells/tissue combined with scaffolds) becomes essential. In this study, we have defined the most optimal staining conditions for contrast-enhanced nanofocus computed tomography for three dimensional visualization and quantitative analysis of in vitro engineered neo-tissue (i.e. extracellular matrix containing cells) in perfusion bioreactor-developed Ti6Al4V constructs. A fractional factorial 'design of experiments' approach was used to elucidate the influence of the staining time and concentration of two contrast agents (Hexabrix and phosphotungstic acid) and the neo-tissue volume on the image contrast and dataset quality. Additionally, the neo-tissue shrinkage that was induced by phosphotungstic acid staining was quantified to determine the operating window within which this contrast agent can be accurately applied. For Hexabrix the staining concentration was the main parameter influencing image contrast and dataset quality. Using phosphotungstic acid the staining concentration had a significant influence on the image contrast while both staining concentration and neo-tissue volume had an influence on the dataset quality. The use of high concentrations of phosphotungstic acid did however introduce significant shrinkage of the neo-tissue indicating that, despite sub-optimal image contrast, low concentrations of this staining agent should be used to enable quantitative analysis. To conclude, design of experiments allowed us to define the most optimal staining conditions for contrast-enhanced nanofocus computed tomography to be used as a routine screening tool of neo-tissue formation in Ti6Al4V constructs, transforming it into a robust three dimensional quality control methodology.

Pixel-based characterisation of CMOS high-speed camera systems

NASA Astrophysics Data System (ADS)

Weber, V.; Brübach, J.; Gordon, R. L.; Dreizler, A.

2011-05-01

Quantifying high-repetition rate laser diagnostic techniques for measuring scalars in turbulent combustion relies on a complete description of the relationship between detected photons and the signal produced by the detector. CMOS-chip based cameras are becoming an accepted tool for capturing high frame rate cinematographic sequences for laser-based techniques such as Particle Image Velocimetry (PIV) and Planar Laser Induced Fluorescence (PLIF) and can be used with thermographic phosphors to determine surface temperatures. At low repetition rates, imaging techniques have benefitted from significant developments in the quality of CCD-based camera systems, particularly with the uniformity of pixel response and minimal non-linearities in the photon-to-signal conversion. The state of the art in CMOS technology displays a significant number of technical aspects that must be accounted for before these detectors can be used for quantitative diagnostics. This paper addresses these issues.

Can we predict necrosis intra-operatively? Real-time optical quantitative perfusion imaging in surgery: study protocol for a prospective, observational, in vivo pilot study.

PubMed

Jansen, Sanne M; de Bruin, Daniel M; van Berge Henegouwen, Mark I; Strackee, Simon D; Veelo, Denise P; van Leeuwen, Ton G; Gisbertz, Suzanne S

2017-01-01

Compromised perfusion as a result of surgical intervention causes a reduction of oxygen and nutrients in tissue and therefore decreased tissue vitality. Quantitative imaging of tissue perfusion during reconstructive surgery, therefore, may reduce the incidence of complications. Non-invasive optical techniques allow real-time tissue imaging, with high resolution and high contrast. The objectives of this study are, first, to assess the feasibility and accuracy of optical coherence tomography (OCT), sidestream darkfield microscopy (SDF), laser speckle contrast imaging (LSCI), and fluorescence imaging (FI) for quantitative perfusion imaging and, second, to identify/search for criteria that enable risk prediction of necrosis during gastric tube and free flap reconstruction. This prospective, multicenter, observational in vivo pilot study will assess tissue perfusion using four optical technologies: OCT, SDF, LSCI, and FI in 40 patients: 20 patients who will undergo gastric tube reconstruction after esophagectomy and 20 patients who will undergo free flap surgery. Intra-operative images of gastric perfusion will be obtained directly after reconstruction at four perfusion areas. Feasibility of perfusion imaging will be analyzed per technique. Quantitative parameters directly related to perfusion will be scored per perfusion area, and differences between biologically good versus reduced perfusion will be tested statistically. Patient outcome will be correlated to images and perfusion parameters. Differences in perfusion parameters before and after a bolus of ephedrine will be tested for significance. This study will identify quantitative perfusion-related parameters for an objective assessment of tissue perfusion during surgery. This will likely allow early risk stratification of necrosis development, which will aid in achieving a reduction of complications in gastric tube reconstruction and free flap transplantation. Clinicaltrials.gov registration number NCT02902549. Dutch Central Committee on Research Involving Human Subjects registration number NL52377.018.15.

Comparison among Reconstruction Algorithms for Quantitative Analysis of 11C-Acetate Cardiac PET Imaging.

PubMed

Shi, Ximin; Li, Nan; Ding, Haiyan; Dang, Yonghong; Hu, Guilan; Liu, Shuai; Cui, Jie; Zhang, Yue; Li, Fang; Zhang, Hui; Huo, Li

2018-01-01

Kinetic modeling of dynamic 11 C-acetate PET imaging provides quantitative information for myocardium assessment. The quality and quantitation of PET images are known to be dependent on PET reconstruction methods. This study aims to investigate the impacts of reconstruction algorithms on the quantitative analysis of dynamic 11 C-acetate cardiac PET imaging. Suspected alcoholic cardiomyopathy patients ( N = 24) underwent 11 C-acetate dynamic PET imaging after low dose CT scan. PET images were reconstructed using four algorithms: filtered backprojection (FBP), ordered subsets expectation maximization (OSEM), OSEM with time-of-flight (TOF), and OSEM with both time-of-flight and point-spread-function (TPSF). Standardized uptake values (SUVs) at different time points were compared among images reconstructed using the four algorithms. Time-activity curves (TACs) in myocardium and blood pools of ventricles were generated from the dynamic image series. Kinetic parameters K 1 and k 2 were derived using a 1-tissue-compartment model for kinetic modeling of cardiac flow from 11 C-acetate PET images. Significant image quality improvement was found in the images reconstructed using iterative OSEM-type algorithms (OSME, TOF, and TPSF) compared with FBP. However, no statistical differences in SUVs were observed among the four reconstruction methods at the selected time points. Kinetic parameters K 1 and k 2 also exhibited no statistical difference among the four reconstruction algorithms in terms of mean value and standard deviation. However, for the correlation analysis, OSEM reconstruction presented relatively higher residual in correlation with FBP reconstruction compared with TOF and TPSF reconstruction, and TOF and TPSF reconstruction were highly correlated with each other. All the tested reconstruction algorithms performed similarly for quantitative analysis of 11 C-acetate cardiac PET imaging. TOF and TPSF yielded highly consistent kinetic parameter results with superior image quality compared with FBP. OSEM was relatively less reliable. Both TOF and TPSF were recommended for cardiac 11 C-acetate kinetic analysis.

Maternal genetic effects on adaptive divergence between anadromous and resident brook charr during early life history.

PubMed

Perry, G M L; Audet, C; Bernatchez, L

2005-09-01

The importance of directional selection relative to neutral evolution may be determined by comparing quantitative genetic variation in phenotype (Q(ST)) to variation at neutral molecular markers (F(ST)). Quantitative divergence between salmonid life history types is often considerable, but ontogenetic changes in the significance of major sources of genetic variance during post-hatch development suggest that selective differentiation varies by developmental stage. In this study, we tested the hypothesis that maternal genetic differentiation between anadromous and resident brook charr (Salvelinus fontinalis Mitchill) populations for early quantitative traits (embryonic size/growth, survival, egg number and developmental time) would be greater than neutral genetic differentiation, but that the maternal genetic basis for differentiation would be higher for pre-resorption traits than post-resorption traits. Quantitative genetic divergence between anadromous (seawater migratory) and resident Laval River (Québec) brook charr based on maternal genetic variance was high (Q(ST) > 0.4) for embryonic length, yolk sac volume, embryonic growth rate and time to first response to feeding relative to neutral genetic differentiation [F(ST) = 0.153 (0.071-0.214)], with anadromous females having positive genetic coefficients for all of the above characters. However, Q(ST) was essentially zero for all traits post-resorption of the yolk sac. Our results indicate that the observed divergence between resident and anadromous brook charr has been driven by directional selection, and may therefore be adaptive. Moreover, they provide among the first evidence that the relative importance of selective differentiation may be highly context-specific, and varies by genetic contributions to phenotype by parental sex at specific points in offspring ontogeny. This in turn suggests that interpretations of Q(ST)-F(ST) comparisons may be improved by considering the structure of quantitative genetic architecture by age category and the sex of the parent used in estimation.

Portable GMR Handheld Platform for the Detection of Influenza A Virus.

PubMed

Wu, Kai; Klein, Todd; Krishna, Venkatramana D; Su, Diqing; Perez, Andres M; Wang, Jian-Ping

2017-11-22

Influenza A virus (IAV) is a common respiratory pathogen infecting many hosts including humans, pigs (swine influenza virus or SIV), and birds (avian influenza virus or AIV). Monitoring swine and avian influenza viruses in the wild, farms, and live poultry markets is of great significance for human and veterinary public health. A portable, sensitive, and quantitative immunoassay device will be of high demand especially in the rural and resource-limited areas. We report herein our Z-Lab point-of-care (POC) device for sensitive and specific detection of swine influenza viruses with minimum sample handling and laboratory skill requirements. In the present study, a portable and quantitative immunoassay platform based on giant magnetoresistive (GMR) technology is used for the detection of IAV nucleoprotein (NP) and purified H3N2v. Z-Lab displays quantitative results in less than 10 min with sensitivities down to 15 ng/mL and 125 TCID 50 /mL for IAV nucleoprotein and purified H3N2v, respectively. This platform allows lab-testing to be performed outdoors and opens up the applications of immunoassays in nonclinical settings.

Correlates of stigma in adults with epilepsy: A systematic review of quantitative studies.

PubMed

Baker, David; Eccles, Fiona J R; Caswell, Helen L

2018-06-01

The aim of this review was to identify quantitative correlates, predictors, and outcomes of stigma in adults with epilepsy living in Western countries. To identify relevant literature, four academic databases (PsycINFO, CINAHL, PubMed, and Scopus) were systematically searched using key terms related to stigma and epilepsy. Thirty-three research papers reporting findings from 25 quantitative studies of correlates of stigma in epilepsy were identified. The findings suggest that stigma can be predicted by demographic, illness-related, and psychosocial factors, although associations were found to be highly culturally specific. Outcomes of stigma in people with epilepsy were replicated more consistently across cultures, and its impact was significant. Detrimental effects included both worse physical health, including less effective management of the condition, and reduced psychological well-being, including difficulties such as depression and anxiety. Educational initiatives and therapeutic interventions that aim to address stigma in people with epilepsy are recommended; however, these need to be culturally informed to ensure that they are valid and effective. Copyright © 2018 Elsevier Inc. All rights reserved.

An Informed Approach to Improving Quantitative Literacy and Mitigating Math Anxiety in Undergraduates Through Introductory Science Courses

NASA Astrophysics Data System (ADS)

Follette, K.; McCarthy, D.

2012-08-01

Current trends in the teaching of high school and college science avoid numerical engagement because nearly all students lack basic arithmetic skills and experience anxiety when encountering numbers. Nevertheless, such skills are essential to science and vital to becoming savvy consumers, citizens capable of recognizing pseudoscience, and discerning interpreters of statistics in ever-present polls, studies, and surveys in which our society is awash. Can a general-education collegiate course motivate students to value numeracy and to improve their quantitative skills in what may well be their final opportunity in formal education? We present a tool to assess whether skills in numeracy/quantitative literacy can be fostered and improved in college students through the vehicle of non-major introductory courses in astronomy. Initial classroom applications define the magnitude of this problem and indicate that significant improvements are possible. Based on these initial results we offer this tool online and hope to collaborate with other educators, both formal and informal, to develop effective mechanisms for encouraging all students to value and improve their skills in basic numeracy.

Raman measurement of carotenoid composition in human skin

NASA Astrophysics Data System (ADS)

Ermakov, Igor V.; Ermakova, Maia R.; Gellermann, Werner

2004-07-01

The carotenoids lycopene and beta-carotene are powerful antioxidants in skin and are thought to act as scavengers for free radicals and singlet oxygen. The role of carotenoid species in skin health is of strong current interest. We demonstrate the possibility to use Resonance Raman spectroscopy for fast, non-invasive, highly specific, and quantitative detection of beta-carotene and lycopene in human skin. Analyzing Raman signals originating from the carbon-carbon double bond stretch vibrations of the carotenoid molecules under blue and green laser excitation, we were able to characterize quantitatively the relative concentrations of each carotenoid species in-vivo. In the selective detection, we take advantage of different Raman cross-section spectral profiles for beta-carotene and lycopene molecules, and obtain a quantitative assessment of individual long-chain carotenoid species in the skin rather than their cumulative levels. Preliminary dual-wavelength Raman measurements reveal significant differences in the carotenoid composition of different subjects. The technique holds promise for rapid screening of carotenoid compositions in human skin in large populations and may be suitable in clinical studies for assessing the risk for cutaneous diseases.

Quantitative measures of walking and strength provide insight into brain corticospinal tract pathology in multiple sclerosis.

PubMed

Fritz, Nora E; Keller, Jennifer; Calabresi, Peter A; Zackowski, Kathleen M

2017-01-01

At least 85% of individuals with multiple sclerosis report walking dysfunction as their primary complaint. Walking and strength measures are common clinical measures to mark increasing disability or improvement with rehabilitation. Previous studies have shown an association between strength or walking ability and spinal cord MRI measures, and strength measures with brainstem corticospinal tract magnetization transfer ratio. However, the relationship between walking performance and brain corticospinal tract magnetization transfer imaging measures and the contribution of clinical measurements of walking and strength to the underlying integrity of the corticospinal tract has not been explored in multiple sclerosis. The objectives of this study were explore the relationship of quantitative measures of walking and strength to whole-brain corticospinal tract-specific MRI measures and to determine the contribution of quantitative measures of function in addition to basic clinical measures (age, gender, symptom duration and Expanded Disability Status Scale) to structural imaging measures of the corticospinal tract. We hypothesized that quantitative walking and strength measures would be related to brain corticospinal tract-specific measures, and would provide insight into the heterogeneity of brain pathology. Twenty-nine individuals with relapsing-remitting multiple sclerosis (mean(SD) age 48.7 (11.5) years; symptom duration 11.9(8.7); 17 females; median[range] Expanded Disability Status Scale 4.0 [1.0-6.5]) and 29 age and gender-matched healthy controls (age 50.8(11.6) years; 20 females) participated in clinical tests of strength and walking (Timed Up and Go, Timed 25 Foot Walk, Two Minute Walk Test ) as well as 3 T imaging including diffusion tensor imaging and magnetization transfer imaging. Individuals with multiple sclerosis were weaker (p = 0.0024) and walked slower (p = 0.0013) compared to controls. Quantitative measures of walking and strength were significantly related to corticospinal tract fractional anisotropy (r > 0.26; p < 0.04) and magnetization transfer ratio (r > 0.29; p < 0.03) measures. Although the Expanded Disability Status Scale was highly correlated with walking measures, it was not significantly related to either corticospinal tract fractional anisotropy or magnetization transfer ratio (p > 0.05). Walk velocity was a significant contributor to magnetization transfer ratio (p = 0.006) and fractional anisotropy (p = 0.011) in regression modeling that included both quantitative measures of function and basic clinical information. Quantitative measures of strength and walking are associated with brain corticospinal tract pathology. The addition of these quantitative measures to basic clinical information explains more of the variance in corticospinal tract fractional anisotropy and magnetization transfer ratio than the basic clinical information alone. Outcome measurement for multiple sclerosis clinical trials has been notoriously challenging; the use of quantitative measures of strength and walking along with tract-specific imaging methods may improve our ability to monitor disease change over time, with intervention, and provide needed guidelines for developing more effective targeted rehabilitation strategies.

A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification.

PubMed

Tu, Chengjian; Shen, Shichen; Sheng, Quanhu; Shyr, Yu; Qu, Jun

2017-01-30

Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the less confident peptides that were previously filtered out using the standard target-decoy search strategy. The filtered-out MS/MS spectra matched to confidently-identified proteins were recovered, and the peptide-spectrum-match FDR were re-calculated and controlled at a confident level of FDR≤1%, while protein FDR maintained at ~1%. We evaluated the performance of this strategy in both spectral count- and ion current-based methods. >60% increase of total quantified spectra/peptides was respectively achieved for analyzing a spike-in sample set and a public dataset from CPTAC. Incorporating the peptide retrieval strategy significantly improved the quantitative accuracy and precision, especially for low-abundance proteins (e.g. one-hit proteins). Moreover, the capacity of confidently discovering significantly-altered proteins was also enhanced substantially, as demonstrated with two spike-in datasets. In summary, improved quantitative performance was achieved by this peptide recovery strategy without compromising confidence of protein identification, which can be readily implemented in a broad range of quantitative proteomics techniques including label-free or labeling approaches. We hypothesize that more quantifiable spectra and peptides in a protein, even including less confident peptides, could help reduce variations and improve protein quantification. Hence the peptide retrieval strategy was developed and evaluated in two spike-in sample sets with different LC-MS/MS variations using both MS1- and MS2-based quantitative approach. The list of confidently identified proteins using the standard target-decoy search strategy was fixed and more spectra/peptides with less confidence matched to confident proteins were retrieved. However, the total peptide-spectrum-match false discovery rate (PSM FDR) after retrieval analysis was still controlled at a confident level of FDR≤1%. As expected, the penalty for occasionally incorporating incorrect peptide identifications is negligible by comparison with the improvements in quantitative performance. More quantifiable peptides, lower missing value rate, better quantitative accuracy and precision were significantly achieved for the same protein identifications by this simple strategy. This strategy is theoretically applicable for any quantitative approaches in proteomics and thereby provides more quantitative information, especially on low-abundance proteins. Published by Elsevier B.V.

Functional ankle instability as a risk factor for osteoarthritis: using T2-mapping to analyze early cartilage degeneration in the ankle joint of young athletes.

PubMed

Golditz, T; Steib, S; Pfeifer, K; Uder, M; Gelse, K; Janka, R; Hennig, F F; Welsch, G H

2014-10-01

The aim of this study was to investigate, using T2-mapping, the impact of functional instability in the ankle joint on the development of early cartilage damage. Ethical approval for this study was provided. Thirty-six volunteers from the university sports program were divided into three groups according to their ankle status: functional ankle instability (FAI, initial ankle sprain with residual instability); ankle sprain Copers (initial sprain, without residual instability); and controls (without a history of ankle injuries). Quantitative T2-mapping magnetic resonance imaging (MRI) was performed at the beginning ('early-unloading') and at the end ('late-unloading') of the MR-examination, with a mean time span of 27 min. Zonal region-of-interest T2-mapping was performed on the talar and tibial cartilage in the deep and superficial layers. The inter-group comparisons of T2-values were analyzed using paired and unpaired t-tests. Statistical analysis of variance was performed. T2-values showed significant to highly significant differences in 11 of 12 regions throughout the groups. In early-unloading, the FAI-group showed a significant increase in quantitative T2-values in the medial, talar regions (P = 0.008, P = 0.027), whereas the Coper-group showed this enhancement in the central-lateral regions (P = 0.05). Especially the comparison of early-loading to late-unloading values revealed significantly decreasing T2-values over time laterally and significantly increasing T2-values medially in the FAI-group, which were not present in the Coper- or control-group. Functional instability causes unbalanced loading in the ankle joint, resulting in cartilage alterations as assessed by quantitative T2-mapping. This approach can visualize and localize early cartilage abnormalities, possibly enabling specific treatment options to prevent osteoarthritis in young athletes. Copyright © 2014 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Phase-contrast CT: Qualitative and Quantitative Evaluation of Capillarized Sinusoids and Trabecular Structure in Human Hepatocellular Carcinoma Tissues.

PubMed

Jian, Jianbo; Zhang, Wenxue; Yang, Hao; Zhao, Xinyan; Xuan, Ruijiao; Li, Dongyue; Hu, Chunhong

2017-01-01

Capillarization of sinusoids and change of trabecular thickness are the main histologic features in hepatocellular carcinoma (HCC). Of particular interest are the three-dimensional (3D) visualization and quantitative evaluation of such alterations in the HCC progression. X-ray phase-contrast computed tomography (PCCT) is an emerging imaging method that provides excellent image contrast for soft tissues. This study aimed to explore the potential of in-line PCCT in microstructure imaging of capillarized sinusoids and trabecular structure in human HCC tissues and to quantitatively evaluate the alterations of those fine structures during the development of HCC. This project was designed as an ex vivo experimental study. The study was approved by the institutional review board, and informed consent was obtained from the patients. Eight human resected HCC tissue samples were imaged using in-line PCCT. After histologic processing, PCCT images and histopathologic data were matched. Fine structures in HCC tissues were revealed. Quantitative analyses of capillarized sinusoids (ie, percentage of sinusoidal area [PSA], sinusoidal volume) and trabecular structure (ie, trabecular thickness, surface-area-to-volume ratio [SA/V]) in low-grade (well or moderately differentiated) and high-grade (poorly differentiated) HCC groups were performed. Using PCCT, the alterations of capillarized sinusoids and trabecular structure were clearly observed in 3D geometry, which was confirmed by the corresponding histologic sections. The 3D qualitative analyses of sinusoids in the high-grade HCC group were significantly different (P < 0.05) in PSA (7.8 ± 2.5%) and sinusoidal volume (2.9 ± 0.6 × 10 7  µm 3 ) from those in the low-grade HCC group (PSA, 12.9 ± 2.2%; sinusoidal volume, 2.4 ± 0.3 × 10 7  µm 3 ). Moreover, the 3D quantitative evaluation of the trabecular structure in the high-grade HCC group showed a significant change (P < 0.05) in the trabecular thickness (87.8 ± 15.6 µm) and SA/V (2.2 ± 1.3 × 10 3  µm - 1 ) compared to the low-grade HCC group (trabecular thickness, 75.9 ± 7.1 µm; SA/V, 7.5 ± 1.3 × 10 3  µm - 1 ). This study provides insights into the 3D alterations of microstructures such as capillarized sinusoids and the trabecular structure at a micrometer level, which might allow for an improved understanding of the development of HCC. Copyright © 2017 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

The Impact of Situation-Based Learning to Students’ Quantitative Literacy

NASA Astrophysics Data System (ADS)

Latifah, T.; Cahya, E.; Suhendra

2017-09-01

Nowadays, the usage of quantities can be seen almost everywhere. There has been an increase of quantitative thinking, such as quantitative reasoning and quantitative literacy, within the context of daily life. However, many people today are still not fully equipped with the knowledge of quantitative thinking. There are still a lot of individuals not having enough quantitative skills to perform well within today’s society. Based on this issue, the research aims to improve students’ quantitative literacy in junior high school. The qualitative analysis of written student work and video observations during the experiment reveal that the impact of situation-based learning affects students’ quantitative literacy.

In situ quantitative characterisation of the ocean water column using acoustic multibeam backscatter data

NASA Astrophysics Data System (ADS)

Lamarche, G.; Le Gonidec, Y.; Lucieer, V.; Lurton, X.; Greinert, J.; Dupré, S.; Nau, A.; Heffron, E.; Roche, M.; Ladroit, Y.; Urban, P.

2017-12-01

Detecting liquid, solid or gaseous features in the ocean is generating considerable interest in the geoscience community, because of their potentially high economic values (oil & gas, mining), their significance for environmental management (oil/gas leakage, biodiversity mapping, greenhouse gas monitoring) as well as their potential cultural and traditional values (food, freshwater). Enhancing people's capability to quantify and manage the natural capital present in the ocean water goes hand in hand with the development of marine acoustic technology, as marine echosounders provide the most reliable and technologically advanced means to develop quantitative studies of water column backscatter data. This is not developed to its full capability because (i) of the complexity of the physics involved in relation to the constantly changing marine environment, and (ii) the rapid technological evolution of high resolution multibeam echosounder (MBES) water-column imaging systems. The Water Column Imaging Working Group is working on a series of multibeam echosounder (MBES) water column datasets acquired in a variety of environments, using a range of frequencies, and imaging a number of water-column features such as gas seeps, oil leaks, suspended particulate matter, vegetation and freshwater springs. Access to data from different acoustic frequencies and ocean dynamics enables us to discuss and test multifrequency approaches which is the most promising means to develop a quantitative analysis of the physical properties of acoustic scatterers, providing rigorous cross calibration of the acoustic devices. In addition, high redundancy of multibeam data, such as is available for some datasets, will allow us to develop data processing techniques, leading to quantitative estimates of water column gas seeps. Each of the datasets has supporting ground-truthing data (underwater videos and photos, physical oceanography measurements) which provide information on the origin and chemistry of the seep content. This is of first importance when assessing the physical properties of water column scatterers from backscatter acoustic measurement.

[THE COMPARATIVE ANALYSIS OF RESULTS OF DETECTION OF CARCINOGENIC TYPES OF HUMAN PAPILLOMA VIRUS BY QUALITATIVE AND QUANTITATIVE TESTS].

PubMed

Kuzmenko, E T; Labigina, A V; Leshenko, O Ya; Rusanov, D N; Kuzmenko, V V; Fedko, L P; Pak, I P

2015-05-01

The analysis of results of screening (n = 3208; sexually active citizen aged from 18 to 59 years) was carried out to detect oncogene types of human papilloma virus in using qualitative (1150 females and 720 males) and quantitative (polymerase chain reaction in real-time (843 females and 115 males) techniques. The human papilloma virus of high oncogene type was detected in 65% and 68.4% of females and in 48.6% and 53% of males correspondingly. Among 12 types of human papilloma virus the most frequently diagnosed was human papilloma virus 16 independently of gender of examined and technique of analysis. In females, under application of qualitative tests rate of human papilloma virus 16 made up to 18.3% (n = 280) and under application of quantitative tests Rte of human papilloma virus made up to 14.9% (n = 126; p ≤ 0.05). Under examination of males using qualitative tests rate of human papilloma virus 16 made up to 8.3% (n = 60) and under application of qualitative tests made up to 12.2% (n = 14; p ≥ 0.05). Under application of qualitative tests rate of detection on the rest ofoncogene types of human papilloma virus varied in females from 3.4% to 8.4% and in males from 1.8% to 5.9%. Under application of qualitative tests to females rate of human papilloma virus with high viral load made up to 68.4%, with medium viral load - 2.85% (n = 24) and with low viral load -0.24% (n = 2). Under application of quantitative tests in males rate of detection of types of human papilloma virus made up to 53% and at that in all high viral load was established. In females, the most of oncogene types of human papilloma virus (except for 31, 39, 59) are detected significantly more often than in males.

Identification and Quantitation of Flavanols and Proanthocyanidins in Foods: How Good are the Datas?

PubMed Central

Kelm, Mark A.; Hammerstone, John F.; Schmitz, Harold H.

2005-01-01

Evidence suggesting that dietary polyphenols, flavanols, and proanthocyanidins in particular offer significant cardiovascular health benefits is rapidly increasing. Accordingly, reliable and accurate methods are needed to provide qualitative and quantitative food composition data necessary for high quality epidemiological and clinical research. Measurements for flavonoids and proanthocyanidins have employed a range of analytical techniques, with various colorimetric assays still being popular for estimating total polyphenolic content in foods and other biological samples despite advances made with more sophisticated analyses. More crudely, estimations of polyphenol content as well as antioxidant activity are also reported with values relating to radical scavenging activity. High-performance liquid chromatography (HPLC) is the method of choice for quantitative analysis of individual polyphenols such as flavanols and proanthocyanidins. Qualitative information regarding proanthocyanidin structure has been determined by chemical methods such as thiolysis and by HPLC-mass spectrometry (MS) techniques at present. The lack of appropriate standards is the single most important factor that limits the aforementioned analyses. However, with ever expanding research in the arena of flavanols, proanthocyanidins, and health and the importance of their future inclusion in food composition databases, the need for standards becomes more critical. At present, sufficiently well-characterized standard material is available for selective flavanols and proanthocyanidins, and construction of at least a limited food composition database is feasible. PMID:15712597

Quantitative Criteria to Screen for Cannabis Use Disorder.

PubMed

Casajuana, Cristina; López-Pelayo, Hugo; Miquel, Laia; Balcells-Oliveró, María Mercedes; Colom, Joan; Gual, Antoni

2018-06-27

The Standard Joint Unit (1 SJU = 7 mg of 9-Tetrahydrocannabinol) simplifies the exploration of risky patterns of cannabis use. This study proposes a preliminary quantitative cutoff criterion to screen for cannabis use disorder (CUD). Socio-demographical data and information on cannabis quantities, frequency of use, and risk for CUD (measured with the Cannabis Abuse Screening Test (CAST) of cannabis users recruited in Barcelona (from February 2015 to June 2016) were collected. CAST scores were categorized into low, moderate, and high risk for CUD, based on the SJU consumed and frequency. Receiver operating characteristic (ROC) analysis related daily SJU with CUD. Participants (n = 473) were on average 29 years old (SD = 10), men (77.1%), and single (74.6%). With an average of 4 joints per smoking day, 82.5% consumed cannabis almost every day. Risk for CUD (9.40% low, 23.72% moderate, 66.88% high) increased significantly with more frequency and quantities consumed. The ROC analyses suggest 1.2 SJU per day as a cutoff criterion to screen for at least moderate risk for CUD (sensitivity 69.4%, specificity 63.6%). Frequency and quantity should be considered when exploring cannabis risks. A 1 SJU per day is proposed as a preliminary quantitative-based criterion to screen users with at least a moderate risk for CUD. © 2018 S. Karger AG, Basel.

Repeatability of shear wave elastography in liver fibrosis phantoms—Evaluation of five different systems

PubMed Central

2018-01-01

This study aimed to assess and validate the repeatability and agreement of quantitative elastography of novel shear wave methods on four individual tissue-mimicking liver fibrosis phantoms with different known Young’s modulus. We used GE Logiq E9 2D-SWE, Philips iU22 ARFI (pSWE), Samsung TS80A SWE (pSWE), Hitachi Ascendus (SWM) and Transient Elastography (TE). Two individual investigators performed all measurements non-continued and in parallel. The methods were evaluated for inter- and intraobserver variability by intraclass correlation, coefficient of variation and limits of agreement using the median elastography value. All systems used in this study provided high repeatability in quantitative measurements in a liver fibrosis phantom and excellent inter- and intraclass correlations. All four elastography platforms showed excellent intra-and interobserver agreement (interclass correlation 0.981–1.000 and intraclass correlation 0.987–1.000) and no significant difference in mean elasticity measurements for all systems, except for TE on phantom 4. All four liver fibrosis phantoms could be differentiated by quantitative elastography, by all platforms (p<0.001). In the Bland-Altman analysis the differences in measurements were larger for the phantoms with higher Young’s modulus. All platforms had a coefficient of variation in the range 0.00–0.21 for all four phantoms, equivalent to low variance and high repeatability. PMID:29293527

The Correlation Between Metacognition Level with Self-Efficacy of Biology Education College Students

NASA Astrophysics Data System (ADS)

Ridlo, S.; Lutfiya, F.

2017-04-01

Self-efficacy is a strong predictor of academic achievement. Self-efficacy refers to the ability of college students to achieve the desired results. The metacognition level can influence college student’s self-efficacy. This study aims to identify college student’s metacognition level and self-efficacy, as well as determine the relationship between self-efficacy and metacognition level for college students of Biology Education 2013, Semarang State University. The ex-post facto quantitative research was conducted on 99 students Academic Year 2015/2016. Saturation sampling technique determined samples. E-D scale collected data for self-efficacy identification. Data for assess the metacognition level collected by Metacognitive Awareness Inventory. Data were analysed quantitatively by Pearson correlation and linear regression. Most college students have the high level of metacognition and average self-efficacy. Pearson correlation coefficient result was 0.367. This result showed that metacognition level and self-efficacy has a weak relationship. Based on linear regression test, self-efficacy influenced by metacognition level up to 13.5%. The results of the study showed that positive and significant relationships exist between metacognition level and self-efficacy. Therefore, if the metacognition level is high, then self-efficacy will also be high (appropriate).

Au-Pt-Au nanoraspberry structures used for mercury ion detection

NASA Astrophysics Data System (ADS)

Huang, Jiang-Hao; Huang, Shuai; Wen, Xiaoyan; Li, Min; Lu, Haifei

2017-12-01

Detection of Hg2+ with high sensitivity is of great significance in the biochemical sensing field. Quantitative of Hg2+ was realized based on the influence of Hg2+ on the UV-vis absorption performance of Au-Pt-Au core-shell nanoraspberry (APA)-rhodamine-6G (R6G) structure. First, APA sol was added into R6G indicator solution and the UV-vis absorption signal intensity of R6G was evidently promoted. The signal intensity monotonously increased as more APA sol was added. However, when HgCl2 solution was introduced, the signal intensity declined. A linear relationship between Hg2+ concentration and signal intensity at 527 nm was revealed, based on which quantitative determination of Hg2+ could be realized. Hg2+ detection sensitivity was measured to be 0.031 a.u./M with a limit of detection of 10-7 M and the response time was 20 s. A high Hg2+ detection selectivity over Cu2+, Na+, Li+, and K+ was demonstrated. Due to its simplicity and high sensitivity, the proposed method could find an extensive application prospect in the Hg2+ detection field.

Quantitative assessment of serum-specific IgE in the diagnosis of human cystic echinococcosis.

PubMed

Marinova, I; Nikolov, G; Michova, A; Kurdova, R; Petrunov, B

2011-07-01

Anti-Echinococcus serum immunoglobulin (Ig)E was assessed by the ImmunoCAP system and compared with anti-Echinococcus serum IgG assessed by enzyme-linked immunosorbent assay (ELISA) and Western blot. The ImmunoCAP system revealed very high specificity (one false positive of 110 healthy individuals), low cross-reactivity (one false positive of 58 patients with other diseases) and decreased sensitivity (73.55%). Receiver operating characteristic analysis displayed a beneficial diagnostic value with high accuracy. Comparison of the ImmunoCAP system with ELISA and Western blot showed significantly higher specificity and significantly lower cross-reactivity compared with the ELISA. Examination of sera from 155 patients with cystic echinococcosis (CE) showed varying levels of anti-Echinococcus IgE (range, 0.01-118.33 kUA/L). However, most samples had moderately elevated IgE levels. Analysis of serum-specific IgE revealed significantly higher sensitivity of the ImmunoCAP system and significantly higher antibody levels in hepatic CE compared with pulmonary CE. © 2011 Blackwell Publishing Ltd.

Bone Status Among Patients With Nonsurgical Hypoparathyroidism, Autosomal Dominant Hypocalcaemia, and Pseudohypoparathyroidism: A Cohort Study.

PubMed

Underbjerg, Line; Malmstroem, Sofie; Sikjaer, Tanja; Rejnmark, Lars

2018-03-01

Nonsurgical hypoparathyroidism (Ns-HypoPT) and pseudohypoparathyroidism (PHP) are both rare diseases, characterized by hypocalcemia. In Ns-HypoPT, PTH levels are low, whereas patients with PHP often have very high levels due to receptor-insensitivity to PTH (PTH-resistance). Accordingly, we hypothesized that indices of bone turnover and bone mineralization/architecture are similar in Ns-HypoPT and PHP despite marked differences in PTH levels. We studied 62 patients with Ns-HypoPT and 31 with PHP as well as a group of age- and sex-matched healthy controls. We found a significantly higher areal BMD (aBMD) by DXA among patients with Ns-HypoPT, both compared with PHP and the background population. Compared with Ns-HypoPT, PHP patients had significantly lower total and trabecular volumetric BMD (vBMD) assessed by quantitative computed tomography (QCT) scans at the spine and hip. High-resolution peripheral quantitative computed tomography (HRpQCT) scans showed a lower trabecular area and vBMD as well as a lower trabecular number at the tibia in PHP compared to Ns-HypoPT and matched controls. In PHP, PTH levels correlated with levels of markers of bone formation (osteocalcin, bone-specific alkaline phosphatase, P1NP), and bone resorption (CTx). In adult males, levels of bone markers were significantly higher in PHP compared with Ns-HypoPT. Levels of procalcitonin and calcitonin were significantly higher in PHP compared with Ns-HypoPT. In conclusion, indices of bone turnover, density, and microarchitecture differ between patients with Ns-HypoPT and PHP. Our data suggest that patients with PHP do not have a complete skeletal resistance to PTH and that the effects of chronically high PTH levels in PHP are mostly confined to the trabecular tissue. © 2017 American Society for Bone and Mineral Research. © 2017 American Society for Bone and Mineral Research.

A Study of Cognitive Load for Enhancing Student’s Quantitative Literacy in Inquiry Lab Learning

NASA Astrophysics Data System (ADS)

Nuraeni, E.; Rahman, T.; Alifiani, D. P.; Khoerunnisa, R. S.

2017-09-01

Students often find it difficult to appreciate the relevance of the role of quantitative analysis and concept attainment in the science class. This study measured student cognitive load during the inquiry lab of the respiratory system to improve quantitative literacy. Participants in this study were 40 11th graders from senior high school in Indonesia. After students learned, their feelings about the degree of mental effort that it took to complete the learning tasks were measured by 28 self-report on a 4-point Likert scale. The Task Complexity Worksheet were used to asses processing quantitative information and paper based test were applied to assess participants’ concept achievements. The results showed that inquiry instructional induced a relatively low mental effort, high processing information and high concept achievments.

Adaptation of a Simple Microfluidic Platform for High-Dimensional Quantitative Morphological Analysis of Human Mesenchymal Stromal Cells on Polystyrene-Based Substrates.

PubMed

Lam, Johnny; Marklein, Ross A; Jimenez-Torres, Jose A; Beebe, David J; Bauer, Steven R; Sung, Kyung E

2017-12-01

Multipotent stromal cells (MSCs, often called mesenchymal stem cells) have garnered significant attention within the field of regenerative medicine because of their purported ability to differentiate down musculoskeletal lineages. Given the inherent heterogeneity of MSC populations, recent studies have suggested that cell morphology may be indicative of MSC differentiation potential. Toward improving current methods and developing simple yet effective approaches for the morphological evaluation of MSCs, we combined passive pumping microfluidic technology with high-dimensional morphological characterization to produce robust tools for standardized high-throughput analysis. Using ultraviolet (UV) light as a modality for reproducible polystyrene substrate modification, we show that MSCs seeded on microfluidic straight channel devices incorporating UV-exposed substrates exhibited morphological changes that responded accordingly to the degree of substrate modification. Substrate modification also effected greater morphological changes in MSCs seeded at a lower rather than higher density within microfluidic channels. Despite largely comparable trends in morphology, MSCs seeded in microscale as opposed to traditional macroscale platforms displayed much higher sensitivity to changes in substrate properties. In summary, we adapted and qualified microfluidic cell culture platforms comprising simple straight channel arrays as a viable and robust tool for high-throughput quantitative morphological analysis to study cell-material interactions.

Quantitative Susceptibility Mapping after Sports-Related Concussion.

PubMed

Koch, K M; Meier, T B; Karr, R; Nencka, A S; Muftuler, L T; McCrea, M

2018-06-07

Quantitative susceptibility mapping using MR imaging can assess changes in brain tissue structure and composition. This report presents preliminary results demonstrating changes in tissue magnetic susceptibility after sports-related concussion. Longitudinal quantitative susceptibility mapping metrics were produced from imaging data acquired from cohorts of concussed and control football athletes. One hundred thirty-six quantitative susceptibility mapping datasets were analyzed across 3 separate visits (24 hours after injury, 8 days postinjury, and 6 months postinjury). Longitudinal quantitative susceptibility mapping group analyses were performed on stability-thresholded brain tissue compartments and selected subregions. Clinical concussion metrics were also measured longitudinally in both cohorts and compared with the measured quantitative susceptibility mapping. Statistically significant increases in white matter susceptibility were identified in the concussed athlete group during the acute (24 hour) and subacute (day 8) period. These effects were most prominent at the 8-day visit but recovered and showed no significant difference from controls at the 6-month visit. The subcortical gray matter showed no statistically significant group differences. Observed susceptibility changes after concussion appeared to outlast self-reported clinical recovery metrics at a group level. At an individual subject level, susceptibility increases within the white matter showed statistically significant correlations with return-to-play durations. The results of this preliminary investigation suggest that sports-related concussion can induce physiologic changes to brain tissue that can be detected using MR imaging-based magnetic susceptibility estimates. In group analyses, the observed tissue changes appear to persist beyond those detected on clinical outcome assessments and were associated with return-to-play duration after sports-related concussion. © 2018 by American Journal of Neuroradiology.

Prediction of Environmental Impact of High-Energy Materials with Atomistic Computer Simulations

DTIC Science & Technology

2010-11-01

from a training set of compounds. Other methods include Quantitative Struc- ture-Activity Relationship ( QSAR ) and Quantitative Structure-Property...26 28 the development of QSPR/ QSAR models, in contrast to boiling points and critical parameters derived from empirical correlations, to improve...Quadratic Configuration Interaction Singles Doubles QSAR Quantitative Structure-Activity Relationship QSPR Quantitative Structure-Property

A Method for Label-Free, Differential Top-Down Proteomics.

PubMed

Ntai, Ioanna; Toby, Timothy K; LeDuc, Richard D; Kelleher, Neil L

2016-01-01

Biomarker discovery in the translational research has heavily relied on labeled and label-free quantitative bottom-up proteomics. Here, we describe a new approach to biomarker studies that utilizes high-throughput top-down proteomics and is the first to offer whole protein characterization and relative quantitation within the same experiment. Using yeast as a model, we report procedures for a label-free approach to quantify the relative abundance of intact proteins ranging from 0 to 30 kDa in two different states. In this chapter, we describe the integrated methodology for the large-scale profiling and quantitation of the intact proteome by liquid chromatography-mass spectrometry (LC-MS) without the need for metabolic or chemical labeling. This recent advance for quantitative top-down proteomics is best implemented with a robust and highly controlled sample preparation workflow before data acquisition on a high-resolution mass spectrometer, and the application of a hierarchical linear statistical model to account for the multiple levels of variance contained in quantitative proteomic comparisons of samples for basic and clinical research.

High-throughput analysis of the protein sequence-stability landscape using a quantitative "yeast surface two-hybrid" system and fragment reconstitution

PubMed Central

Dutta, Sanjib; Koide, Akiko; Koide, Shohei

2008-01-01

Stability evaluation of many mutants can lead to a better understanding of the sequence determinants of a structural motif and of factors governing protein stability and protein evolution. The traditional biophysical analysis of protein stability is low throughput, limiting our ability to widely explore the sequence space in a quantitative manner. In this study, we have developed a high-throughput library screening method for quantifying stability changes, which is based on protein fragment reconstitution and yeast surface display. Our method exploits the thermodynamic linkage between protein stability and fragment reconstitution and the ability of the yeast surface display technique to quantitatively evaluate protein-protein interactions. The method was applied to a fibronectin type III (FN3) domain. Characterization of fragment reconstitution was facilitated by the co-expression of two FN3 fragments, thus establishing a "yeast surface two-hybrid" method. Importantly, our method does not rely on competition between clones and thus eliminates a common limitation of high-throughput selection methods in which the most stable variants are predominantly recovered. Thus, it allows for the isolation of sequences that exhibits a desired level of stability. We identified over one hundred unique sequences for a β-bulge motif, which was significantly more informative than natural sequences of the FN3 family in revealing the sequence determinants for the β-bulge. Our method provides a powerful means to rapidly assess stability of many variants, to systematically assess contribution of different factors to protein stability and to enhance protein stability. PMID:18674545

Quantitative Analysis of Focused A-To-I RNA Editing Sites by Ultra-High-Throughput Sequencing in Psychiatric Disorders

PubMed Central

Zhu, Hu; Urban, Daniel J.; Blashka, Jared; McPheeters, Matthew T.; Kroeze, Wesley K.; Mieczkowski, Piotr; Overholser, James C.; Jurjus, George J.; Dieter, Lesa; Mahajan, Gouri J.; Rajkowska, Grazyna; Wang, Zefeng; Sullivan, Patrick F.; Stockmeier, Craig A.; Roth, Bryan L.

2012-01-01

A-to-I RNA editing is a post-transcriptional modification of single nucleotides in RNA by adenosine deamination, which thereby diversifies the gene products encoded in the genome. Thousands of potential RNA editing sites have been identified by recent studies (e.g. see Li et al, Science 2009); however, only a handful of these sites have been independently confirmed. Here, we systematically and quantitatively examined 109 putative coding region A-to-I RNA editing sites in three sets of normal human brain samples by ultra-high-throughput sequencing (uHTS). Forty of 109 putative sites, including 25 previously confirmed sites, were validated as truly edited in our brain samples, suggesting an overestimation of A-to-I RNA editing in these putative sites by Li et al (2009). To evaluate RNA editing in human disease, we analyzed 29 of the confirmed sites in subjects with major depressive disorder and schizophrenia using uHTS. In striking contrast to many prior studies, we did not find significant alterations in the frequency of RNA editing at any of the editing sites in samples from these patients, including within the 5HT2C serotonin receptor (HTR2C). Our results indicate that uHTS is a fast, quantitative and high-throughput method to assess RNA editing in human physiology and disease and that many prior studies of RNA editing may overestimate both the extent and disease-related variability of RNA editing at the sites we examined in the human brain. PMID:22912834

Regenerate Healing Outcomes in Unilateral Mandibular Distraction Osteogenesis Using Quantitative Histomorphometry

PubMed Central

Schwarz, Daniel A.; Arman, Krikor G.; Kakwan, Mehreen S.; Jamali, Ameen M.; Elmeligy, Ayman A.; Buchman, Steven R.

2015-01-01

Background The authors’ goal was to ascertain regenerate bone-healing metrics using quantitative histomorphometry at a single consolidation period. Methods Rats underwent either mandibular distraction osteogenesis (n=7) or partially reduced fractures (n=7); their contralateral mandibles were used as controls (n=11). External fixators were secured and unilateral osteotomies performed, followed by either mandibular distraction osteogenesis (4 days’ latency, then 0.3 mm every 12 hours for 8 days; 5.1 mm) or partially reduced fractures (fixed immediately postoperatively; 2.1 mm); both groups underwent 4 weeks of consolidation. After tissue processing, bone volume/tissue volume ratio, osteoid volume/tissue volume ratio, and osteocyte count per high-power field were analyzed by means of quantitative histomorphometry. Results Contralateral mandibles had statistically greater bone volume/tissue volume ratio and osteocyte count per high-power field compared with both mandibular distraction osteogenesis and partially reduced fractures by almost 50 percent, whereas osteoid volume/tissue volume ratio was statistically greater in both mandibular distraction osteogenesis specimens and partially reduced fractures compared with contralateral mandibles. No statistical difference in bone volume/tissue volume ratio, osteoid volume/tissue volume ratio, or osteocyte count per high-power field was found between mandibular distraction osteogenesis specimens and partially reduced fractures. Conclusions The authors’ findings demonstrate significantly decreased bone quantity and maturity in mandibular distraction osteogenesis specimens and partially reduced fractures compared with contralateral mandibles using the clinically analogous protocols. If these results are extrapolated clinically, treatment strategies may require modification to ensure reliable, predictable, and improved outcomes. PMID:20463629

Quantitative Analyses of Core Promoters Enable Precise Engineering of Regulated Gene Expression in Mammalian Cells.

PubMed

Ede, Christopher; Chen, Ximin; Lin, Meng-Yin; Chen, Yvonne Y

2016-05-20

Inducible transcription systems play a crucial role in a wide array of synthetic biology circuits. However, the majority of inducible promoters are constructed from a limited set of tried-and-true promoter parts, which are susceptible to common shortcomings such as high basal expression levels (i.e., leakiness). To expand the toolbox for regulated mammalian gene expression and facilitate the construction of mammalian genetic circuits with precise functionality, we quantitatively characterized a panel of eight core promoters, including sequences with mammalian, viral, and synthetic origins. We demonstrate that this selection of core promoters can provide a wide range of basal gene expression levels and achieve a gradient of fold-inductions spanning 2 orders of magnitude. Furthermore, commonly used parts such as minimal CMV and minimal SV40 promoters were shown to achieve robust gene expression upon induction, but also suffer from high levels of leakiness. In contrast, a synthetic promoter, YB_TATA, was shown to combine low basal expression with high transcription rate in the induced state to achieve significantly higher fold-induction ratios compared to all other promoters tested. These behaviors remain consistent when the promoters are coupled to different genetic outputs and different response elements, as well as across different host-cell types and DNA copy numbers. We apply this quantitative understanding of core promoter properties to the successful engineering of human T cells that respond to antigen stimulation via chimeric antigen receptor signaling specifically under hypoxic environments. Results presented in this study can facilitate the design and calibration of future mammalian synthetic biology systems capable of precisely programmed functionality.

Psychiatric co-morbidity is highly prevalent in idiopathic cervical dystonia and significantly influences health-related quality of life: Results of a controlled study.

PubMed

Smit, M; Kuiper, A; Han, V; Jiawan, V C R; Douma, G; van Harten, B; Oen, J M T H; Pouwels, M E; Dieks, H J G; Bartels, A L; Tijssen, M A

2016-09-01

The aim of this study was to systematically investigate the prevalence of psychiatric disorders and factors influencing health-related quality of life (HR-QoL) in cervical dystonia (CD) patients, in the context of objective dystonia motor severity. We studied 50 CD patients and 50 matched healthy controls. Psychiatric assessment included the MINI-PLUS interview and quantitative questionnaires. Dystonia motor severity (based on video evaluation), pain and disability were determined with the TWSTRS rating scale. In addition, severity of tremor and jerks was evaluated with the 7-point CGI-S scale. HR-QoL was determined with the RAND-36 item Health Survey and predictors of HR-QoL were assessed using multiple regression analysis. In CD patients, the MINI-PLUS revealed a significantly higher prevalence of psychiatric disorders (64% vs. 28%, p = 0.001), with substantially more depression (32% vs. 14%) and anxiety disorders (42% vs. 8%). This was confirmed by the quantitative rating scales. Disease characteristics did not differ between patients with and without a psychiatric diagnosis. HR-QoL in dystonia patients was significantly lowered. The most important predictors of HR-QoL appeared severity of depressive symptoms, pain and disability, but not severity of motor symptoms. Psychiatric co-morbidity is highly prevalent and is an important predictor of HR-QoL in CD patients, rather than dystonia motor severity. Our findings support the theory of a shared neurobiology for motor and non-motor features and highlight the need for systematic research into psychiatric disorders in dystonia. Adequate treatment of psychiatric symptoms could significantly contribute to better overall quality of life of CD patients. Copyright © 2016 Elsevier Ltd. All rights reserved.

An Integrated MRI and MRS Approach to Evaluation of Multiple Sclerosis with Cognitive Impairment

NASA Astrophysics Data System (ADS)

Liang, Zhengrong; Li, Lihong; Lu, Hongbing; Huang, Wei; Tudorica, Alina; Krupp, Lauren

Magnetic resonance imaging and spectroscopy (MRI/MRS) plays a unique role in multiple sclerosis (MS) evaluation, because of its ability to provide both high image contrast and significant chemical change among brain tissues. The image contrast renders the possibility of quantifying the tissue volumetric and texture variations, e.g., cerebral atrophy and progressing speed, reflecting the ongoing destructive pathologic processes. Any chemical change reflects an early sign of pathological alteration, e.g., decreased N-acetyl aspartate (NAA) in lesions and normal appearing white matter, related to axonal damage or dysfunction. Both MRI and MRS encounter partial volume (PV) effect, which compromises the quantitative capability, especially for MRS. This work aims to develop a statistical framework to segment the tissue mixtures inside each image element, eliminating theoretically the PV effect, and apply the framework to the evaluation of MS with cognitive impairment. The quantitative measures from MRI/MRS neuroimaging are strongly correlated with the qualitative neuropsychological scores of Brief Repeatable Battery (BRB) test on cognitive impairment, demonstrating the usefulness of the PV image segmentation framework in this clinically significant problem.

Spotting and validation of a genome wide oligonucleotide chip with duplicate measurement of each gene

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

Thomassen, Mads; Skov, Vibe; Eiriksdottir, Freyja

2006-06-16

The quality of DNA microarray based gene expression data relies on the reproducibility of several steps in a microarray experiment. We have developed a spotted genome wide microarray chip with oligonucleotides printed in duplicate in order to minimise undesirable biases, thereby optimising detection of true differential expression. The validation study design consisted of an assessment of the microarray chip performance using the MessageAmp and FairPlay labelling kits. Intraclass correlation coefficient (ICC) was used to demonstrate that MessageAmp was significantly more reproducible than FairPlay. Further examinations with MessageAmp revealed the applicability of the system. The linear range of the chips wasmore » three orders of magnitude, the precision was high, as 95% of measurements deviated less than 1.24-fold from the expected value, and the coefficient of variation for relative expression was 13.6%. Relative quantitation was more reproducible than absolute quantitation and substantial reduction of variance was attained with duplicate spotting. An analysis of variance (ANOVA) demonstrated no significant day-to-day variation.« less

Quantitative assessment of image motion blur in diffraction images of moving biological cells

NASA Astrophysics Data System (ADS)

Wang, He; Jin, Changrong; Feng, Yuanming; Qi, Dandan; Sa, Yu; Hu, Xin-Hua

2016-02-01

Motion blur (MB) presents a significant challenge for obtaining high-contrast image data from biological cells with a polarization diffraction imaging flow cytometry (p-DIFC) method. A new p-DIFC experimental system has been developed to evaluate the MB and its effect on image analysis using a time-delay-integration (TDI) CCD camera. Diffraction images of MCF-7 and K562 cells have been acquired with different speed-mismatch ratios and compared to characterize MB quantitatively. Frequency analysis of the diffraction images shows that the degree of MB can be quantified by bandwidth variations of the diffraction images along the motion direction. The analytical results were confirmed by the p-DIFC image data acquired at different speed-mismatch ratios and used to validate a method of numerical simulation of MB on blur-free diffraction images, which provides a useful tool to examine the blurring effect on diffraction images acquired from the same cell. These results provide insights on the dependence of diffraction image on MB and allow significant improvement on rapid biological cell assay with the p-DIFC method.

Quantitative Aspects of Single Molecule Microscopy

PubMed Central

Ober, Raimund J.; Tahmasbi, Amir; Ram, Sripad; Lin, Zhiping; Ward, E. Sally

2015-01-01

Single molecule microscopy is a relatively new optical microscopy technique that allows the detection of individual molecules such as proteins in a cellular context. This technique has generated significant interest among biologists, biophysicists and biochemists, as it holds the promise to provide novel insights into subcellular processes and structures that otherwise cannot be gained through traditional experimental approaches. Single molecule experiments place stringent demands on experimental and algorithmic tools due to the low signal levels and the presence of significant extraneous noise sources. Consequently, this has necessitated the use of advanced statistical signal and image processing techniques for the design and analysis of single molecule experiments. In this tutorial paper, we provide an overview of single molecule microscopy from early works to current applications and challenges. Specific emphasis will be on the quantitative aspects of this imaging modality, in particular single molecule localization and resolvability, which will be discussed from an information theoretic perspective. We review the stochastic framework for image formation, different types of estimation techniques and expressions for the Fisher information matrix. We also discuss several open problems in the field that demand highly non-trivial signal processing algorithms. PMID:26167102

[Colonization of Porphyromonas endodontalis in primary and secondary endodontic infections].

PubMed

Hong, Li; Hai, Ji; Yan-Yan, He; Shenghui, Yang; Benxiang, Hou

2015-02-01

This study aims to assess and compare the prevalence of Porphyromonas endodontalis (P. endodontalis) in root canals associated with primary and secondary endodontic infections by using 16s rDNA PCR and real-time fluorescence quantitative polymerase chain reaction (RTFQ-PCR). A total of 120 adult patients with one radiographically documented periapical lesion were included. Sixty teeth presented with primary endodontic infections and 60 with secondary endodontic infections requiring retreatment. P. endodontalis was identified by using 16s rDNA PCR techniques. The positive DNA expression of P. endodontalis in two types of infected root canals were quantitatively compared by using SYBR GREEN I RTFQ-PCR. The prevalence of P. endodontalis in the root canals with primary endodontic infections was significantly higher than that in root canals with secondary endodontic infections (P = 0.001). However, RTFQ-PCR results showed no significant difference in DNA expression quantities between the primary and secondary endodontic infections root canals (P = 0.303). P. endodontalis is more highly associated with root canals having primary endodontic infections, although P. endodontalis colonize in both root canals with primary and secondary chronic apical periodontitis.

Quantitation of heat-shock proteins in clinical samples using mass spectrometry.

PubMed

Kaur, Punit; Asea, Alexzander

2011-01-01

Mass spectrometry (MS) is a powerful analytical tool for proteomics research and drug and biomarker discovery. MS enables identification and quantification of known and unknown compounds by revealing their structural and chemical properties. Proper sample preparation for MS-based analysis is a critical step in the proteomics workflow because the quality and reproducibility of sample extraction and preparation for downstream analysis significantly impact the separation and identification capabilities of mass spectrometers. The highly expressed proteins represent potential biomarkers that could aid in diagnosis, therapy, or drug development. Because the proteome is so complex, there is no one standard method for preparing protein samples for MS analysis. Protocols differ depending on the type of sample, source, experiment, and method of analysis. Molecular chaperones play significant roles in almost all biological functions due to their capacity for detecting intracellular denatured/unfolded proteins, initiating refolding or denaturation of such malfolded protein sequences and more recently for their role in the extracellular milieu as chaperokines. In this chapter, we describe the latest techniques for quantitating the expression of molecular chaperones in human clinical samples.

Effect of Intensive Statin Therapy on Coronary High-Intensity Plaques Detected by Noncontrast T1-Weighted Imaging: The AQUAMARINE Pilot Study.

PubMed

Noguchi, Teruo; Tanaka, Atsushi; Kawasaki, Tomohiro; Goto, Yoichi; Morita, Yoshiaki; Asaumi, Yasuhide; Nakao, Kazuhiro; Fujiwara, Reiko; Nishimura, Kunihiro; Miyamoto, Yoshihiro; Ishihara, Masaharu; Ogawa, Hisao; Koga, Nobuhiko; Narula, Jagat; Yasuda, Satoshi

2015-07-21

Coronary high-intensity plaques detected by noncontrast T1-weighted imaging may represent plaque instability. High-intensity plaques can be quantitatively assessed by a plaque-to-myocardium signal-intensity ratio (PMR). This pilot, hypothesis-generating study sought to investigate whether intensive statin therapy would lower PMR. Prospective serial noncontrast T1-weighted magnetic resonance imaging and computed tomography angiography were performed in 48 patients with coronary artery disease at baseline and after 12 months of intensive pitavastatin treatment with a target low-density lipoprotein cholesterol level <80 mg/dl. The control group consisted of coronary artery disease patients not treated with statins that were matched by propensity scoring (n = 48). The primary endpoint was the 12-month change in PMR. Changes in computed tomography angiography parameters and high-sensitivity C-reactive protein levels were analyzed. In the statin group, 12 months of statin therapy significantly improved low-density lipoprotein cholesterol levels (125 to 70 mg/dl; p < 0.001), PMR (1.38 to 1.11, an 18.9% reduction; p < 0.001), low-attenuation plaque volume, and the percentage of total atheroma volume on computed tomography. In the control group, the PMR increased significantly (from 1.22 to 1.49, a 19.2% increase; p < 0.001). Changes in PMR were correlated with changes in low-density lipoprotein cholesterol (r = 0.533; p < 0.001), high-sensitivity C-reactive protein (r = 0.347; p < 0.001), percentage of atheroma volume (r = 0.477; p < 0.001), and percentage of low-attenuation plaque volume (r = 0.416; p < 0.001). Statin treatment significantly reduced the PMR of high-intensity plaques. Noncontrast T1-weighted magnetic resonance imaging could become a useful technique for repeated quantitative assessment of plaque composition. (Attempts at Plaque Vulnerability Quantification with Magnetic Resonance Imaging Using Noncontrast T1-weighted Technique [AQUAMARINE]; UMIN000003567). Copyright © 2015 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells.

PubMed

Park, Han Sang; Rinehart, Matthew T; Walzer, Katelyn A; Chi, Jen-Tsan Ashley; Wax, Adam

2016-01-01

Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection without staining or expert analysis.

CpG island methylator phenotype (CIMP) of colorectal cancer is best characterised by quantitative DNA methylation analysis and prospective cohort studies.

PubMed

Ogino, S; Cantor, M; Kawasaki, T; Brahmandam, M; Kirkner, G J; Weisenberger, D J; Campan, M; Laird, P W; Loda, M; Fuchs, C S

2006-07-01

The concept of CpG island methylator phenotype (CIMP) is not universally accepted. Even if specific clinicopathological features have been associated with CIMP, investigators often failed to demonstrate a bimodal distribution of the number of methylated markers, which would suggest CIMP as a distinct subtype of colorectal cancer. Previous studies primarily used methylation specific polymerase chain reaction which might detect biologically insignificant low levels of methylation. To demonstrate a distinct genetic profile of CIMP colorectal cancer using quantitative DNA methylation analysis that can distinguish high from low levels of DNA methylation. We developed quantitative real time polymerase chain reaction (MethyLight) assays and measured DNA methylation (percentage of methylated reference) of five carefully selected loci (promoters of CACNA1G, CDKN2A (p16), CRABP1, MLH1, and NEUROG1) in 460 colorectal cancers from large prospective cohorts. There was a clear bimodal distribution of 80 microsatellite instability-high (MSI-H) tumours according to the number of methylated promoters, with no tumours showing 3/5 methylated loci. Thus we defined CIMP as having >or=4/5 methylated loci, and 17% (78) of the 460 tumours were classified as CIMP. CIMP was significantly associated with female sex, MSI, BRAF mutations, and wild-type KRAS. Both CIMP MSI-H tumours and CIMP microsatellite stable (MSS) tumours showed much higher frequencies of BRAF mutations (63% and 54%) than non-CIMP counterparts (non-CIMP MSI-H (0%, p<10(-5)) and non-CIMP MSS tumours (6.6%, p<10(-4)), respectively). CIMP is best characterised by quantitative DNA methylation analysis. CIMP is a distinct epigenotype of colorectal cancer and may be less frequent than previously reported.

The Metabotropic Glutamate Receptor Subtype 5 (mGluR5) Mediates Sensitivity to the Sedative Properties of Ethanol

PubMed Central

Downing, Chris; Marks, Michael J.; Larson, Colin; Johnson, Thomas E.

2010-01-01

Objective Inbred Long-Sleep and Short-Sleep mice (ILS and ISS) were selectively bred for differential sensitivity to the sedative effects of ethanol. Lines of mice derived from these progenitors have been used to identify several Quantitative Trait Loci (QTLs) mediating Loss Of the Righting reflex due to Ethanol (LORE). The present study investigated mGluR5 as a candidate gene underlying Lore7, a QTL mediating differential LORE sensitivity. Methods We used knockout mice, a quantitative complementation test, pharmacological antagonism of mGluR5, real-time quantitative PCR, radioligand binding, DNA sequencing and bioinformatics to examine the role of mGluR5 in ethanol-induced sedation. Results mGluR5 knockout mice had a significantly longer LORE duration than wild-type controls. Administration of the mGluR5 antagonist 2-methyl-6-(phenylethyl)-pyridine (MPEP) had differential effects on LORE in ILS and ISS mice. A quantitative complementation test also supported mGluR5 mediating LORE. Two intronic single-nucleotide polymorphisms in mGluR5 were highly correlated with LORE in recombinant inbred mice derived from a cross between ILS and ISS (LXS RIs). Differences in mGluR5 mRNA level and receptor density were observed between ILS and ISS in distinct brain regions. Finally, data from WebQTL showed that mGluR5 expression was highly correlated with several LORE phenotypes in the LXS RIs. Conclusions Taken together, this data provides convincing evidence that mGluR5 mediates differential sensitivity to the sedative effects of ethanol. Studies from the human literature have also identified MGLUR5 as a potential candidate gene for ethanol sensitivity. PMID:20657349

Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells

PubMed Central

Park, Han Sang; Rinehart, Matthew T.; Walzer, Katelyn A.; Chi, Jen-Tsan Ashley; Wax, Adam

2016-01-01

Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection without staining or expert analysis. PMID:27636719

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform

NASA Astrophysics Data System (ADS)

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-11-01

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05839b

Impact of reconstruction parameters on quantitative I-131 SPECT

NASA Astrophysics Data System (ADS)

van Gils, C. A. J.; Beijst, C.; van Rooij, R.; de Jong, H. W. A. M.

2016-07-01

Radioiodine therapy using I-131 is widely used for treatment of thyroid disease or neuroendocrine tumors. Monitoring treatment by accurate dosimetry requires quantitative imaging. The high energy photons however render quantitative SPECT reconstruction challenging, potentially requiring accurate correction for scatter and collimator effects. The goal of this work is to assess the effectiveness of various correction methods on these effects using phantom studies. A SPECT/CT acquisition of the NEMA IEC body phantom was performed. Images were reconstructed using the following parameters: (1) without scatter correction, (2) with triple energy window (TEW) scatter correction and (3) with Monte Carlo-based scatter correction. For modelling the collimator-detector response (CDR), both (a) geometric Gaussian CDRs as well as (b) Monte Carlo simulated CDRs were compared. Quantitative accuracy, contrast to noise ratios and recovery coefficients were calculated, as well as the background variability and the residual count error in the lung insert. The Monte Carlo scatter corrected reconstruction method was shown to be intrinsically quantitative, requiring no experimentally acquired calibration factor. It resulted in a more accurate quantification of the background compartment activity density compared with TEW or no scatter correction. The quantification error relative to a dose calibrator derived measurement was found to be  <1%,-26% and 33%, respectively. The adverse effects of partial volume were significantly smaller with the Monte Carlo simulated CDR correction compared with geometric Gaussian or no CDR modelling. Scatter correction showed a small effect on quantification of small volumes. When using a weighting factor, TEW correction was comparable to Monte Carlo reconstruction in all measured parameters, although this approach is clinically impractical since this factor may be patient dependent. Monte Carlo based scatter correction including accurately simulated CDR modelling is the most robust and reliable method to reconstruct accurate quantitative iodine-131 SPECT images.

Mammographic features and subsequent risk of breast cancer: a comparison of qualitative and quantitative evaluations in the Guernsey prospective studies.

PubMed

Torres-Mejía, Gabriela; De Stavola, Bianca; Allen, Diane S; Pérez-Gavilán, Juan J; Ferreira, Jorge M; Fentiman, Ian S; Dos Santos Silva, Isabel

2005-05-01

Mammographic features are known to be associated with breast cancer but the magnitude of the effect differs markedly from study to study. Methods to assess mammographic features range from subjective qualitative classifications to computer-automated quantitative measures. We used data from the UK Guernsey prospective studies to examine the relative value of these methods in predicting breast cancer risk. In all, 3,211 women ages > or =35 years who had a mammogram taken in 1986 to 1989 were followed-up to the end of October 2003, with 111 developing breast cancer during this period. Mammograms were classified using the subjective qualitative Wolfe classification and several quantitative mammographic features measured using computer-based techniques. Breast cancer risk was positively associated with high-grade Wolfe classification, percent breast density and area of dense tissue, and negatively associated with area of lucent tissue, fractal dimension, and lacunarity. Inclusion of the quantitative measures in the same model identified area of dense tissue and lacunarity as the best predictors of breast cancer, with risk increasing by 59% [95% confidence interval (95% CI), 29-94%] per SD increase in total area of dense tissue but declining by 39% (95% CI, 53-22%) per SD increase in lacunarity, after adjusting for each other and for other confounders. Comparison of models that included both the qualitative Wolfe classification and these two quantitative measures to models that included either the qualitative or the two quantitative variables showed that they all made significant contributions to prediction of breast cancer risk. These findings indicate that breast cancer risk is affected not only by the amount of mammographic density but also by the degree of heterogeneity of the parenchymal pattern and, presumably, by other features captured by the Wolfe classification.

Development of CD3 cell quantitation algorithms for renal allograft biopsy rejection assessment utilizing open source image analysis software.

PubMed

Moon, Andres; Smith, Geoffrey H; Kong, Jun; Rogers, Thomas E; Ellis, Carla L; Farris, Alton B Brad

2018-02-01

Renal allograft rejection diagnosis depends on assessment of parameters such as interstitial inflammation; however, studies have shown interobserver variability regarding interstitial inflammation assessment. Since automated image analysis quantitation can be reproducible, we devised customized analysis methods for CD3+ T-cell staining density as a measure of rejection severity and compared them with established commercial methods along with visual assessment. Renal biopsy CD3 immunohistochemistry slides (n = 45), including renal allografts with various degrees of acute cellular rejection (ACR) were scanned for whole slide images (WSIs). Inflammation was quantitated in the WSIs using pathologist visual assessment, commercial algorithms (Aperio nuclear algorithm for CD3+ cells/mm 2 and Aperio positive pixel count algorithm), and customized open source algorithms developed in ImageJ with thresholding/positive pixel counting (custom CD3+%) and identification of pixels fulfilling "maxima" criteria for CD3 expression (custom CD3+ cells/mm 2 ). Based on visual inspections of "markup" images, CD3 quantitation algorithms produced adequate accuracy. Additionally, CD3 quantitation algorithms correlated between each other and also with visual assessment in a statistically significant manner (r = 0.44 to 0.94, p = 0.003 to < 0.0001). Methods for assessing inflammation suggested a progression through the tubulointerstitial ACR grades, with statistically different results in borderline versus other ACR types, in all but the custom methods. Assessment of CD3-stained slides using various open source image analysis algorithms presents salient correlations with established methods of CD3 quantitation. These analysis techniques are promising and highly customizable, providing a form of on-slide "flow cytometry" that can facilitate additional diagnostic accuracy in tissue-based assessments.

A Pilot Study of the Noninvasive Assessment of the Lung Microbiota as a Potential Tool for the Early Diagnosis of Ventilator-Associated Pneumonia

PubMed Central

Brady, Jacob S.; Romano-Keeler, Joann; Drake, Wonder P.; Norris, Patrick R.; Jenkins, Judith M.; Isaacs, Richard J.; Boczko, Erik M.

2015-01-01

BACKGROUND: Ventilator-associated pneumonia (VAP) remains a common complication in critically ill surgical patients, and its diagnosis remains problematic. Exhaled breath contains aerosolized droplets that reflect the lung microbiota. We hypothesized that exhaled breath condensate fluid (EBCF) in hygroscopic condenser humidifier/heat and moisture exchanger (HCH/HME) filters would contain bacterial DNA that qualitatively and quantitatively correlate with pathogens isolated from quantitative BAL samples obtained for clinical suspicion of pneumonia. METHODS: Forty-eight adult patients who were mechanically ventilated and undergoing quantitative BAL (n = 51) for suspected pneumonia in the surgical ICU were enrolled. Per protocol, patients fulfilling VAP clinical criteria undergo quantitative BAL bacterial culture. Immediately prior to BAL, time-matched HCH/HME filters were collected for study of EBCF by real-time polymerase chain reaction. Additionally, convenience samples of serially collected filters in patients with BAL-diagnosed VAP were analyzed. RESULTS: Forty-nine of 51 time-matched EBCF/BAL fluid samples were fully concordant (concordance > 95% by κ statistic) relative to identified pathogens and strongly correlated with clinical cultures. Regression analysis of quantitative bacterial DNA in paired samples revealed a statistically significant positive correlation (r = 0.85). In a convenience sample, qualitative and quantitative polymerase chain reaction analysis of serial HCH/HME samples for bacterial DNA demonstrated an increase in load that preceded the suspicion of pneumonia. CONCLUSIONS: Bacterial DNA within EBCF demonstrates a high correlation with BAL fluid and clinical cultures. Bacterial DNA within EBCF increases prior to the suspicion of pneumonia. Further study of this novel approach may allow development of a noninvasive tool for the early diagnosis of VAP. PMID:25474571

Quantitative assessment of skin, hair, and iris variation in a diverse sample of individuals and associated genetic variation.

PubMed

Norton, Heather L; Edwards, Melissa; Krithika, S; Johnson, Monique; Werren, Elizabeth A; Parra, Esteban J

2016-08-01

The main goals of this study are to 1) quantitatively measure skin, hair, and iris pigmentation in a diverse sample of individuals, 2) describe variation within and between these samples, and 3) demonstrate how quantitative measures can facilitate genotype-phenotype association tests. We quantitatively characterize skin, hair, and iris pigmentation using the Melanin (M) Index (skin) and CIELab values (hair) in 1,450 individuals who self-identify as African American, East Asian, European, Hispanic, or South Asian. We also quantify iris pigmentation in a subset of these individuals using CIELab values from high-resolution iris photographs. We compare mean skin M index and hair and iris CIELab values among populations using ANOVA and MANOVA respectively and test for genotype-phenotype associations in the European sample. All five populations are significantly different for skin (P <2 × 10(-16) ) and hair color (P <2 × 10(-16) ). Our quantitative analysis of iris and hair pigmentation reinforces the continuous, rather than discrete, nature of these traits. We confirm the association of three loci (rs16891982, rs12203592, and rs12913832) with skin pigmentation and four loci (rs12913832, rs12203592, rs12896399, and rs16891982) with hair pigmentation. Interestingly, the derived rs12203592 T allele located within the IRF4 gene is associated with lighter skin but darker hair color. The quantitative methods used here provide a fine-scale assessment of pigmentation phenotype and facilitate genotype-phenotype associations, even with relatively small sample sizes. This represents an important expansion of current investigations into pigmentation phenotype and associated genetic variation by including non-European and admixed populations. Am J Phys Anthropol 160:570-581, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

MR morphology of triangular fibrocartilage complex: correlation with quantitative MR and biomechanical properties.

PubMed

Bae, Won C; Ruangchaijatuporn, Thumanoon; Chang, Eric Y; Biswas, Reni; Du, Jiang; Statum, Sheronda; Chung, Christine B

2016-04-01

To evaluate pathology of the triangular fibrocartilage complex (TFCC) using high-resolution morphologic magnetic resonance (MR) imaging, and compare with quantitative MR and biomechanical properties. Five cadaveric wrists (22-70 years) were imaged at 3 T using morphologic (proton density weighted spin echo, PD FS, and 3D spoiled gradient echo, 3D SPGR) and quantitative MR sequences to determine T2 and T1rho properties. In eight geographic regions, morphology of TFC disc and laminae were evaluated for pathology and quantitative MR values. Samples were disarticulated and biomechanical indentation testing was performed on the distal surface of the TFC disc. On morphologic PD SE images, TFC disc pathology included degeneration and tears, while that of the laminae included degeneration, degeneration with superimposed tear, mucinous transformation, and globular calcification. Punctate calcifications were highly visible on 3D SPGR images and found only in pathologic regions. Disc pathology occurred more frequently in proximal regions of the disc than distal regions. Quantitative MR values were lowest in normal samples, and generally higher in pathologic regions. Biomechanical testing demonstrated an inverse relationship, with indentation modulus being high in normal regions with low MR values. The laminae studied were mostly pathologic, and additional normal samples are needed to discern quantitative changes. These results show technical feasibility of morphologic MR, quantitative MR, and biomechanical techniques to characterize pathology of the TFCC. Quantitative MRI may be a suitable surrogate marker of soft tissue mechanical properties, and a useful adjunct to conventional morphologic MR techniques.

Gene expression in developing watermelon fruit

PubMed Central

Wechter, W Patrick; Levi, Amnon; Harris, Karen R; Davis, Angela R; Fei, Zhangjun; Katzir, Nurit; Giovannoni, James J; Salman-Minkov, Ayelet; Hernandez, Alvaro; Thimmapuram, Jyothi; Tadmor, Yaakov; Portnoy, Vitaly; Trebitsh, Tova

2008-01-01

Background Cultivated watermelon form large fruits that are highly variable in size, shape, color, and content, yet have extremely narrow genetic diversity. Whereas a plethora of genes involved in cell wall metabolism, ethylene biosynthesis, fruit softening, and secondary metabolism during fruit development and ripening have been identified in other plant species, little is known of the genes involved in these processes in watermelon. A microarray and quantitative Real-Time PCR-based study was conducted in watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] in order to elucidate the flow of events associated with fruit development and ripening in this species. RNA from three different maturation stages of watermelon fruits, as well as leaf, were collected from field grown plants during three consecutive years, and analyzed for gene expression using high-density photolithography microarrays and quantitative PCR. Results High-density photolithography arrays, composed of probes of 832 EST-unigenes from a subtracted, fruit development, cDNA library of watermelon were utilized to examine gene expression at three distinct time-points in watermelon fruit development. Analysis was performed with field-grown fruits over three consecutive growing seasons. Microarray analysis identified three hundred and thirty-five unique ESTs that are differentially regulated by at least two-fold in watermelon fruits during the early, ripening, or mature stage when compared to leaf. Of the 335 ESTs identified, 211 share significant homology with known gene products and 96 had no significant matches with any database accession. Of the modulated watermelon ESTs related to annotated genes, a significant number were found to be associated with or involved in the vascular system, carotenoid biosynthesis, transcriptional regulation, pathogen and stress response, and ethylene biosynthesis. Ethylene bioassays, performed with a closely related watermelon genotype with a similar phenotype, i.e. seeded, bright red flesh, dark green rind, etc., determined that ethylene levels were highest during the green fruit stage followed by a decrease during the white and pink fruit stages. Additionally, quantitative Real-Time PCR was used to validate modulation of 127 ESTs that were differentially expressed in developing and ripening fruits based on array analysis. Conclusion This study identified numerous ESTs with putative involvement in the watermelon fruit developmental and ripening process, in particular the involvement of the vascular system and ethylene. The production of ethylene during fruit development in watermelon gives further support to the role of ethylene in fruit development in non-climacteric fruits. PMID:18534026

Effect of oral monthly ibandronate on bone microarchitecture in women with osteopenia-a randomized placebo-controlled trial.

PubMed

Chapurlat, R D; Laroche, M; Thomas, T; Rouanet, S; Delmas, P D; de Vernejoul, M-C

2013-01-01

We have examined the effect of oral monthly ibandronate on distal radius and tibia microarchitecture with high-resolution peripheral quantitative tomography compared with placebo, in women with osteopenia, and found that ibandronate did not significantly affect trabecular bone but improved cortical density and thickness at the tibia. We have examined the effect of ibandronate on bone microarchitecture with peripheral high-resolution quantitative computed tomography (HR-pQCT) in a randomized placebo-controlled trial among 148 women with osteopenia. Patients received either oral 150 mg monthly ibandronate or placebo over 24 months. Bone microarchitecture was assessed at baseline, 6, 12, and 24 months, using HR-pQCT at the distal radius and tibia; areal bone mineral density (aBMD) was measured with DXA at the spine, hip, and radius. At 12 months, there was no significant difference in trabecular bone volume at the radius (the primary end point) between women on ibandronate (10.8 ± 2.5%) and placebo (10.5 ± 2.9%), p = 0.25. There was no significant difference in other radius trabecular and cortical microarchitecture parameters at 12 and 24 months. In contrast, at the tibia, cortical vBMD in the ibandronate group was significantly greater than in the placebo group at 6, 12, and 24 months, with better cortical thickness at 6, 12, and 24 months. With ibandronate, aBMD was significantly increased at the hip and spine at 12 and 24 months but at the radius was significantly superior to placebo only at 24 months. Most of the adverse events related to ibandronate were expected with bisphosphonate use, and none of them were serious. We conclude that 12 months of treatment with ibandronate in women with osteopenia did not affect trabecular bone microarchitecture, but improved cortical vBMD at the tibia at 12 and 24 months, and preserved cortical thickness at the tibia.

Design of cinnamaldehyde amino acid Schiff base compounds based on the quantitative structure-activity relationship.

PubMed

Wang, Hui; Jiang, Mingyue; Li, Shujun; Hse, Chung-Yun; Jin, Chunde; Sun, Fangli; Li, Zhuo

2017-09-01

Cinnamaldehyde amino acid Schiff base (CAAS) is a new class of safe, bioactive compounds which could be developed as potential antifungal agents for fungal infections. To design new cinnamaldehyde amino acid Schiff base compounds with high bioactivity, the quantitative structure-activity relationships (QSARs) for CAAS compounds against Aspergillus niger ( A. niger ) and Penicillium citrinum (P. citrinum) were analysed. The QSAR models ( R 2  = 0.9346 for A. niger , R 2  = 0.9590 for P. citrinum, ) were constructed and validated. The models indicated that the molecular polarity and the Max atomic orbital electronic population had a significant effect on antifungal activity. Based on the best QSAR models, two new compounds were designed and synthesized. Antifungal activity tests proved that both of them have great bioactivity against the selected fungi.

Intravital microscopy of biosensor activities and intrinsic metabolic states

PubMed Central

Winfree, Seth; Hato, Takashi; Day, Richard N.

2018-01-01

Intravital microscopy (IVM) is an imaging tool that is capable of detecting subcellular signaling or metabolic events as they occur in tissues in the living animal. Imaging in highly scattering biological tissues, however, is challenging because of the attenuation of signal in images acquired at increasing depths. Depth-dependent signal attenuation is the major impediment to IVM, limiting the depth from which significant data can be obtained. Therefore, making quantitative measurements by IVM requires methods that use internal calibration, or alternatively, a completely different way of evaluating the signals. Here, we describe how ratiometric imaging of genetically encoded biosensor probes can be used to make quantitative measurements of changes in the activity of cell signaling pathways. Then, we describe how fluorescence lifetime imaging can be used for label-free measurements of the metabolic states of cells within the living animal. PMID:28434902

Two-dimensional auto-correlation analysis and Fourier-transform analysis of second-harmonic-generation image for quantitative analysis of collagen fiber in human facial skin

NASA Astrophysics Data System (ADS)

Ogura, Yuki; Tanaka, Yuji; Hase, Eiji; Yamashita, Toyonobu; Yasui, Takeshi

2018-02-01

We compare two-dimensional auto-correlation (2D-AC) analysis and two-dimensional Fourier transform (2D-FT) for evaluation of age-dependent structural change of facial dermal collagen fibers caused by intrinsic aging and extrinsic photo-aging. The age-dependent structural change of collagen fibers for female subjects' cheek skin in their 20s, 40s, and 60s were more noticeably reflected in 2D-AC analysis than in 2D-FT analysis. Furthermore, 2D-AC analysis indicated significantly higher correlation with the skin elasticity measured by Cutometer® than 2D-AC analysis. 2D-AC analysis of SHG image has a high potential for quantitative evaluation of not only age-dependent structural change of collagen fibers but also skin elasticity.

Computational modeling of brain tumors: discrete, continuum or hybrid?

NASA Astrophysics Data System (ADS)

Wang, Zhihui; Deisboeck, Thomas S.

In spite of all efforts, patients diagnosed with highly malignant brain tumors (gliomas), continue to face a grim prognosis. Achieving significant therapeutic advances will also require a more detailed quantitative understanding of the dynamic interactions among tumor cells, and between these cells and their biological microenvironment. Data-driven computational brain tumor models have the potential to provide experimental tumor biologists with such quantitative and cost-efficient tools to generate and test hypotheses on tumor progression, and to infer fundamental operating principles governing bidirectional signal propagation in multicellular cancer systems. This review highlights the modeling objectives of and challenges with developing such in silico brain tumor models by outlining two distinct computational approaches: discrete and continuum, each with representative examples. Future directions of this integrative computational neuro-oncology field, such as hybrid multiscale multiresolution modeling are discussed.

Computational modeling of brain tumors: discrete, continuum or hybrid?

NASA Astrophysics Data System (ADS)

Wang, Zhihui; Deisboeck, Thomas S.

2008-04-01

In spite of all efforts, patients diagnosed with highly malignant brain tumors (gliomas), continue to face a grim prognosis. Achieving significant therapeutic advances will also require a more detailed quantitative understanding of the dynamic interactions among tumor cells, and between these cells and their biological microenvironment. Data-driven computational brain tumor models have the potential to provide experimental tumor biologists with such quantitative and cost-efficient tools to generate and test hypotheses on tumor progression, and to infer fundamental operating principles governing bidirectional signal propagation in multicellular cancer systems. This review highlights the modeling objectives of and challenges with developing such in silicobrain tumor models by outlining two distinct computational approaches: discrete and continuum, each with representative examples. Future directions of this integrative computational neuro-oncology field, such as hybrid multiscale multiresolution modeling are discussed.

Spacecraft Complexity Subfactors and Implications on Future Cost Growth

NASA Technical Reports Server (NTRS)

Leising, Charles J.; Wessen, Randii; Ellyin, Ray; Rosenberg, Leigh; Leising, Adam

2013-01-01

During the last ten years the Jet Propulsion Laboratory has used a set of cost-risk subfactors to independently estimate the magnitude of development risks that may not be covered in the high level cost models employed during early concept development. Within the last several years the Laboratory has also developed a scale of Concept Maturity Levels with associated criteria to quantitatively assess a concept's maturity. This latter effort has been helpful in determining whether a concept is mature enough for accurate costing but it does not provide any quantitative estimate of cost risk. Unfortunately today's missions are significantly more complex than when the original cost-risk subfactors were first formulated. Risks associated with complex missions are not being adequately evaluated and future cost growth is being underestimated. The risk subfactor process needed to be updated.

Numeracy and the Persuasive Effect of Policy Information and Party Cues

PubMed Central

Mérola, Vittorio; Hitt, Matthew P.

2016-01-01

Numeric political appeals represent a prevalent but overlooked domain of public opinion research. When can quantitative information change political attitudes, and is this change trumped by partisan effects? We analyze how numeracy—or individual differences in citizens’ ability to process and apply numeric policy information—moderates the effectiveness of numeric political appeals on a moderately salient policy issue. Results show that those low in numeracy exhibit a strong party-cue effect, treating numeric information in a superficial and heuristic fashion. Conversely, those high in numeracy are persuaded by numeric information, even when it is sponsored by the opposing party, overcoming the party-cue effect. Our results make clear that overlooking numeric ability when analyzing quantitative political appeals can mask significant persuasion effects, and we build on recent work advancing the understanding of individual differences in public opinion. PMID:27274578

Phosphoproteins in extracellular vesicles as candidate markers for breast cancer

PubMed Central

Chen, I-Hsuan; Xue, Liang; Hsu, Chuan-Chih; Paez, Juan Sebastian Paez; Pan, Li; Andaluz, Hillary; Wendt, Michael K.; Iliuk, Anton B.; Tao, W. Andy

2017-01-01

The state of protein phosphorylation can be a key determinant of cellular physiology such as early-stage cancer, but the development of phosphoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate a strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer compared with healthy controls. Several biomarkers were validated in individual patients using paralleled reaction monitoring for targeted quantitation. This study demonstrates that the development of phosphoproteins in plasma EV as disease biomarkers is highly feasible and may transform cancer screening and monitoring. PMID:28270605

Phosphoproteins in extracellular vesicles as candidate markers for breast cancer.

PubMed

Chen, I-Hsuan; Xue, Liang; Hsu, Chuan-Chih; Paez, Juan Sebastian Paez; Pan, Li; Andaluz, Hillary; Wendt, Michael K; Iliuk, Anton B; Zhu, Jian-Kang; Tao, W Andy

2017-03-21

The state of protein phosphorylation can be a key determinant of cellular physiology such as early-stage cancer, but the development of phosphoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate a strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer compared with healthy controls. Several biomarkers were validated in individual patients using paralleled reaction monitoring for targeted quantitation. This study demonstrates that the development of phosphoproteins in plasma EV as disease biomarkers is highly feasible and may transform cancer screening and monitoring.

Exploring Nurse Faculty Incivility and Resonant Leadership.

PubMed

Casale, Katherine R

The purpose of this quantitative correlational study was to explore the relationship between the frequency of interfaculty incivility among nurses in academia and observed levels of resonant leadership of immediate supervisors. Despite mandates to address incivility in health care, nurse faculty report high levels of horizontal incivility among their peers. No known quantitative research has measured the relationship between nurse faculty-to-faculty incivility and resonant leadership traits of leaders. Nursing faculty from 17 universities (n = 260) were emailed an anonymous link to answer survey questions about horizontal peer incivility and leaders' management styles. There was a significant inverse relationship (Pearson's r, -.560) between the frequency of experienced faculty-to-faculty incivility and the level of observed resonant leadership behaviors of participants' immediate supervisors. Resonant supervisory behaviors inversely correlated with nurse faculty peer incivility, with potential to impact satisfaction, recruitment, and retention.

Design of cinnamaldehyde amino acid Schiff base compounds based on the quantitative structure–activity relationship

PubMed Central

Wang, Hui; Jiang, Mingyue; Hse, Chung-Yun; Jin, Chunde; Sun, Fangli; Li, Zhuo

2017-01-01

Cinnamaldehyde amino acid Schiff base (CAAS) is a new class of safe, bioactive compounds which could be developed as potential antifungal agents for fungal infections. To design new cinnamaldehyde amino acid Schiff base compounds with high bioactivity, the quantitative structure–activity relationships (QSARs) for CAAS compounds against Aspergillus niger (A. niger) and Penicillium citrinum (P. citrinum) were analysed. The QSAR models (R2 = 0.9346 for A. niger, R2 = 0.9590 for P. citrinum,) were constructed and validated. The models indicated that the molecular polarity and the Max atomic orbital electronic population had a significant effect on antifungal activity. Based on the best QSAR models, two new compounds were designed and synthesized. Antifungal activity tests proved that both of them have great bioactivity against the selected fungi. PMID:28989758

Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.).

PubMed

Zhang, Zhen; Shang, Haihong; Shi, Yuzhen; Huang, Long; Li, Junwen; Ge, Qun; Gong, Juwu; Liu, Aiying; Chen, Tingting; Wang, Dan; Wang, Yanling; Palanga, Koffi Kibalou; Muhammad, Jamshed; Li, Weijie; Lu, Quanwei; Deng, Xiaoying; Tan, Yunna; Song, Weiwu; Cai, Juan; Li, Pengtao; Rashid, Harun or; Gong, Wankui; Yuan, Youlu

2016-04-11

Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.

Developing High-Frequency Quantitative Ultrasound Techniques to Characterize Three-Dimensional Engineered Tissues

NASA Astrophysics Data System (ADS)

Mercado, Karla Patricia E.

Tissue engineering holds great promise for the repair or replacement of native tissues and organs. Further advancements in the fabrication of functional engineered tissues are partly dependent on developing new and improved technologies to monitor the properties of engineered tissues volumetrically, quantitatively, noninvasively, and nondestructively over time. Currently, engineered tissues are evaluated during fabrication using histology, biochemical assays, and direct mechanical tests. However, these techniques destroy tissue samples and, therefore, lack the capability for real-time, longitudinal monitoring. The research reported in this thesis developed nondestructive, noninvasive approaches to characterize the structural, biological, and mechanical properties of 3-D engineered tissues using high-frequency quantitative ultrasound and elastography technologies. A quantitative ultrasound technique, using a system-independent parameter known as the integrated backscatter coefficient (IBC), was employed to visualize and quantify structural properties of engineered tissues. Specifically, the IBC was demonstrated to estimate cell concentration and quantitatively detect differences in the microstructure of 3-D collagen hydrogels. Additionally, the feasibility of an ultrasound elastography technique called Single Tracking Location Acoustic Radiation Force Impulse (STL-ARFI) imaging was demonstrated for estimating the shear moduli of 3-D engineered tissues. High-frequency ultrasound techniques can be easily integrated into sterile environments necessary for tissue engineering. Furthermore, these high-frequency quantitative ultrasound techniques can enable noninvasive, volumetric characterization of the structural, biological, and mechanical properties of engineered tissues during fabrication and post-implantation.

Selective Weighted Least Squares Method for Fourier Transform Infrared Quantitative Analysis.

PubMed

Wang, Xin; Li, Yan; Wei, Haoyun; Chen, Xia

2017-06-01

Classical least squares (CLS) regression is a popular multivariate statistical method used frequently for quantitative analysis using Fourier transform infrared (FT-IR) spectrometry. Classical least squares provides the best unbiased estimator for uncorrelated residual errors with zero mean and equal variance. However, the noise in FT-IR spectra, which accounts for a large portion of the residual errors, is heteroscedastic. Thus, if this noise with zero mean dominates in the residual errors, the weighted least squares (WLS) regression method described in this paper is a better estimator than CLS. However, if bias errors, such as the residual baseline error, are significant, WLS may perform worse than CLS. In this paper, we compare the effect of noise and bias error in using CLS and WLS in quantitative analysis. Results indicated that for wavenumbers with low absorbance, the bias error significantly affected the error, such that the performance of CLS is better than that of WLS. However, for wavenumbers with high absorbance, the noise significantly affected the error, and WLS proves to be better than CLS. Thus, we propose a selective weighted least squares (SWLS) regression that processes data with different wavenumbers using either CLS or WLS based on a selection criterion, i.e., lower or higher than an absorbance threshold. The effects of various factors on the optimal threshold value (OTV) for SWLS have been studied through numerical simulations. These studies reported that: (1) the concentration and the analyte type had minimal effect on OTV; and (2) the major factor that influences OTV is the ratio between the bias error and the standard deviation of the noise. The last part of this paper is dedicated to quantitative analysis of methane gas spectra, and methane/toluene mixtures gas spectra as measured using FT-IR spectrometry and CLS, WLS, and SWLS. The standard error of prediction (SEP), bias of prediction (bias), and the residual sum of squares of the errors (RSS) from the three quantitative analyses were compared. In methane gas analysis, SWLS yielded the lowest SEP and RSS among the three methods. In methane/toluene mixture gas analysis, a modification of the SWLS has been presented to tackle the bias error from other components. The SWLS without modification presents the lowest SEP in all cases but not bias and RSS. The modification of SWLS reduced the bias, which showed a lower RSS than CLS, especially for small components.

Quantitative X-ray Differential Interference Contrast Microscopy

NASA Astrophysics Data System (ADS)

Nakamura, Takashi

Full-field soft x-ray microscopes are widely used in many fields of sciences. Advances in nanofabrication technology enabled short wavelength focusing elements with significantly improved spatial resolution. In the soft x-ray spectral region, samples as small as 12 nm can be resolved using micro zone-plates as the objective lens. In addition to conventional x-ray microscopy in which x-ray absorption difference provides the image contrast, phase contrast mechanisms such as differential phase contrast (DIC) and Zernike phase contrast have also been demonstrated These phase contrast imaging mechanisms are especially attractive at the x-ray wavelengths where phase contrast of most materials is typically 10 times stronger than the absorption contrast. With recent progresses in plasma-based x- ray sources and increasing accessibility to synchrotron user facilities, x-ray microscopes are quickly becoming standard measurement equipment in the laboratory. To further the usefulness of x-ray DIC microscopy this thesis explicitly addresses three known issues with this imaging modality by introducing new techniques and devices First, as opposed to its visible-light counterpart, no quantitative phase imaging technique exists for x-ray DIC microscopy. To address this issue, two nanoscale x-ray quantitative phase imaging techniques, using exclusive OR (XOR) patterns and zone-plate doublets, respectively, are proposed. Unlike existing x-ray quantitative phase imaging techniques such as Talbot interferometry and ptychography, no dedicated experimental setups or stringent illumination coherence are needed for quantitative phase retrieval. Second, to the best of our knowledge, no quantitative performance characterization of DIC microscopy exists to date. Therefore the imaging system's response to sample's spatial frequency is not known In order to gain in-depth understanding of this imaging modality, performance of x-ray DIC microscopy is quantified using modulation transfer function. A new illumination apparatus required for the transfer function analysis under partially coherent illumination is also proposed. Such a characterization is essential for a proper selection of DIC optics for various transparent samples under study. Finally, optical elements used for x-ray DIC microscopy are highly absorptive and high brilliance x-ray sources such as synchrotrons are generally needed for image contrast. To extend the use of x-ray DIC microscopy to a wider variety of applications, a high efficiency large numerical aperture optical element consisting of high reflective Bragg reflectors is proposed. Using Bragg reflectors, which have 70% ˜99% reflectivity at extreme ultraviolet and soft x-rays for all angles of glancing incidence, the first order focusing efficiency is expected to increase by ˜ 8 times compared to that of a typical Fresnel zone-plate. This thesis contributes to current nanoscale x-ray phase contrast imaging research and provides new insights for biological, material, and magnetic sciences

A quantitative image cytometry technique for time series or population analyses of signaling networks.

PubMed

Ozaki, Yu-ichi; Uda, Shinsuke; Saito, Takeshi H; Chung, Jaehoon; Kubota, Hiroyuki; Kuroda, Shinya

2010-04-01

Modeling of cellular functions on the basis of experimental observation is increasingly common in the field of cellular signaling. However, such modeling requires a large amount of quantitative data of signaling events with high spatio-temporal resolution. A novel technique which allows us to obtain such data is needed for systems biology of cellular signaling. We developed a fully automatable assay technique, termed quantitative image cytometry (QIC), which integrates a quantitative immunostaining technique and a high precision image-processing algorithm for cell identification. With the aid of an automated sample preparation system, this device can quantify protein expression, phosphorylation and localization with subcellular resolution at one-minute intervals. The signaling activities quantified by the assay system showed good correlation with, as well as comparable reproducibility to, western blot analysis. Taking advantage of the high spatio-temporal resolution, we investigated the signaling dynamics of the ERK pathway in PC12 cells. The QIC technique appears as a highly quantitative and versatile technique, which can be a convenient replacement for the most conventional techniques including western blot, flow cytometry and live cell imaging. Thus, the QIC technique can be a powerful tool for investigating the systems biology of cellular signaling.

Quantitative Analysis of High-Quality Officer Selection by Commandants Career-Level Education Board

DTIC Science & Technology

2017-03-01

due to Marines being evaluated before the end of their initial service commitment. Our research utilizes quantitative variables to analyze the...not provide detailed information why. B. LIMITATIONS The photograph analysis in this research is strictly limited to a quantitative analysis in...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. QUANTITATIVE

Multidisciplinary Biomarkers of Early Mammary Carcinogenesis

DTIC Science & Technology

2011-04-01

cDNA prepared. Quantitative real-time PCR (qRT-PCR) was then performed on the cDNA. All qRT-PCR reactions were performed in triplicate. ESR1 ...in Figure 4, all ER(+) cells express ESR1 at high levels (at least 4 fold higher than ER(-) cell lines). A Pearson correlation coefficient was...calculated to determine the linear relationship between the optical redox ratio and ESR1 expression levels and found to be significant (p = 0.0024, r

Customized Body Mapping to Facilitate the Ergonomic Design of Sportswear.

PubMed

Cao, Mingliang; Li, Yi; Guo, Yueping; Yao, Lei; Pan, Zhigeng

2016-01-01

A successful high-performance sportswear design that considers human factors should result in a significant increase in thermal comfort and reduce energy loss. The authors describe a body-mapping approach that facilitates the effective ergonomic design of sportswear. Their general framework can be customized based on the functional requirements of various sports and sportswear, the desired combination and selection of mapping areas for the human body, and customized quantitative data distribution of target physiological indicators.

Development and application of an instrument for analysis of bone structure on radiographs.

PubMed

Xu, S; Liu, S; Bao, K

1997-01-01

An instrument used for quantitative assessment of trabecular structure of radius on radiograph including trabecular number and trabecular width was developed using a microdensitometer and a single-chip microcomputer. The device is characterized by its high sensitivity, good reproducibility, convenience and economy. The results obtained with the instrument were significantly correlated to actual bone mineral content. This device can be used for the diagnosis of osteoporosis, fluorosis, rickets and bone damages caused by cadmium.

Flow Modulation and Force Control in Insect Fast Maneuver

NASA Astrophysics Data System (ADS)

Li, Chengyu; Dong, Haibo; Zhang, Wen; Gai, Kuo

2012-11-01

In this work, an integrated study combining high-speed photogrammetry and direct numerical simulation (DNS) is used to study free flying insects in fast maneuver. Quantitative measurement has shown the significant differences between quad-winged flyers such as dragonfly and damselfly and two-winged flyers such as cicada. Comparisons of unsteady 3D vortex formation and associated aerodynamic force production reveal the different mechanisms used by insects in fast turn. This work is supported by NSF CBET-1055949.

Flavobacteria Blooms in Four Eutrophic Lakes: Linking Population Dynamics of Freshwater Bacterioplankton to Resource Availability▿ †

PubMed Central

Eiler, Alexander; Bertilsson, Stefan

2007-01-01

Heterotrophic bacteria are major contributors to biogeochemical cycles and influence water quality. Still, the lack of representative isolates and the few quantitative surveys leave the ecological role and significance of single bacterial populations to be revealed. Here we analyzed the diversity and dynamics of freshwater Flavobacteria populations in four eutrophic temperate lakes. From each lake, clone libraries were constructed using primers specific for either the class Flavobacteria or Bacteria. Sequencing of 194 Flavobacteria clones from 8 libraries revealed a diverse freshwater Flavobacteria community and distinct differences among lakes. Abundance and seasonal dynamics of Flavobacteria were assessed by quantitative PCR with class-specific primers. In parallel, the dynamics of individual populations within the Flavobacteria community were assessed with terminal restriction fragment length polymorphism analysis using identical primers. The contribution of Flavobacteria to the total bacterioplankton community ranged from 0.4 to almost 100% (average, 24%). Blooms where Flavobacteria represented more than 30% of the bacterioplankton were observed at different times in the four lakes. In general, high proportions of Flavobacteria appeared during episodes of high bacterial production. Phylogenetic analyses combined with Flavobacteria community fingerprints suggested dominance of two Flavobacteria lineages. Both drastic alterations in total Flavobacteria and in community composition of this class significantly correlated with bacterial production, emphasizing that resource availability is an important driver of heterotrophic bacterial succession in eutrophic lakes. PMID:17435002

Quantitative monitoring of lipid accumulation over time in cultured adipocytes as function of culture conditions: toward controlled adipose tissue engineering.

PubMed

Or-Tzadikario, Shira; Sopher, Ran; Gefen, Amit

2010-10-01

Adipose tissue engineering is investigated for native fat substitutes and wound healing model systems. Research and clinical applications of bioartificial fat require a quantitative and objective method to continuously measure adipogenesis in living cultures as opposed to currently used culture-destructive techniques that stain lipid droplet (LD) accumulation. To allow standardization, automatic quantification of LD size is further needed, but currently LD size is measured mostly manually. We developed an image processing-based method that does not require staining to monitor adipose cell maturation in vitro nondestructively using optical micrographs taken consecutively during culturing. We employed our method to monitor LD accumulation in 3T3-L1 and mesenchymal stem cells over 37 days. For each cell type, percentage of lipid area, number of droplets per cell, and droplet diameter were obtained every 2-3 days. In 3T3-L1 cultures, high insulin concentration (10 microg/mL) yielded a significantly different (p < 0.01) time course of all three outcome measures. In mesenchymal stem cell cultures, high fetal bovine serum concentration (12.5%) produced significantly more lipid area (p < 0.01). Our method was able to successfully characterize time courses and extents of adipogenesis and is useful for a wide range of applications testing the effects of biochemical, mechanical, and thermal stimulations in tissue engineering of bioartificial fat constructs.

Genetic Profiling and Comorbidities of Zika Infection.

PubMed

Moni, Mohammad Ali; Lio', Pietro

2017-09-15

The difficulty in distinguishing infection by Zika virus (ZIKV) from other flaviviruses is a global health concern, particularly given the high risk of neurologic complications (including Guillain-Barré syndrome [GBS]) with ZIKV infection. We developed quantitative frameworks to compare and explore infectome, diseasome, and comorbidity of ZIKV infections. We analyzed gene expression microarray and RNA-Seq data from ZIKV, West Nile fever (WNF), chikungunya, dengue, yellow fever, Japanese encephalitis virus, GBS, and control datasets. Using neighborhood-based benchmarking and multilayer network topology, we constructed relationship networks based on the Online Mendelian Inheritance in Man database and our identified significant genes. ZIKV infections showed dysregulation in expression of 929 genes. Forty-seven genes were highly expressed in both ZIKV and dengue infections. However, ZIKV shared <15 significant transcripts with other flavivirus infections. Notably, dysregulation of MAFB and SELENBP1 was common to ZIKV, dengue, and GBS infection; ATF5, TNFAIP3, and BAMB1 were common to ZIKV, dengue, and WNF; and NAMPT and PMAlP1 were common to ZIKV, GBS, and WNF. Phylogenetic, ontologic, and pathway analyses showed that ZIKV infection most resembles dengue fever. We have developed methodologies to investigate disease mechanisms and predictions for infectome, diseasome, and comorbidities quantitatively, and identified particular similarities between ZIKV and dengue infections. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Evaluation of Flow-Injection Tandem Mass Spectrometry for Rapid and High-Throughput Quantitative Determination of B-Vitamins in Nutritional Supplements

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

Bhandari, Deepak; Van Berkel, Gary J

2012-01-01

The use of flow-injection electrospray ionization tandem mass spectrometry for rapid and high-throughput mass spectral analysis of selected B-vitamins, viz. B1, B2, B3, B5, and B6, in nutritional formulations was demonstrated. A simple and rapid (~5 min) in-tube sample preparation was performed by adding extraction solvent to a powdered sample aliquot followed by agitation, centrifugation, and filtration to recover an extract for analysis. Automated flow injection introduced 1 L of the extracts directly into the mass spectrometer ion source without chromatographic separation. Sample-to-sample analysis time was 60 s representing significant improvement over conventional liquid chromatography approaches which typically require 25-45more » min, and often require more significant sample preparation procedures. Quantitative capabilities of the flow-injection analysis were tested using the method of standard additions and NIST standard reference material (SRM 3280) multivitamin/multielement tablets. The quantity determined for each B-vitamin in SRM 3280 was within the statistical range provided for the respective certified values. The same sample preparation and analysis approach was also applied to two different commercial vitamin supplement tablets and proved to be successful in the quantification of the selected B-vitamins as evidenced by an agreement with the labels values and the results obtained using isotope dilution liquid chromatography/mass spectrometry.« less

Non-random occurrence of Robertsonian translocations in the house mouse (Mus musculus domesticus): is it related to quantitative variation in the minor satellite?

PubMed

Cazaux, Benoîte; Catalan, Josette; Claude, Julien; Britton-Davidian, Janice

2014-01-01

The house mouse, Mus musculus domesticus, shows extraordinary chromosomal diversity driven by fixation of Robertsonian (Rb) translocations. The high frequency of this rearrangement, which involves the centromeric regions, has been ascribed to the architecture of the satellite sequence (high quantity and homogeneity). This promotes centromere-related translocations through unequal recombination and gene conversion. A characteristic feature of Rb variation in this subspecies is the non-random contribution of different chromosomes to the translocation frequency, which, in turn, depends on the chromosome size. Here, the association between satellite quantity and Rb frequency was tested by PRINS of the minor satellite which is the sequence involved in the translocation breakpoints. Five chromosomes with different translocation frequencies were selected and analyzed among wild house mice from 8 European localities. Using a relative quantitative measurement per chromosome, the analysis detected a large variability in signal size most of which was observed between individuals and/or localities. The chromosomes differed significantly in the quantity of the minor satellite, but these differences were not correlated with their translocation frequency. However, the data uncovered a marginally significant correlation between the quantity of the minor satellite and chromosome size. The implications of these results on the evolution of the chromosomal architecture in the house mouse are discussed. © 2014 S. Karger AG, Basel.

Quantitative assessment of the enamel machinability in tooth preparation with dental diamond burs.

PubMed

Song, Xiao-Fei; Jin, Chen-Xin; Yin, Ling

2015-01-01

Enamel cutting using dental handpieces is a critical process in tooth preparation for dental restorations and treatment but the machinability of enamel is poorly understood. This paper reports on the first quantitative assessment of the enamel machinability using computer-assisted numerical control, high-speed data acquisition, and force sensing systems. The enamel machinability in terms of cutting forces, force ratio, cutting torque, cutting speed and specific cutting energy were characterized in relation to enamel surface orientation, specific material removal rate and diamond bur grit size. The results show that enamel surface orientation, specific material removal rate and diamond bur grit size critically affected the enamel cutting capability. Cutting buccal/lingual surfaces resulted in significantly higher tangential and normal forces, torques and specific energy (p<0.05) but lower cutting speeds than occlusal surfaces (p<0.05). Increasing material removal rate for high cutting efficiencies using coarse burs yielded remarkable rises in cutting forces and torque (p<0.05) but significant reductions in cutting speed and specific cutting energy (p<0.05). In particular, great variations in cutting forces, torques and specific energy were observed at the specific material removal rate of 3mm(3)/min/mm using coarse burs, indicating the cutting limit. This work provides fundamental data and the scientific understanding of the enamel machinability for clinical dental practice. Copyright © 2014 Elsevier Ltd. All rights reserved.

BMP and TGFbeta pathways in human central chondrosarcoma: enhanced endoglin and Smad 1 signaling in high grade tumors

PubMed Central

2012-01-01

Background As major regulators of normal chondrogenesis, the bone morphogenic protein (BMP) and transforming growth factor β (TGFB) signaling pathways may be involved in the development and progression of central chondrosarcoma. In order to uncover their possible implication, the aim of this study was to perform a systematic quantitative study of the expression of BMPs, TGFBs and their receptors and to assess activity of the corresponding pathways in central chondrosarcoma. Methods Gene expression analysis was performed by quantitative RT-PCR in 26 central chondrosarcoma and 6 healthy articular cartilage samples. Expression of endoglin and nuclear localization of phosphorylated Smad1/5/8 and Smad2 was assessed by immunohistochemical analysis. Results The expression of TGFB3 and of the activin receptor-like kinase ALK2 was found to be significantly higher in grade III compared to grade I chondrosarcoma. Nuclear phosphorylated Smad1/5/8 and Smad2 were found in all tumors analyzed and the activity of both signaling pathways was confirmed by functional reporter assays in 2 chondrosarcoma cell lines. Immunohistochemical analysis furthermore revealed that phosphorylated Smad1/5/8 and endoglin expression were significantly higher in high-grade compared to low-grade chondrosarcoma and correlated to each other. Conclusions The BMP and TGFβ signaling pathways were found to be active in central chondrosarcoma cells. The correlation of Smad1/5/8 activity to endoglin expression suggests that, as described in other cell types, endoglin could enhance Smad1/5/8 signaling in high-grade chondrosarcoma cells. Endoglin expression coupled to Smad1/5/8 activation could thus represent a functionally important signaling axis for the progression of chondrosarcoma and a regulator of the undifferentiated phenotype of high-grade tumor cells. PMID:23088614

Behavioral and molecular studies of quantitative differences in hygienic behavior in honeybees.

PubMed

Gempe, Tanja; Stach, Silke; Bienefeld, Kaspar; Otte, Marianne; Beye, Martin

2016-10-21

Hygienic behavior (HB) enables honeybees to tolerate parasites, including infection with the parasitic mite Varroa destructor, and it is a well-known example of a quantitative genetic trait. The understanding of the molecular processes underpinning the quantitative differences in this behavior remains limited. We performed gene expression studies in worker bees that displayed quantitative genetic differences in HB. We established a high and low genetic source of HB performance and studied the engagements into HB of single worker bees under the same environmental conditions. We found that the percentage of worker bees that engaged in a hygienic behavioral task tripled in the high versus low HB sources, thus suggesting that genetic differences may mediate differences in stimulated states to perform HB. We found 501 differently expressed genes (DEGs) in the brains of hygienic and non-hygienic performing workers in the high HB source bees, and 342 DEGs in the brains of hygienic performing worker bees, relative to the gene expression in non-hygienic worker bees from the low HB source group. "Cell surface receptor ligand signal transduction" in the high and "negative regulation of cell communication" in the low HB source were overrepresented molecular processes, suggesting that these molecular processes in the brain may play a role in the regulation of quantitative differences in HB. Moreover, only 21 HB-associated DEGs were common between the high and low HB sources. The better HB colony performance is primarily achieved by a high number of bees engaging in the hygienic tasks that associate with distinct molecular processes in the brain. We propose that different gene products and pathways may mediate the quantitative genetic differences of HB.

Think Pair Share with Formative Assessment for Junior High School Student

NASA Astrophysics Data System (ADS)

Pradana, O. R. Y.; Sujadi, I.; Pramudya, I.

2017-09-01

Geometry is a science related to abstract thinking ability so that not many students are able to understand this material well. In this case, the learning model plays a crucial role in improving student achievement. This means that a less precise learning model will cause difficulties for students. Therefore, this study provides a quantitative explanation of the Think Pair Share learning model combined with the formative assessment. This study aims to test the Think Pair Share with the formative assessment on junior high school students. This research uses a quantitative approach of Pretest-Posttest in control group and experiment group. ANOVA test and Scheffe test used to analyse the effectiveness this learning. Findings in this study are student achievement on the material geometry with Think Pair Share using formative assessment has increased significantly. This happens probably because this learning makes students become more active during learning. Hope in the future, Think Pair Share with formative assessment be a useful learning for teachers and this learning applied by the teacher around the world especially on the material geometry.

Optimization of a resazurin-based microplate assay for large-scale compound screenings against Klebsiella pneumoniae.

PubMed

Kim, Hyung Jun; Jang, Soojin

2018-01-01

A new resazurin-based assay was evaluated and optimized using a microplate (384-well) format for high-throughput screening of antibacterial molecules against Klebsiella pneumoniae . Growth of the bacteria in 384-well plates was more effectively measured and had a > sixfold higher signal-to-background ratio using the resazurin-based assay compared with absorbance measurements at 600 nm. Determination of minimum inhibitory concentrations of the antibiotics revealed that the optimized assay quantitatively measured antibacterial activity of various antibiotics. An edge effect observed in the initial assay was significantly reduced using a 1-h incubation of the bacteria-containing plates at room temperature. There was an approximately 10% decrease in signal variability between the edge and the middle wells along with improvement in the assay robustness ( Z ' = 0.99). This optimized resazurin-based assay is an efficient, inexpensive, and robust assay that can quantitatively measure antibacterial activity using a high-throughput screening system to assess a large number of compounds for discovery of new antibiotics against K. pneumoniae .

Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA

PubMed Central

Kim, Minji; Kreig, Alex; Lee, Chun-Ying; Rube, H. Tomas; Calvert, Jacob; Song, Jun S.; Myong, Sua

2016-01-01

Abstract G-quadruplex (GQ) is a four-stranded DNA structure that can be formed in guanine-rich sequences. GQ structures have been proposed to regulate diverse biological processes including transcription, replication, translation and telomere maintenance. Recent studies have demonstrated the existence of GQ DNA in live mammalian cells and a significant number of potential GQ forming sequences in the human genome. We present a systematic and quantitative analysis of GQ folding propensity on a large set of 438 GQ forming sequences in double-stranded DNA by integrating fluorescence measurement, single-molecule imaging and computational modeling. We find that short minimum loop length and the thymine base are two main factors that lead to high GQ folding propensity. Linear and Gaussian process regression models further validate that the GQ folding potential can be predicted with high accuracy based on the loop length distribution and the nucleotide content of the loop sequences. Our study provides important new parameters that can inform the evaluation and classification of putative GQ sequences in the human genome. PMID:27095201

Quantitative relations between interaction parameter, miscibility and function in organic solar cells

NASA Astrophysics Data System (ADS)

Ye, Long; Hu, Huawei; Ghasemi, Masoud; Wang, Tonghui; Collins, Brian A.; Kim, Joo-Hyun; Jiang, Kui; Carpenter, Joshua H.; Li, Hong; Li, Zhengke; McAfee, Terry; Zhao, Jingbo; Chen, Xiankai; Lai, Joshua Lin Yuk; Ma, Tingxuan; Bredas, Jean-Luc; Yan, He; Ade, Harald

2018-03-01

Although it is known that molecular interactions govern morphology formation and purity of mixed domains of conjugated polymer donors and small-molecule acceptors, and thus largely control the achievable performance of organic solar cells, quantifying interaction-function relations has remained elusive. Here, we first determine the temperature-dependent effective amorphous-amorphous interaction parameter, χaa(T), by mapping out the phase diagram of a model amorphous polymer:fullerene material system. We then establish a quantitative `constant-kink-saturation' relation between χaa and the fill factor in organic solar cells that is verified in detail in a model system and delineated across numerous high- and low-performing materials systems, including fullerene and non-fullerene acceptors. Our experimental and computational data reveal that a high fill factor is obtained only when χaa is large enough to lead to strong phase separation. Our work outlines a basis for using various miscibility tests and future simulation methods that will significantly reduce or eliminate trial-and-error approaches to material synthesis and device fabrication of functional semiconducting blends and organic blends in general.

JCPDS-ICDD Research Associateship (Cooperative Program with NBS/NIST)

PubMed Central

Wong-Ng, W.; McMurdie, H. F.; Hubbard, C. R.; Mighell, A. D.

2001-01-01

The Research Associateship program of the Joint Committee on Powder Diffraction-International Centre for Diffraction Data (JCPDS-ICDD, now known as the ICDD) at NBS/NIST was a long standing (over 35 years) successful industry-government cooperation. The main mission of the Associateship was to publish high quality x-ray reference patterns to be included in the Powder Diffraction File (PDF). The PDF is a continuing compilation of patterns gathered from many sources, compiled and published by the ICDD. As a result of this collaboration, more than 1500 high quality powder diffraction patterns, which have had a significant impact on the scientific community, were reported. In addition, various research collaborations with NBS/NIST also led to the development of several standard reference materials (SRMs) for instrument calibration and quantitative analyses, and computer software for data collection, calibration, reduction, for the editorial process of powder pattern publication, analysis of powder data, and for quantitative analyses. This article summarizes information concerning the JCPDS-ICDD organization, the Powder Diffraction File (PDF), history and accomplishments of the JCPDS-ICDD Research Associateship. PMID:27500061

Enzyme Active Site Interactions by Raman/FTIR, NMR, and Ab Initio Calculations

PubMed Central

Deng, Hua

2017-01-01

Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis. PMID:24018325

Study of electric field distorted by space charges under positive lightning impulse voltage

NASA Astrophysics Data System (ADS)

Wang, Zezhong; Geng, Yinan

2018-03-01

Actually, many insulation problems are related to electric fields. And measuring electric fields is an important research topic of high-voltage engineering. In particular, the electric field distortion caused by space charge is the basis of streamer theory, and thus quantitatively measuring the Poisson electric field caused by space charge is significant to researching the mechanism of air gap discharge. In this paper, we used our photoelectric integrated sensor to measure the electric field distribution in a 1-m rod-plane gap under positive lightning impulse voltage. To verify the reliability of this quantitative measurement, we compared the measured results with calculated results from a numerical simulation. The electric-field time domain waveforms on the axis of the 1-m rod-plane out of the space charge zone were measured with various electrodes. The Poisson electric fields generated by space charge were separated from the Laplace electric field generated by applied voltages, and the amplitudes and variations were measured for various applied voltages and at various locations. This work also supplies the feasible basis for directly measuring strong electric field under high voltage.

High-level mRNA quantification of proliferation marker pKi-67 is correlated with favorable prognosis in colorectal carcinoma.

PubMed

Ihmann, Thomas; Liu, Jian; Schwabe, Wolfgang; Häusler, Peter; Behnke, Detlev; Bruch, Hans-Peter; Broll, Rainer; Windhövel, Ute; Duchrow, Michael

2004-12-01

The present study retrospectively examines the expression of pKi-67 mRNA and protein in colorectal carcinoma and their correlation to the outcome of patients. Immunohistochemistry and quantitative RT-PCR were used to analyze the expression of pKi-67 in 43 archival specimens of patients with curatively resected primary colorectal carcinoma, who were not treated with neo-adjuvant therapy. We determined a median pKi-67 (MIB-1) labeling index of 31.3% (range 10.3-66.4%), and a mean mRNA level of 0.1769 (DeltaC(T): range 0.01-0.69); indices and levels did not correlate. High pKi-67 mRNA DeltaC(T) values were associated with a significantly favorable prognosis, while pKi-67 labeling indices were not correlated to prognostic outcome. A multivariate analysis of clinical and biological factors indicated that tumor stage (UICC) and pKi-67 mRNA expression level were independent prognostic factors. Quantitatively determined pKi-67 mRNA can be a good and new prognostic indicator for primary resected colorectal carcinoma.

An examination of the relationship among Iiraqi high school students' science achievement and perceptions of the value of education, parent support, and peer support in the United States

NASA Astrophysics Data System (ADS)

Al-Mandwee, Samir F.

The objective of this dissertation was to quantitatively study Iraqi students (N=90) who arrived in the U.S.A. in the last 20 years. A non-experimental, descriptive research design was used for this study, which took place in one of three high schools in a large Midwestern suburban school district, during the 2013--2014 academic year. Three factors, including the students' perception of the value of education, the parental support, and the peer support, were examined using the Facilitating Conditions Questionnaire. The three subscales were part of a larger self-administered questionnaire used by McInerney (1997). In addition to the FCQ survey, a student demographic questionnaire was also used in the survey. Quantitative data from the FCQ survey reported that the students' perception of the value of education and their perception of peer support had a significant relationship with science academic achievement, which was measured for two semesters. Moreover, their peer support was the only predictor for science achievement.

Quantitative O-glycomics based on improvement of the one-pot method for nonreductive O-glycan release and simultaneous stable isotope labeling with 1-(d0/d5)phenyl-3-methyl-5-pyrazolone followed by mass spectrometric analysis.

PubMed

Wang, Chengjian; Zhang, Ping; Jin, Wanjun; Li, Lingmei; Qiang, Shan; Zhang, Ying; Huang, Linjuan; Wang, Zhongfu

2017-01-06

Rapid, simple and versatile methods for quantitative analysis of glycoprotein O-glycans are urgently required for current studies on protein O-glycosylation patterns and the search for disease O-glycan biomarkers. Relative quantitation of O-glycans using stable isotope labeling followed by mass spectrometric analysis represents an ideal and promising technique. However, it is hindered by the shortage of reliable nonreductive O-glycan release methods as well as the too large or too small inconstant mass difference between the light and heavy isotope form derivatives of O-glycans, which results in difficulties during the recognition and quantitative analysis of O-glycans by mass spectrometry. Herein we report a facile and versatile O-glycan relative quantification strategy, based on an improved one-pot method that can quantitatively achieve nonreductive release and in situ chromophoric labeling of intact mucin-type O-glycans in one step. In this study, the one-pot method is optimized and applied for quantitative O-glycan release and tagging with either non-deuterated (d 0 -) or deuterated (d 5 -) 1-phenyl-3-methyl-5-pyrazolone (PMP). The obtained O-glycan derivatives feature a permanent 10-Da mass difference between the d 0 - and d 5 -PMP forms, allowing complete discrimination and comparative quantification of these isotopically labeled O-glycans by mass spectrometric techniques. Moreover, the d 0 - and d 5 -PMP derivatives of O-glycans also have a relatively high hydrophobicity as well as a strong UV adsorption, especially suitable for high-resolution separation and high-sensitivity detection by RP-HPLC-UV. We have refined the conditions for the one-pot reaction as well as the corresponding sample purification approach. The good quantitation feasibility, reliability and linearity of this strategy have been verified using bovine fetuin and porcine stomach mucin as model O-glycoproteins. Additionally, we have also successfully applied this method to the quantitative O-glycomic comparison between perch and salmon eggs by ESI-MS, MS/MS and online RP-HPLC-UV-ESI-MS/MS, demonstrating its excellent applicability to various complex biological samples. O-Linked glycoproteins, generated via a widely existing glycosylation modification process on serine (Ser) or threonine (Thr) residues of nascent proteins, play essential roles in a series of biological processes. As a type of informational molecule, the O-glycans of these glycoproteins participate directly in these biological mechanisms. Thus, the characteristic differences or changes of O-glycans in expression level usually relate to pathologies of many diseases and represent an important opportunity to uncover the functional mechanisms of various glycoprotein O-glycans. The novel strategy introduced here provides a simple and versatile analytical method for the precise quantitation of glycoprotein O-glycans by mass spectrometry, enabling rapid evaluation of the differences or changes of O-glycans in expression level. It is attractive for the field of quantitative/comparative O-glycomics, which has great significance for exploring the complex structure-function relationship of O-glycans, as well as for the search of O-glycan biomarkers of some major diseases and O-glycan related targets of some drugs. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative 3D breast magnetic resonance imaging fibroglandular tissue analysis and correlation with qualitative assessments: a feasibility study.

PubMed

Ha, Richard; Mema, Eralda; Guo, Xiaotao; Mango, Victoria; Desperito, Elise; Ha, Jason; Wynn, Ralph; Zhao, Binsheng

2016-04-01

The amount of fibroglandular tissue (FGT) has been linked to breast cancer risk based on mammographic density studies. Currently, the qualitative assessment of FGT on mammogram (MG) and magnetic resonance imaging (MRI) is prone to intra and inter-observer variability. The purpose of this study is to develop an objective quantitative FGT measurement tool for breast MRI that could provide significant clinical value. An IRB approved study was performed. Sixty breast MRI cases with qualitative assessment of mammographic breast density and MRI FGT were randomly selected for quantitative analysis from routine breast MRIs performed at our institution from 1/2013 to 12/2014. Blinded to the qualitative data, whole breast and FGT contours were delineated on T1-weighted pre contrast sagittal images using an in-house, proprietary segmentation algorithm which combines the region-based active contours and a level set approach. FGT (%) was calculated by: [segmented volume of FGT (mm(3))/(segmented volume of whole breast (mm(3))] ×100. Statistical correlation analysis was performed between quantified FGT (%) on MRI and qualitative assessments of mammographic breast density and MRI FGT. There was a significant positive correlation between quantitative MRI FGT assessment and qualitative MRI FGT (r=0.809, n=60, P<0.001) and mammographic density assessment (r=0.805, n=60, P<0.001). There was a significant correlation between qualitative MRI FGT assessment and mammographic density assessment (r=0.725, n=60, P<0.001). The four qualitative assessment categories of FGT correlated with the calculated mean quantitative FGT (%) of 4.61% (95% CI, 0-12.3%), 8.74% (7.3-10.2%), 18.1% (15.1-21.1%), 37.4% (29.5-45.3%). Quantitative measures of FGT (%) were computed with data derived from breast MRI and correlated significantly with conventional qualitative assessments. This quantitative technique may prove to be a valuable tool in clinical use by providing computer generated standardized measurements with limited intra or inter-observer variability.

Quantitative analysis of background parenchymal enhancement in whole breast on MRI: Influence of menstrual cycle and comparison with a qualitative analysis.

PubMed

Jung, Yongsik; Jeong, Seong Kyun; Kang, Doo Kyoung; Moon, Yeorae; Kim, Tae Hee

2018-06-01

We quantitatively analyzed background parenchymal enhancement (BPE) in whole breast according to menstrual cycle and compared it with a qualitative analysis method. A data set of breast magnetic resonance imaging (MRI) from 273 breast cancer patients was used. For quantitative analysis, we used semiautomated in-house software with MATLAB. From each voxel of whole breast, the software calculated BPE using following equation: [(signal intensity [SI] at 1 min 30 s after contrast injection - baseline SI)/baseline SI] × 100%. In total, 53 patients had minimal, 108 mild, 87 moderate, and 25 marked BPE. On quantitative analysis, mean BPE values were 33.1% in the minimal, 42.1% in the mild, 59.1% in the moderate, and 81.9% in the marked BPE group showing significant difference (p = .009 for minimal vs. mild, p < 0.001 for other comparisons). Spearman's correlation test showed that there was strong significant correlation between qualitative and quantitative BPE (r = 0.63, p < 0.001). The mean BPE value was 48.7% for patients in the first week of the menstrual cycle, 43.5% in the second week, 49% in the third week, and 49.4% for those in the fourth week. The difference between the second and fourth weeks was significant (p = .005). Median, 90th percentile, and 10th percentile values were also significantly different between the second and fourth weeks but not different in other comparisons (first vs. second, first vs. third, first vs. fourth, second vs. third, or third vs. fourth). Quantitative analysis of BPE correlated well with the qualitative BPE grade. Quantitative BPE values were lowest in the second week and highest in the fourth week. Copyright © 2018 Elsevier B.V. All rights reserved.

Optical Ptychographic Microscope for Quantitative Bio-Mechanical Imaging

NASA Astrophysics Data System (ADS)

Anthony, Nicholas; Cadenazzi, Guido; Nugent, Keith; Abbey, Brian

The role that mechanical forces play in biological processes such as cell movement and death is becoming of significant interest to further develop our understanding of the inner workings of cells. The most common method used to obtain stress information is photoelasticity which maps a samples birefringence, or its direction dependent refractive indices, using polarized light. However this method only provides qualitative data and for stress information to be useful quantitative data is required. Ptychography is a method for quantitatively determining the phase of a samples complex transmission function. The technique relies upon the collection of multiple overlapping coherent diffraction patterns from laterally displaced points on the sample. The overlap of measurement points provides complementary information that significantly aids in the reconstruction of the complex wavefield exiting the sample and allows for quantitative imaging of weakly interacting specimens. Here we describe recent advances at La Trobe University Melbourne on achieving quantitative birefringence mapping using polarized light ptychography with applications in cell mechanics. Australian Synchrotron, ARC Centre of Excellence for Advanced Molecular Imaging.

Genetic Modifiers of Cardiovascular Phenotype Caused by Elastin Haploinsufficiency Act by Extrinsic Noncomplementation*

PubMed Central

Kozel, Beth A.; Knutsen, Russell H.; Ye, Li; Ciliberto, Christopher H.; Broekelmann, Thomas J.; Mecham, Robert P.

2011-01-01

Elastin haploinsufficiency causes the cardiovascular complications associated with Williams-Beuren syndrome and isolated supravalvular aortic stenosis. Significant variability exists in the vascular pathology in these individuals. Using the Eln+/− mouse, we sought to identify the source of this variability. Following outcrossing of C57Bl/6J Eln+/−, two backgrounds were identified whose cardiovascular parameters deviated significantly from the parental strain. F1 progeny of the C57Bl/6J; Eln+/−x129X1/SvJ were more hypertensive and their arteries less compliant. In contrast, Eln+/− animals crossed to DBA/2J were protected from the pathologic changes associated with elastin insufficiency. Among the crosses, aortic elastin and collagen content did not correlate with quantitative vasculopathy traits. Quantitative trait locus analysis performed on F2 C57; Eln+/−x129 intercrosses identified highly significant peaks on chromosome 1 (LOD 9.7) for systolic blood pressure and on chromosome 9 (LOD 8.7) for aortic diameter. Additional peaks were identified that affect only Eln+/−, including a region upstream of Eln on chromosome 5 (LOD 4.5). Bioinformatic analysis of the quantitative trait locus peaks revealed several interesting candidates, including Ren1, Ncf1, and Nos1; genes whose functions are unrelated to elastic fiber assembly, but whose effects may synergize with elastin insufficiency to predispose to hypertension and stiffer blood vessels. Real time RT-PCR studies show background-specific increased expression of Ncf1 (a subunit of the NOX2 NAPDH oxidase) that parallel the presence of increased oxidative stress in Eln+/− aortas. This finding raises the possibility that polymorphisms in genes affecting the generation of reactive oxygen species alter cardiovascular function in individuals with elastin haploinsufficiency through extrinsic noncomplementation. PMID:22049077

Validation of the IHC4 Breast Cancer Prognostic Algorithm Using Multiple Approaches on the Multinational TEAM Clinical Trial.

PubMed

Bartlett, John M S; Christiansen, Jason; Gustavson, Mark; Rimm, David L; Piper, Tammy; van de Velde, Cornelis J H; Hasenburg, Annette; Kieback, Dirk G; Putter, Hein; Markopoulos, Christos J; Dirix, Luc Y; Seynaeve, Caroline; Rea, Daniel W

2016-01-01

Hormone receptors HER2/neu and Ki-67 are markers of residual risk in early breast cancer. An algorithm (IHC4) combining these markers may provide additional information on residual risk of recurrence in patients treated with hormone therapy. To independently validate the IHC4 algorithm in the multinational Tamoxifen Versus Exemestane Adjuvant Multicenter Trial (TEAM) cohort, originally developed on the trans-ATAC (Arimidex, Tamoxifen, Alone or in Combination Trial) cohort, by comparing 2 methodologies. The IHC4 biomarker expression was quantified on TEAM cohort samples (n = 2919) by using 2 independent methodologies (conventional 3,3'-diaminobezidine [DAB] immunohistochemistry with image analysis and standardized quantitative immunofluorescence [QIF] by AQUA technology). The IHC4 scores were calculated by using the same previously established coefficients and then compared with recurrence-free and distant recurrence-free survival, using multivariate Cox proportional hazards modeling. The QIF model was highly significant for prediction of residual risk (P < .001), with continuous model scores showing a hazard ratio (HR) of 1.012 (95% confidence interval [95% CI]: 1.010-1.014), which was significantly higher than that for the DAB model (HR: 1.008, 95% CI: 1.006-1.009); P < .001). Each model added significant prognostic value in addition to recognized clinical prognostic factors, including nodal status, in multivariate analyses. Quantitative immunofluorescence, however, showed more accuracy with respect to overall residual risk assessment than the DAB model. The use of the IHC4 algorithm was validated on the TEAM trial for predicting residual risk in patients with breast cancer. These data support the use of the IHC4 algorithm clinically, but quantitative and standardized approaches need to be used.

Remineralization of enamel subsurface lesions with casein phosphopeptide-amorphous calcium phosphate: A quantitative energy dispersive X-ray analysis using scanning electron microscopy: An in vitro study

PubMed Central

Hegde, Mithra N; Moany, Anu

2012-01-01

Aim: The objective of this study was to quantitatively evaluate the remineralization potential of casein phosphopeptide-amor-phous calcium phosphate paste on enamel subsurface lesions using scanning electron microscopy with energy dispersive X-ray analysis (SEM-EDX). Materials and Methods: Ninety enamel specimens were prepared from extracted human molars. All specimens were evaluated for mineral content (% weight) using SEM-EDX. The specimens were placed in demineralizing solution for four days to produce artificial carious lesions. The mineral content (calcium/phosphorus ratios, Ca/P ratios) was remeasured using SEM-EDX. The specimens were then randomly assigned to five study groups and one control group of 15 specimens per group. Except for the control group, all group specimens were incubated in remineralizing paste (CPP-ACP paste) for 7, 14, 21, 28, and 35 days twice daily for three minutes. The control group received no treatment with remineralizing paste. All the 90 specimens were stored in artificial saliva at 37°C. After remineralization, the mineral content (% weight) of the samples was measured using SEM-EDX. Results: All the study groups showed very highly significant differences between Ca/P ratios of the demineralized and remineralized samples. There was no significant difference seen in the control group. Conclusion: CPP-ACP paste could significantly remineralize the artificial enamel subsurface lesions in vitro: the remineralizing rates increasing with the time for which the samples were kept in the remineralizing paste. Energy dispersive X-ray analysis is an efficient way to quantitatively assess the changes in mineral content during demineralization and in vitro remineralization processes. PMID:22368338

Bone Mineral Density Variation in Men is influenced by Sex-Specific and Non Sex-Specific Quantitative Trait Loci

PubMed Central

Peacock, Munro; Koller, Daniel L.; Lai, Dongbing; Hui, Siu; Foroud, Tatiana; Econs, Michael J.

2009-01-01

Introduction A major predictor of age-related osteoporotic fracture is peak areal bone mineral density (aBMD) which is a highly heritable trait. However, few linkage and association studies have been performed in men to identify the genes contributing to normal variation in aBMD. The aim of this study was to perform a genome wide scan in healthy men to identify quantitative trait loci (QTL) that were significantly linked to aBMD and to test whether any of these might be sex-specific. Methods aBMD at the spine and hip were measured in 515 pairs of brothers, aged 18-61 (405 white pairs, 110 black pairs). Linkage analysis in the brother sample was compared with results in a previously published sample of 774 sister pairs to identify sex-specific quantitative trait loci (QTL). Results A genome wide scan identified significant QTL (LOD>3.6) for aBMD on chromosomes 4q21 (hip), 7q34 (spine), 14q32 (hip), 19p13 (hip), 21q21 (hip), and 22q13 (hip). Analysis suggested that the QTL on chromosome 7q34, 14q32, and 21q21 were male-specific whereas the others were not sex-specific. Conclusions This study demonstrates that six QTL were significantly linked with aBMD in men. One was linked to spine and five were linked to hip. When compared to published data in women from the same geographical region, the QTL on chromosomes 7, 14 and 21 were male-specific. The occurrence of sex-specific genes in humans for aBMD has important implications for the pathogenesis and treatment of osteoporosis. PMID:19427925

A quantitative genetic analysis of hibernation emergence date in a wild population of Columbian ground squirrels.

PubMed

Lane, J E; Kruuk, L E B; Charmantier, A; Murie, J O; Coltman, D W; Buoro, M; Raveh, S; Dobson, F S

2011-09-01

The life history schedules of wild organisms have long attracted scientific interest, and, in light of ongoing climate change, an understanding of their genetic and environmental underpinnings is increasingly becoming of applied concern. We used a multi-generation pedigree and detailed phenotypic records, spanning 18 years, to estimate the quantitative genetic influences on the timing of hibernation emergence in a wild population of Columbian ground squirrels (Urocitellus columbianus). Emergence date was significantly heritable [h(2) = 0.22 ± 0.05 (in females) and 0.34 ± 0.14 (in males)], and there was a positive genetic correlation (r(G) = 0.76 ± 0.22) between male and female emergence dates. In adult females, the heritabilities of body mass at emergence and oestrous date were h(2) = 0.23 ± 0.09 and h(2) = 0.18 ± 0.12, respectively. The date of hibernation emergence has been hypothesized to have evolved so as to synchronize subsequent reproduction with upcoming peaks in vegetation abundance. In support of this hypothesis, although levels of phenotypic variance in emergence date were higher than oestrous date, there was a highly significant genetic correlation between the two (r(G) = 0.98 ± 0.01). Hibernation is a prominent feature in the annual cycle of many small mammals, but our understanding of its influences lags behind that for phenological traits in many other taxa. Our results provide the first insight into its quantitative genetic influences and thus help contribute to a more general understanding of its evolutionary significance. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

A quantitative Kirkpatrick Level 1 and 2 study of equipment specialist apprentice operations training

NASA Astrophysics Data System (ADS)

Hughes, Dirk D.

The primary purpose of the quantitative experimental study is to compare employee-learning outcomes for a course of study that is offered in two formats: explicit and tacit instructor led and explicit e-learning operations training. A Kirkpatrick Level 2 course examination is used to establish a pretest knowledge baseline and to measure posttest learning outcomes for each instructional format. A secondary purpose is to compare responses of the two groups using a Kirkpatrick Level 1 customer satisfaction index survey. Several authors reported the United States electric utility industry would have an employee attrition issue during the 2010 through 2015 period. This is at the same time the industry will be experiencing an increased demand for electricity. There now is a demand for highly training powerplant operators. A review of literature yielded few studies comparing instructor led training and e-based training. Though the Electric Power Research Institute stated the two training modes would be acceptable instruction, the organization did not develop a quantifiable justified recommendation as to the training. Subjects participated in a basic operations course and decided to take either the instructor led or e-based training course. Results of the study concluded that both instructor led and e-based training provided significant learning to the participants. The Kirkpatrick Level 1 results indicated significantly better results for instructor led training. There was not a significant difference in the Kirkpatrick Level 2 results between the two training modalities. Recommendation for future research include conducting a quantitative studies including a Phillips Level 5 study and qualitative studies including a more detailed examination of the customer satisfaction survey (Kirkpatrick Level 1).

The added value of quantitative analysis of on-therapy impedance-pH parameters in distinguishing refractory non-erosive reflux disease from functional heartburn.

PubMed

Frazzoni, M; Conigliaro, R; Mirante, V G; Melotti, G

2012-02-01

By analysis of symptom-reflux association, endoscopy-negative refractory heartburn can be related to acid/non-acid refluxes with impedance-pH monitoring. Unfortunately, patients frequently do not report symptoms during the test. We aimed to assess the contribution of quantitative analysis of impedance-pH parameters added to symptom-reflux association in evaluating patients with endoscopy-negative heartburn refractory to high-dose proton pump inhibitor therapy. The symptom association probability (SAP), the symptom index (SI), the esophageal acid exposure time and the number of distal and proximal refluxes were assessed at on-therapy impedance-pH monitoring. Relationships with hiatal hernia and manometric findings were also evaluated. Eighty patients were prospectively studied. Refractory heartburn was more frequently related to reflux by a positive SAP/SI and/or abnormal impedance-pH parameters (52/80 cases) (65%) than by a positive SAP/SI only (38/80 cases) (47%) (P = 0.038). In patients with refractory non-erosive reflux disease (NERD) defined by a positive SAP/SI and/or abnormal impedance-pH parameters, the prevalence of hiatal hernia was significantly higher (56%vs 21%, P = 0.007) and the mean lower esophageal sphincter tone was significantly lower (18.7 vs 25.8 mmHg, P = 0.005) than in those (35%) with reflux-unrelated, i.e., functional heartburn (FH). On the contrary, no significant difference was observed subdividing patients according to a positive SAP/SI only. Quantitative analysis of impedance-pH parameters added to symptom-reflux association allows a subdivision of refractory-heartburn patients into refractory NERD and FH which is substantiated by pathophysiological findings and which restricts the diagnosis of FH to one third of cases. © 2011 Blackwell Publishing Ltd.

Geometric distortion correction in prostate diffusion-weighted MRI and its effect on quantitative apparent diffusion coefficient analysis.

PubMed

Nketiah, Gabriel; Selnaes, Kirsten M; Sandsmark, Elise; Teruel, Jose R; Krüger-Stokke, Brage; Bertilsson, Helena; Bathen, Tone F; Elschot, Mattijs

2018-05-01

To evaluate the effect of correction for B 0 inhomogeneity-induced geometric distortion in echo-planar diffusion-weighted imaging on quantitative apparent diffusion coefficient (ADC) analysis in multiparametric prostate MRI. Geometric distortion correction was performed in echo-planar diffusion-weighted images (b = 0, 50, 400, 800 s/mm 2 ) of 28 patients, using two b 0 scans with opposing phase-encoding polarities. Histology-matched tumor and healthy tissue volumes of interest delineated on T 2 -weighted images were mapped to the nondistortion-corrected and distortion-corrected data sets by resampling with and without spatial coregistration. The ADC values were calculated on the volume and voxel level. The effect of distortion correction on ADC quantification and tissue classification was evaluated using linear-mixed models and logistic regression, respectively. Without coregistration, the absolute differences in tumor ADC (range: 0.0002-0.189 mm 2 /s×10 -3 (volume level); 0.014-0.493 mm 2 /s×10 -3 (voxel level)) between the nondistortion-corrected and distortion-corrected were significantly associated (P < 0.05) with distortion distance (mean: 1.4 ± 1.3 mm; range: 0.3-5.3 mm). No significant associations were found upon coregistration; however, in patients with high rectal gas residue, distortion correction resulted in improved spatial representation and significantly better classification of healthy versus tumor voxels (P < 0.05). Geometric distortion correction in DWI could improve quantitative ADC analysis in multiparametric prostate MRI. Magn Reson Med 79:2524-2532, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Relating interesting quantitative time series patterns with text events and text features

NASA Astrophysics Data System (ADS)

Wanner, Franz; Schreck, Tobias; Jentner, Wolfgang; Sharalieva, Lyubka; Keim, Daniel A.

2013-12-01

In many application areas, the key to successful data analysis is the integrated analysis of heterogeneous data. One example is the financial domain, where time-dependent and highly frequent quantitative data (e.g., trading volume and price information) and textual data (e.g., economic and political news reports) need to be considered jointly. Data analysis tools need to support an integrated analysis, which allows studying the relationships between textual news documents and quantitative properties of the stock market price series. In this paper, we describe a workflow and tool that allows a flexible formation of hypotheses about text features and their combinations, which reflect quantitative phenomena observed in stock data. To support such an analysis, we combine the analysis steps of frequent quantitative and text-oriented data using an existing a-priori method. First, based on heuristics we extract interesting intervals and patterns in large time series data. The visual analysis supports the analyst in exploring parameter combinations and their results. The identified time series patterns are then input for the second analysis step, in which all identified intervals of interest are analyzed for frequent patterns co-occurring with financial news. An a-priori method supports the discovery of such sequential temporal patterns. Then, various text features like the degree of sentence nesting, noun phrase complexity, the vocabulary richness, etc. are extracted from the news to obtain meta patterns. Meta patterns are defined by a specific combination of text features which significantly differ from the text features of the remaining news data. Our approach combines a portfolio of visualization and analysis techniques, including time-, cluster- and sequence visualization and analysis functionality. We provide two case studies, showing the effectiveness of our combined quantitative and textual analysis work flow. The workflow can also be generalized to other application domains such as data analysis of smart grids, cyber physical systems or the security of critical infrastructure, where the data consists of a combination of quantitative and textual time series data.

Generation of High-Quality SWATH® Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF® Mass Spectrometers

PubMed Central

Schilling, Birgit; Gibson, Bradford W.; Hunter, Christie L.

2017-01-01

Data-independent acquisition is a powerful mass spectrometry technique that enables comprehensive MS and MS/MS analysis of all detectable species, providing an information rich data file that can be mined deeply. Here, we describe how to acquire high-quality SWATH® Acquisition data to be used for large quantitative proteomic studies. We specifically focus on using variable sized Q1 windows for acquisition of MS/MS data for generating higher specificity quantitative data. PMID:28188533

High-resolution quantitative determination of dielectric function by using scattering scanning near-field optical microscopy

PubMed Central

Tranca, D. E.; Stanciu, S. G.; Hristu, R.; Stoichita, C.; Tofail, S. A. M.; Stanciu, G. A.

2015-01-01

A new method for high-resolution quantitative measurement of the dielectric function by using scattering scanning near-field optical microscopy (s-SNOM) is presented. The method is based on a calibration procedure that uses the s-SNOM oscillating dipole model of the probe-sample interaction and quantitative s-SNOM measurements. The nanoscale capabilities of the method have the potential to enable novel applications in various fields such as nano-electronics, nano-photonics, biology or medicine. PMID:26138665

High performance liquid chromatographic assay for the quantitation of total glutathione in plasma

NASA Technical Reports Server (NTRS)

Abukhalaf, Imad K.; Silvestrov, Natalia A.; Menter, Julian M.; von Deutsch, Daniel A.; Bayorh, Mohamed A.; Socci, Robin R.; Ganafa, Agaba A.

2002-01-01

A simple and widely used homocysteine HPLC procedure was applied for the HPLC identification and quantitation of glutathione in plasma. The method, which utilizes SBDF as a derivatizing agent utilizes only 50 microl of sample volume. Linear quantitative response curve was generated for glutathione over a concentration range of 0.3125-62.50 micromol/l. Linear regression analysis of the standard curve exhibited correlation coefficient of 0.999. Limit of detection (LOD) and limit of quantitation (LOQ) values were 5.0 and 15 pmol, respectively. Glutathione recovery using this method was nearly complete (above 96%). Intra-assay and inter-assay precision studies reflected a high level of reliability and reproducibility of the method. The applicability of the method for the quantitation of glutathione was demonstrated successfully using human and rat plasma samples.

Prognostic value of mitotic counts in breast cancer of Saudi Arabian patients.

PubMed

Buhmeida, Abdelbaset; Al-Maghrabi, Jaudah; Merdad, Adnan; Al-Thubaity, Fatima; Chaudhary, Adeel; Gari, Mamdooh; Abuzenadah, Adel; Collan, Yrjö; Syrjänen, Kari; Al-Qahtani, Mohammed

2011-01-01

Quantitative methods in combination with other objective prognostic criteria can improve the evaluation of a cancer patient's prognosis, and possibly predict response to therapy. One of the important prognostic and predictive markers is the mitotic count, which has proven valuable in many aspects. In this study, the prognostic value of the mitotic count was assessed in breast cancer (BC) patients in Saudi Arabia. The study comprised a series of 87 patients diagnosed and treated for breast cancer at the Departments of Surgery and Oncology, King Abdul-Aziz University Hospital, between 2000 and 2008. Mitotic counts were carried out using a standard laboratory microscope (objective, × 40; field diameter, 420 μm). The number of mitotic figures in 10 consecutive high-power fields (hpf) from the most cellular area of the sample gave the mitotic activity index (MAI, mitotic figures/10 hpf). The standardized mitotic index (SMI) recorded the mitotic count as the number of mitotic figures by area of the neoplastic tissue in the microscopic field, thus the number of mitoses in 10 consecutive fields was corrected for the volume fraction and field size (mitotic figures/mm²). The means of MAI and SMI of the tumors in the entire series of 87 patients were 15 mitotic figures/10 hpf (range 4-45) and 4 mitotic figures/mm² (range 1-9), respectively. The mitotic counts were higher in advanced stages than in early cancer (p < 0.04). The mitotic counts were significantly larger in patients with high-grade tumor (p < 0.004) and in cases with tumor metastasis (p < 0.004). The mitotic counts were also significantly larger in the recurrent cases than in non-recurrent ones (p < 0.02). The quantitatively measurable mitotic counts of cancer cell nuclei are of significant prognostic value in invasive ductal carcinoma of the breast in Saudi Arabia and the mean cut-off values of MAI and SMI can be applied as objective (quantitative) criteria to distinguish breast cancer patients into groups with favorable and less favorable prognosis.

Harnessing quantitative genetics and genomics for understanding and improving complex traits in crops

USDA-ARS?s Scientific Manuscript database

Classical quantitative genetics aids crop improvement by providing the means to estimate heritability, genetic correlations, and predicted responses to various selection schemes. Genomics has the potential to aid quantitative genetics and applied crop improvement programs via large-scale, high-thro...

40 CFR 796.2750 - Sediment and soil adsorption isotherm.

Code of Federal Regulations, 2014 CFR

2014-07-01

... are highly reproducible. The test provides excellent quantitative data readily amenable to statistical... combination of methods suitable for the identification and quantitative detection of the parent test chemical... quantitative analysis of the parent chemical. (3) Amount of parent test chemical applied, the amount recovered...

40 CFR 796.2750 - Sediment and soil adsorption isotherm.

Code of Federal Regulations, 2013 CFR

2013-07-01

... highly reproducible. The test provides excellent quantitative data readily amenable to statistical... combination of methods suitable for the identification and quantitative detection of the parent test chemical... quantitative analysis of the parent chemical. (3) Amount of parent test chemical applied, the amount recovered...

40 CFR 796.2750 - Sediment and soil adsorption isotherm.

Code of Federal Regulations, 2012 CFR

2012-07-01

... highly reproducible. The test provides excellent quantitative data readily amenable to statistical... combination of methods suitable for the identification and quantitative detection of the parent test chemical... quantitative analysis of the parent chemical. (3) Amount of parent test chemical applied, the amount recovered...

Subjective Burden and Depression in Mothers of Children with Autism Spectrum Disorder in India: Moderating Effect of Social Support.

PubMed

Singh, Prerna; Ghosh, Subharati; Nandi, Subhrangshu

2017-10-01

The quantitative study assessed subjective burden, depression, and the moderating effect of social support in mothers of children with autism spectrum disorder (ASD) in India. Seventy mothers were interviewed using a structured interview schedule, which measured their subjective burden, depression, and social support from family, friends, and significant others. Data was analyzed using descriptive statistics and multiple regression analysis with interaction terms. Half of the mothers in the study reported depression of clinical significance. Higher subjective burden significantly predicted higher depression. Of the three sources of support, only medium/high family support had a direct impact on depression and also moderated the impact of the subjective burden of depression. Implications for practice and policy are discussed.

The importance of spatial heterogeneity and self-restraint on mutualism stability - a quantitative review

NASA Astrophysics Data System (ADS)

Wang, Rui-Wu; Dunn, Derek W.; Luo, Jun; He, Jun-Zhou; Shi, Lei

2015-10-01

Understanding the factors that enable mutualisms to evolve and to subsequently remain stable over time, is essential to fully understand patterns of global biodiversity and for evidence based conservation policy. Theoretically, spatial heterogeneity of mutualists, through increased likelihood of fidelity between cooperative partners in structured populations, and ‘self-restraint’ of symbionts, due to selection against high levels of virulence leading to short-term host overexploitation, will result in either a positive correlation between the reproductive success of both mutualists prior to the total exploitation of any host resource or no correlation after any host resource has been fully exploited. A quantitative review by meta-analysis on the results of 96 studies from 35 papers, showed no evidence of a significant fitness correlation between mutualists across a range of systems that captured much taxonomic diversity. However, when the data were split according to four categories of host: 1) cnidarian corals, 2) woody plants, 3) herbaceous plants, and 4) insects, a significantly positive effect in corals was revealed. The trends for the remaining three categories did not significantly differ to zero. Our results suggest that stability in mutualisms requires alternative processes, or mechanisms in addition to, spatial heterogeneity of hosts and/or ‘self-restraint’ of symbionts.

Evaluation of prognostic and predictive value of microtubule associated protein tau in two independent cohorts

PubMed Central

2011-01-01

Introduction Microtubule associated proteins (MAPs) endogenously regulate microtubule stabilization and have been reported as prognostic and predictive markers for taxane response. The microtubule stabilizer, MAP-tau, has shown conflicting results. We quantitatively assessed MAP-tau expression in two independent breast cancer cohorts to determine prognostic and predictive value of this biomarker. Methods MAP-tau expression was evaluated in the retrospective Yale University breast cancer cohort (n = 651) using tissue microarrays and also in the TAX 307 cohort, a clinical trial randomized for TAC versus FAC chemotherapy (n = 140), using conventional whole tissue sections. Expression was measured using the AQUA method for quantitative immunofluorescence. Scores were correlated with clinicopathologic variables, survival, and response to therapy. Results Assessment of the Yale cohort using Cox univariate analysis indicated an improved overall survival (OS) in tumors with a positive correlation between high MAP-tau expression and overall survival (OS) (HR = 0.691, 95% CI = 0.489-0.974; P = 0.004). Kaplan Meier analysis showed 10-year survival for 65% of patients with high MAP-tau expression compared to 52% with low expression (P = .006). In TAX 307, high expression was associated with significantly longer median time to tumor progression (TTP) regardless of treatment arm (33.0 versus 23.4 months, P = 0.010) with mean TTP of 31.2 months. Response rates did not differ by MAP-tau expression (P = 0.518) or by treatment arm (P = 0.584). Conclusions Quantitative measurement of MAP-tau expression has prognostic value in both cohorts, with high expression associated with longer TTP and OS. Differences by treatment arm or response rate in low versus high MAP-tau groups were not observed, indicating that MAP-tau is not associated with response to taxanes and is not a useful predictive marker for taxane-based chemotherapy. PMID:21888627

EPS-LASSO: Test for High-Dimensional Regression Under Extreme Phenotype Sampling of Continuous Traits.

PubMed

Xu, Chao; Fang, Jian; Shen, Hui; Wang, Yu-Ping; Deng, Hong-Wen

2018-01-25

Extreme phenotype sampling (EPS) is a broadly-used design to identify candidate genetic factors contributing to the variation of quantitative traits. By enriching the signals in extreme phenotypic samples, EPS can boost the association power compared to random sampling. Most existing statistical methods for EPS examine the genetic factors individually, despite many quantitative traits have multiple genetic factors underlying their variation. It is desirable to model the joint effects of genetic factors, which may increase the power and identify novel quantitative trait loci under EPS. The joint analysis of genetic data in high-dimensional situations requires specialized techniques, e.g., the least absolute shrinkage and selection operator (LASSO). Although there are extensive research and application related to LASSO, the statistical inference and testing for the sparse model under EPS remain unknown. We propose a novel sparse model (EPS-LASSO) with hypothesis test for high-dimensional regression under EPS based on a decorrelated score function. The comprehensive simulation shows EPS-LASSO outperforms existing methods with stable type I error and FDR control. EPS-LASSO can provide a consistent power for both low- and high-dimensional situations compared with the other methods dealing with high-dimensional situations. The power of EPS-LASSO is close to other low-dimensional methods when the causal effect sizes are small and is superior when the effects are large. Applying EPS-LASSO to a transcriptome-wide gene expression study for obesity reveals 10 significant body mass index associated genes. Our results indicate that EPS-LASSO is an effective method for EPS data analysis, which can account for correlated predictors. The source code is available at https://github.com/xu1912/EPSLASSO. hdeng2@tulane.edu. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Serial analysis of gene expression identifies connective tissue growth factor expression as a prognostic biomarker in gallbladder cancer.

PubMed

Alvarez, Hector; Corvalan, Alejandro; Roa, Juan C; Argani, Pedram; Murillo, Francisco; Edwards, Jennifer; Beaty, Robert; Feldmann, Georg; Hong, Seung-Mo; Mullendore, Michael; Roa, Ivan; Ibañez, Luis; Pimentel, Fernando; Diaz, Alfonso; Riggins, Gregory J; Maitra, Anirban

2008-05-01

Gallbladder cancer (GBC) is an uncommon neoplasm in the United States, but one with high mortality rates. This malignancy remains largely understudied at the molecular level such that few targeted therapies or predictive biomarkers exist. We built the first series of serial analysis of gene expression (SAGE) libraries from GBC and nonneoplastic gallbladder mucosa, composed of 21-bp long-SAGE tags. SAGE libraries were generated from three stage-matched GBC patients (representing Hispanic/Latino, Native American, and Caucasian ethnicities, respectively) and one histologically alithiasic gallbladder. Real-time quantitative PCR was done on microdissected epithelium from five matched GBC and corresponding nonneoplastic gallbladder mucosa. Immunohistochemical analysis was done on a panel of 182 archival GBC in high-throughput tissue microarray format. SAGE tags corresponding to connective tissue growth factor (CTGF) transcripts were identified as differentially overexpressed in all pairwise comparisons of GBC (P < 0.001). Real-time quantitative PCR confirmed significant overexpression of CTGF transcripts in microdissected primary GBC (P < 0.05), but not in metastatic GBC, compared with nonneoplastic gallbladder epithelium. By immunohistochemistry, 66 of 182 (36%) GBC had high CTGF antigen labeling, which was significantly associated with better survival on univariate analysis (P = 0.0069, log-rank test). An unbiased analysis of the GBC transcriptome by SAGE has identified CTGF expression as a predictive biomarker of favorable prognosis in this malignancy. The SAGE libraries from GBC and nonneoplastic gallbladder mucosa are publicly available at the Cancer Genome Anatomy Project web site and should facilitate much needed research into this lethal neoplasm.

Variability of serial same-day left ventricular ejection fraction using quantitative gated SPECT.

PubMed

Vallejo, Enrique; Chaya, Hugo; Plancarte, Gerardo; Victoria, Diana; Bialostozky, David

2002-01-01

The accuracy of quantitative gated single photon emission computed tomography (SPECT) (QGS) and the potential limitations for estimation of left ventricular ejection fraction (LVEF) have been extensively evaluated. However, few studies have focused on the serial variability of QGS. This study was conducted to assess the serial variability of QGS for determination of LVEF between 2 sequential technetium 99m sestamibi-gated SPECT acquisitions at rest in both healthy and unhealthy subjects. The study population consisted of 2 groups: group I included 21 volunteers with a low likelihood of CAD, and group II included 22 consecutive patients with documented CAD. Both groups underwent serial SPECT imaging. The overall correlation between sequential images was high (r = 0.94, SEE = 5.3%), and the mean serial variability of LVEF was 5.15% +/- 3.51%. Serial variability was lower for images with high counts (3.45% +/- 3.23%) than for images with low counts (6.85% +/- 3.77%). The mean serial variability was not different between normal and abnormal high-dose images (3.0% +/- 1.56% vs 3.9% +/- 2.77%). However, mean serial variability for images derived from abnormal low-dose images was significantly greater than that derived from normal low-dose images (9.6% +/- 2.22% vs 3.1% +/- 2.12%, P <.05). Although QGS is an efficacious method to approximate LVEF values and is extremely valuable for incremental risk stratification of patients with coronary artery disease, it has significant variability in the estimation of LVEF on serial images. This should be taken into account when used for serial evaluation of LVEF.

Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal populations in both in vitro and in vivo systems.

PubMed

Sekhavati, Mohammad H; Mesgaran, Mohsen Danesh; Nassiri, Mohammad R; Mohammadabadi, Tahereh; Rezaii, Farkhondeh; Fani Maleki, Adham

2009-10-01

This paper describes the use of a quantitative competitive polymerase chain reaction (QC-PCR) assay; using PCR primers to the rRNA locus of rumen fungi and a standard-control DNA including design and validation. In order to test the efficiency of this method for quantifying anaerobic rumen fungi, it has been attempted to evaluate this method in in vitro conditions by comparing with an assay based on measuring cell wall chitin. The changes in fungal growth have been studied when they are grown in in vitro on either untreated (US) or sodium hydroxide treated wheat straw (TS). Results showed that rumen fungi growth was significantly higher in treated samples compared with untreated during the 12d incubation (P<0.05) and plotting the chitin assay's results against the competitive PCR's showed high positive correlation (R(2)> or =0.87). The low mean values of the coefficients of variance in repeatability in the QC-PCR method against the chitin assay demonstrated more reliability of this new approach. And finally, the efficiency of this method was investigated in in vivo conditions. Samples of rumen fluid were collected from four fistulated Holstein steers which were fed four different diets (basal diet, high starch, high sucrose and starch plus sucrose) in rotation. The results of QC-PCR showed that addition of these non-structural carbohydrates to the basal diets caused a significant decrease in rumen anaerobic fungi biomass. The QC-PCR method appears to be a reliable and can be used for rumen samples.

Can NMR solve some significant challenges in metabolomics?

PubMed Central

Gowda, G.A. Nagana; Raftery, Daniel

2015-01-01

The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact biospecimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory. PMID:26476597

Potential predictors of risk sexual behavior among private college students in Mekelle City, North Ethiopia.

PubMed

Gebresllasie, Fanna; Tsadik, Mache; Berhane, Eyoel

2017-01-01

Risk sexual practice among students from public universities/colleges is common in Ethiopia. However, little has been known about risk sexual behavior of students in private colleges where more students are potentially enrolled. Therefore, this study aimed to assess the magnitude of risky sexual behaviors and predictors among students of Private Colleges in Mekelle City. A mixed design of both quantitative and qualitative methods was used among 627 randomly selected students of private colleges from February to march 2013. Self administered questionnaire and focus group discussion was used to collect data. A thematic content analysis was used for the qualitative part. For the quantitative study, Univariate, Bivariate and multivariable analysis was made using SPSS version 16 statistical package and p value less than 0.05 was used as cut off point for a statistical significance. Among the total 590 respondents, 151 (29.1%) have ever had sex. Among the sexually active students, 30.5% reported having had multiple sexual partners and consistent condom use was nearly 39%. In multivariable logistic regression analysis, variables such as sex, age group, sex last twelve months and condom use last twelve months was found significantly associated with risky sexual behavior. The findings of qualitative and quantitative study showed consistency in presence of risk factors. Finding of this study showed sexual risk behaviors is high among private colleges such as multiple sexual partners and substance use. So that colleges should emphasis on promoting healthy sexual and reproductive health programs.

Impact of inflammation on iron stores in involved and non-involved psoriatic skin

NASA Astrophysics Data System (ADS)

Pinheiro, T.; Ynsa, M. D.; Alves, L. C.; Teixeira, P.; Ferreira, J.; Filipe, P.

2015-04-01

Accumulating evidence supports a role for cellular Fe in cell proliferation, inflammation, and disease tolerance. Psoriasis is a severe inflammatory and hyper proliferative condition of human skin whose aetiology remains poorly understood. Herein, we performed nuclear microscopy techniques to quantify with cellular resolution and high sensitivity the concentration of Fe in lesional (psoriatic plaques) and non-lesional adjacent skin of psoriatic patients. Fe contents were measured across skin depth and along epidermal strata either by quantitatively imaging Fe distribution in regions of interest, or by determining Fe profiles through analysis of sequential points along selected transepts. Both procedures require deconvolution of spectra to project quantitative elemental data through the application of different software codes. Using these approaches a detailed quantitative distribution of Fe was resolved. We show that in both lesional and non-lesional skin, the epidermal profiles of Fe contents showed a peak at the basal layer and that Fe concentration along the basal layer was not uniformly distributed. Typically, Fe levels were significantly higher in epidermal ridges relative to regions above dermal papillae. Lesional skin displayed excess Fe over extended regions above basal layer. In conclusion, we found significantly increased Fe deposits in the epidermis of psoriatic patients, particularly in areas of epidermal hyper proliferation. These findings suggest an important role for Fe in the pathogenesis of psoriasis. They also raise the possibility that manipulation of Fe levels in the skin may become relevant for the clinical management of psoriasis.

Micro-computed tomography characterization of tissue engineering scaffolds: effects of pixel size and rotation step.

PubMed

Cengiz, Ibrahim Fatih; Oliveira, Joaquim Miguel; Reis, Rui L

2017-08-01

Quantitative assessment of micro-structure of materials is of key importance in many fields including tissue engineering, biology, and dentistry. Micro-computed tomography (µ-CT) is an intensively used non-destructive technique. However, the acquisition parameters such as pixel size and rotation step may have significant effects on the obtained results. In this study, a set of tissue engineering scaffolds including examples of natural and synthetic polymers, and ceramics were analyzed. We comprehensively compared the quantitative results of µ-CT characterization using 15 acquisition scenarios that differ in the combination of the pixel size and rotation step. The results showed that the acquisition parameters could statistically significantly affect the quantified mean porosity, mean pore size, and mean wall thickness of the scaffolds. The effects are also practically important since the differences can be as high as 24% regarding the mean porosity in average, and 19.5 h and 166 GB regarding the characterization time and data storage per sample with a relatively small volume. This study showed in a quantitative manner the effects of such a wide range of acquisition scenarios on the final data, as well as the characterization time and data storage per sample. Herein, a clear picture of the effects of the pixel size and rotation step on the results is provided which can notably be useful to refine the practice of µ-CT characterization of scaffolds and economize the related resources.

Environmental distribution of two widespread uncultured freshwater Euryarchaeota clades unveiled by specific primers and quantitative PCR.

PubMed

Restrepo-Ortiz, Claudia X; Casamayor, Emilio O

2013-12-01

Quantitative environmental distribution of two widely distributed uncultured freshwater Euryarchaeota with unknown functional role was explored by newly designed quantitative PCR primers targeting the 16S rRNA gene of clades Miscellaneous Euryarchaeota Group (MEG, containing the groups pMC2A384 and VALII/Eury4) and Deep-Sea Euryarchaeotal Groups (DSEG, targeting the cluster named VALIII containing the DHVE-3/DSEG, BC07-2A-27/DSEG-3 and DSEG-2 groups), respectively. The summer surface plankton of 28 lakes was analysed, and one additional dimictic deep alpine lake, Lake Redon, was temporally and vertically surveyed covering seasonal limnological variability. A trophic range between 0.2 and 5.2 μg l(-1) Chl a, and pH span from 3.8 to 9.5 was explored at altitudes between 632 and 2590 m above sea level. The primers showed to be highly selective with c. 85% coverage and 100% specificity. Only pH significantly explained the changes observed in gene abundances and environment. In Lake Redon, DSEG bloomed in deep stratified waters both in summer and early spring, and MEG at intermediate depths during the ice-cover period. Overall, MEG and DSEG showed a differential ecological distribution although correlational analyses indicated lack of coupling of both Euryarchaeota with phytoplankton (chlorophyll a). However, an intriguing positive and significant relationship was found between DSEG and putative ammonia oxidizing thaumarchaeota. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

[Quantitative research on operation behavior of acupuncture manipulation].

PubMed

Li, Jing; Grierson, Lawrence; Wu, Mary X; Breuer, Ronny; Carnahan, Heather

2014-03-01

To explore a method of quantitative evaluation on operation behavior of acupuncture manipulation and further analyze behavior features of professional acupuncture manipulation. According to acupuncture basic manipulations, Scales for Operation Behavior of Acupuncture Basic Manipulation was made and Delphi method was adopted to test its validity. Two independent estimators utilized this scale to assess operation behavior of acupuncture manipulate among 12 acupuncturists and 12 acupuncture-novices and calculate interrater reliability, also the differences of total score of operation behavior in the two groups as well as single-step score, including sterilization, needle insertion, needle manipulation and needle withdrawal, were compared. The validity of this scale was satisfied. The inter-rater reliability was 0. 768. The total score of operation behavior in acupuncturist group was significantly higher than that in the acupuncture-novice group (13.80 +/- 1.05 vs 11.03 +/- 2.14, P < 0.01). The scores of needle insertion and needle manipulation in the acupuncturist group were significantly higher than those in the acupuncture-novice group (4.28 +/- 0.91 vs 2.54 +/- 1.51, P < 0.01; 2.56 +/- 0.65 vs 1.88 +/- 0.88, P < 0.05); however, the scores of sterilization and needle withdrawal in the acupuncturist group were not different from those in the acupuncture-novice group. This scale is suitable for quantitative evaluation on operation behavior of acupuncture manipulation. The behavior features of professional acupuncture manipulation are mainly presented with needle insertion and needle manipulation which has superior difficulty, high coordination and accuracy.

Multiparametric MRI Assessment of Human Articular Cartilage Degeneration: Correlation with Quantitative Histology and Mechanical Properties

PubMed Central

Rautiainen, Jari; Nissi, Mikko J.; Salo, Elli-Noora; Tiitu, Virpi; Finnilä, Mikko A.J.; Aho, Olli-Matti; Saarakkala, Simo; Lehenkari, Petri; Ellermann, Jutta; Nieminen, Miika T.

2014-01-01

Purpose To evaluate the sensitivity of quantitative MRI techniques (T1, T1,Gd, T2, continous wave (CW) T1ρ dispersion, adiabatic T1ρ, adiabatic T2ρ, RAFF and inversion-prepared magnetization transfer (MT)) for assessment of human articular cartilage with varying degrees of natural degeneration. Methods Osteochondral samples (n = 14) were obtained from the tibial plateaus of patients undergoing total knee replacement. MRI of the specimens was performed at 9.4 T and the relaxation time maps were evaluated in the cartilage zones. For reference, quantitative histology, OARSI grading and biomechanical measurements were performed and correlated with MRI findings. Results All MRI parameters, except T1,Gd, showed statistically significant differences in tangential and full-thickness ROIs between early and advanced osteoarthritis (OA) groups, as classified by OARSI grading. CW-T1ρ showed significant dispersion in all ROIs and featured classical laminar structure of cartilage with spin-lock powers below 1000 Hz. Adiabatic T1ρ, T2ρ, CW-T1ρ, MT and RAFF correlated strongly with OARSI grade and biomechanical parameters. Conclusion MRI parameters were able to differentiate between early and advanced OA. Furthermore, rotating frame methods, namely adiabatic T1ρ, adiabatic T2ρ, CW-T1ρ and RAFF, as well as MT experiment correlated strongly with biomechanical parameters and OARSI grade, suggesting high sensitivity of the parameters for cartilage degeneration. PMID:25104181