Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.

PubMed

Manor, Ohad; Borenstein, Elhanan

2017-02-08

Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity. Copyright © 2017 Elsevier Inc. All rights reserved.

NKp44 expression, phylogenesis and function in non-human primate NK cells

PubMed Central

De Maria, Andrea; Ugolotti, Elisabetta; Rutjens, Erik; Mazza, Stefania; Radic, Luana; Faravelli, Alessandro; Koopman, Gerrit; Di Marco, Eddi; Costa, Paola; Ensoli, Barbara; Cafaro, Aurelio; Mingari, Maria Cristina; Moretta, Lorenzo; Heeney, Jonathan

2009-01-01

Molecular and functional characterization of the natural cytotoxicity receptor (NCR) NKp44 in species other than Homo sapiens has been elusive, so far. Here, we provide complete phenotypic, molecular and functional characterization for NKp44 triggering receptor on Pan troglodytes NK cells, the closest human relative, and the analysis of NKp44-genomic locus and transcription in Macaca fascicularis. Similar to H. sapiens, NKp44 expression is detectable on chimpanzee NK cells only upon activation. However, basal NKp44 transcription is 5-fold higher in chimpanzees with lower differential increases upon cell activation compared with humans. Upon activation, an overall 12-fold lower NKp44 gene expression is observed in P. troglodytes compared with H. sapiens NK cells with only a slight reduction in NKp44 surface expression. Functional analysis of ‘in vitro’ activated purified NK cells confirms the NKp44 triggering potential compared with other major NCRs. These findings suggest the presence of a post-transcriptional regulation that evolved differently in H. sapiens. Analysis of cynomolgus NKp44-genomic sequence and transcription pattern showed very low levels of transcription with occurrence of out-of-frame transcripts and no surface expression. The present comparative analysis suggests that NKp44-genomic organization appears during macaque speciation, with considerable evolution of its transcriptional and post-transcriptional tuning. Thus, NKp44 may represent an NCR being only recently emerged during speciation, acquiring functional relevance only in non-human primates closest to H. sapiens. PMID:19147838

Obesity as a risk factor for developing functional limitation among older adults: A conditional inference tree analysis.

PubMed

Cheng, Feon W; Gao, Xiang; Bao, Le; Mitchell, Diane C; Wood, Craig; Sliwinski, Martin J; Smiciklas-Wright, Helen; Still, Christopher D; Rolston, David D K; Jensen, Gordon L

2017-07-01

To examine the risk factors of developing functional decline and make probabilistic predictions by using a tree-based method that allows higher order polynomials and interactions of the risk factors. The conditional inference tree analysis, a data mining approach, was used to construct a risk stratification algorithm for developing functional limitation based on BMI and other potential risk factors for disability in 1,951 older adults without functional limitations at baseline (baseline age 73.1 ± 4.2 y). We also analyzed the data with multivariate stepwise logistic regression and compared the two approaches (e.g., cross-validation). Over a mean of 9.2 ± 1.7 years of follow-up, 221 individuals developed functional limitation. Higher BMI, age, and comorbidity were consistently identified as significant risk factors for functional decline using both methods. Based on these factors, individuals were stratified into four risk groups via the conditional inference tree analysis. Compared to the low-risk group, all other groups had a significantly higher risk of developing functional limitation. The odds ratio comparing two extreme categories was 9.09 (95% confidence interval: 4.68, 17.6). Higher BMI, age, and comorbid disease were consistently identified as significant risk factors for functional decline among older individuals across all approaches and analyses. © 2017 The Obesity Society.

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function

PubMed Central

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A.

2012-01-01

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that the functional evolution can be inferred from the changes in the protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced Cα representation of the protein structure while enzymatic function is described by Enzyme Commission (EC) numbers. Similarity of the binding pocket dynamics at each branch of the protein family’s phylogeny was analyzed in two ways: 1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and 2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the alpha-amylase, D-isomer specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal modes analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. PMID:22651983

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

PubMed

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A

2012-09-21

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparative bioinformatics analyses and profiling of lysosome-related organelle proteomes

NASA Astrophysics Data System (ADS)

Hu, Zhang-Zhi; Valencia, Julio C.; Huang, Hongzhan; Chi, An; Shabanowitz, Jeffrey; Hearing, Vincent J.; Appella, Ettore; Wu, Cathy

2007-01-01

Complete and accurate profiling of cellular organelle proteomes, while challenging, is important for the understanding of detailed cellular processes at the organelle level. Mass spectrometry technologies coupled with bioinformatics analysis provide an effective approach for protein identification and functional interpretation of organelle proteomes. In this study, we have compiled human organelle reference datasets from large-scale proteomic studies and protein databases for seven lysosome-related organelles (LROs), as well as the endoplasmic reticulum and mitochondria, for comparative organelle proteome analysis. Heterogeneous sources of human organelle proteins and rodent homologs are mapped to human UniProtKB protein entries based on ID and/or peptide mappings, followed by functional annotation and categorization using the iProXpress proteomic expression analysis system. Cataloging organelle proteomes allows close examination of both shared and unique proteins among various LROs and reveals their functional relevance. The proteomic comparisons show that LROs are a closely related family of organelles. The shared proteins indicate the dynamic and hybrid nature of LROs, while the unique transmembrane proteins may represent additional candidate marker proteins for LROs. This comparative analysis, therefore, provides a basis for hypothesis formulation and experimental validation of organelle proteins and their functional roles.

The aquatic animals' transcriptome resource for comparative functional analysis.

PubMed

Chou, Chih-Hung; Huang, Hsi-Yuan; Huang, Wei-Chih; Hsu, Sheng-Da; Hsiao, Chung-Der; Liu, Chia-Yu; Chen, Yu-Hung; Liu, Yu-Chen; Huang, Wei-Yun; Lee, Meng-Lin; Chen, Yi-Chang; Huang, Hsien-Da

2018-05-09

Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis. In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis. The database is now publically accessible through the URL http://dbATM.mbc.nctu.edu.tw/ .

The efficacy of psychotherapy, pharmacotherapy and their combination on functioning and quality of life in depression: a meta-analysis.

PubMed

Kamenov, K; Twomey, C; Cabello, M; Prina, A M; Ayuso-Mateos, J L

2017-02-01

There is growing recognition of the importance of both functioning and quality of life (QoL) outcomes in the treatment of depressive disorders, but the meta-analytic evidence is scarce. The objective of this meta-analysis of randomized controlled trials (RCTs) was to determine the absolute and relative effects of psychotherapy, pharmacotherapy and their combination on functioning and QoL in patients with depression. One hundred and fifty-three outcome trials involving 29 879 participants with depressive disorders were identified through database searches in Pubmed, PsycINFO and the Cochrane Central Register of Controlled Trials. Compared to control conditions, psychotherapy and pharmacotherapy yielded small to moderate effect sizes for functioning and QoL, ranging from g = 0.31 to g = 0.43. When compared directly, initial analysis yielded no evidence that one of them was superior. After adjusting for publication bias, psychotherapy was more efficacious than pharmacotherapy (g = 0.21) for QoL. The combination of psychotherapy and medication performed significantly better for both outcomes compared to each treatment alone yielding small effect sizes (g = 0.32 to g = 0.39). Both interventions improved depression symptom severity more than functioning and QoL. Despite the small number of comparative trials for some of the analyses, this study reveals that combined treatment is superior, but psychotherapy and pharmacotherapy alone are also efficacious for improving functioning and QoL. The overall relatively modest effects suggest that future tailoring of therapies could be warranted to better meet the needs of individuals with functioning and QoL problems.

Functional vs. Traditional Analysis in Biomechanical Gait Data: An Alternative Statistical Approach

PubMed Central

Seeley, Matthew K.; Francom, Devin; Reese, C. Shane; Hopkins, J. Ty

2017-01-01

Abstract In human motion studies, discrete points such as peak or average kinematic values are commonly selected to test hypotheses. The purpose of this study was to describe a functional data analysis and describe the advantages of using functional data analyses when compared with a traditional analysis of variance (ANOVA) approach. Nineteen healthy participants (age: 22 ± 2 yrs, body height: 1.7 ± 0.1 m, body mass: 73 ± 16 kg) walked under two different conditions: control and pain+effusion. Pain+effusion was induced by injection of sterile saline into the joint capsule and hypertonic saline into the infrapatellar fat pad. Sagittal-plane ankle, knee, and hip joint kinematics were recorded and compared following injections using 2×2 mixed model ANOVAs and FANOVAs. The results of ANOVAs detected a condition × time interaction for the peak ankle (F1,18 = 8.56, p = 0.01) and hip joint angle (F1,18 = 5.77, p = 0.03), but did not for the knee joint angle (F1,18 = 0.36, p = 0.56). The functional data analysis, however, found several differences at initial contact (ankle and knee joint), in the mid-stance (each joint) and at toe off (ankle). Although a traditional ANOVA is often appropriate for discrete or summary data, in biomechanical applications, the functional data analysis could be a beneficial alternative. When using the functional data analysis approach, a researcher can (1) evaluate the entire data as a function, and (2) detect the location and magnitude of differences within the evaluated function. PMID:29339984

Functional vs. Traditional Analysis in Biomechanical Gait Data: An Alternative Statistical Approach.

PubMed

Park, Jihong; Seeley, Matthew K; Francom, Devin; Reese, C Shane; Hopkins, J Ty

2017-12-01

In human motion studies, discrete points such as peak or average kinematic values are commonly selected to test hypotheses. The purpose of this study was to describe a functional data analysis and describe the advantages of using functional data analyses when compared with a traditional analysis of variance (ANOVA) approach. Nineteen healthy participants (age: 22 ± 2 yrs, body height: 1.7 ± 0.1 m, body mass: 73 ± 16 kg) walked under two different conditions: control and pain+effusion. Pain+effusion was induced by injection of sterile saline into the joint capsule and hypertonic saline into the infrapatellar fat pad. Sagittal-plane ankle, knee, and hip joint kinematics were recorded and compared following injections using 2×2 mixed model ANOVAs and FANOVAs. The results of ANOVAs detected a condition × time interaction for the peak ankle (F1,18 = 8.56, p = 0.01) and hip joint angle (F1,18 = 5.77, p = 0.03), but did not for the knee joint angle (F1,18 = 0.36, p = 0.56). The functional data analysis, however, found several differences at initial contact (ankle and knee joint), in the mid-stance (each joint) and at toe off (ankle). Although a traditional ANOVA is often appropriate for discrete or summary data, in biomechanical applications, the functional data analysis could be a beneficial alternative. When using the functional data analysis approach, a researcher can (1) evaluate the entire data as a function, and (2) detect the location and magnitude of differences within the evaluated function.

Functional vs. Traditional Analysis in Biomechanical Gait Data: An Alternative Statistical Approach

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

Park, Jihong; Seeley, Matthew K.; Francom, Devin

In human motion studies, discrete points such as peak or average kinematic values are commonly selected to test hypotheses. The purpose of this study was to describe a functional data analysis and describe the advantages of using functional data analyses when compared with a traditional analysis of variance (ANOVA) approach. Nineteen healthy participants (age: 22 ± 2 yrs, body height: 1.7 ± 0.1 m, body mass: 73 ± 16 kg) walked under two different conditions: control and pain+effusion. Pain+effusion was induced by injection of sterile saline into the joint capsule and hypertonic saline into the infrapatellar fat pad. Sagittal-plane ankle,more » knee, and hip joint kinematics were recorded and compared following injections using 2×2 mixed model ANOVAs and FANOVAs. The results of ANOVAs detected a condition × time interaction for the peak ankle (F1,18 = 8.56, p = 0.01) and hip joint angle (F1,18 = 5.77, p = 0.03), but did not for the knee joint angle (F1,18 = 0.36, p = 0.56). The functional data analysis, however, found several differences at initial contact (ankle and knee joint), in the mid-stance (each joint) and at toe off (ankle). Although a traditional ANOVA is often appropriate for discrete or summary data, in biomechanical applications, the functional data analysis could be a beneficial alternative. Thus when using the functional data analysis approach, a researcher can (1) evaluate the entire data as a function, and (2) detect the location and magnitude of differences within the evaluated function.« less

Functional vs. Traditional Analysis in Biomechanical Gait Data: An Alternative Statistical Approach

DOE PAGES

Park, Jihong; Seeley, Matthew K.; Francom, Devin; ...

2017-12-28

In human motion studies, discrete points such as peak or average kinematic values are commonly selected to test hypotheses. The purpose of this study was to describe a functional data analysis and describe the advantages of using functional data analyses when compared with a traditional analysis of variance (ANOVA) approach. Nineteen healthy participants (age: 22 ± 2 yrs, body height: 1.7 ± 0.1 m, body mass: 73 ± 16 kg) walked under two different conditions: control and pain+effusion. Pain+effusion was induced by injection of sterile saline into the joint capsule and hypertonic saline into the infrapatellar fat pad. Sagittal-plane ankle,more » knee, and hip joint kinematics were recorded and compared following injections using 2×2 mixed model ANOVAs and FANOVAs. The results of ANOVAs detected a condition × time interaction for the peak ankle (F1,18 = 8.56, p = 0.01) and hip joint angle (F1,18 = 5.77, p = 0.03), but did not for the knee joint angle (F1,18 = 0.36, p = 0.56). The functional data analysis, however, found several differences at initial contact (ankle and knee joint), in the mid-stance (each joint) and at toe off (ankle). Although a traditional ANOVA is often appropriate for discrete or summary data, in biomechanical applications, the functional data analysis could be a beneficial alternative. Thus when using the functional data analysis approach, a researcher can (1) evaluate the entire data as a function, and (2) detect the location and magnitude of differences within the evaluated function.« less

Fine-Granularity Functional Interaction Signatures for Characterization of Brain Conditions

PubMed Central

Hu, Xintao; Zhu, Dajiang; Lv, Peili; Li, Kaiming; Han, Junwei; Wang, Lihong; Shen, Dinggang; Guo, Lei; Liu, Tianming

2014-01-01

In the human brain, functional activity occurs at multiple spatial scales. Current studies on functional brain networks and their alterations in brain diseases via resting-state functional magnetic resonance imaging (rs-fMRI) are generally either at local scale (regionally confined analysis and inter-regional functional connectivity analysis) or at global scale (graph theoretic analysis). In contrast, inferring functional interaction at fine-granularity sub-network scale has not been adequately explored yet. Here our hypothesis is that functional interaction measured at fine-granularity subnetwork scale can provide new insight into the neural mechanisms of neurological and psychological conditions, thus offering complementary information for healthy and diseased population classification. In this paper, we derived fine-granularity functional interaction (FGFI) signatures in subjects with Mild Cognitive Impairment (MCI) and Schizophrenia by diffusion tensor imaging (DTI) and rsfMRI, and used patient-control classification experiments to evaluate the distinctiveness of the derived FGFI features. Our experimental results have shown that the FGFI features alone can achieve comparable classification performance compared with the commonly used inter-regional connectivity features. However, the classification performance can be substantially improved when FGFI features and inter-regional connectivity features are integrated, suggesting the complementary information achieved from the FGFI signatures. PMID:23319242

Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

PubMed

Ebrahimie, Esmaeil; Fruzangohar, Mario; Moussavi Nik, Seyyed Hani; Newman, Morgan

2017-10-01

Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: "Molecular Function," "Biological Process," and "Cellular Component." GO analysis can assist in revealing functional mechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 ( www.comparativego.com ). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.

Is functional MR imaging assessment of hemispheric language dominance as good as the Wada test?: a meta-analysis.

PubMed

Dym, R Joshua; Burns, Judah; Freeman, Katherine; Lipton, Michael L

2011-11-01

To perform a systematic review and meta-analysis to quantitatively assess functional magnetic resonance (MR) imaging lateralization of language function in comparison with the Wada test. This study was determined to be exempt from review by the institutional review board. A systematic review and meta-analysis were performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A structured Medline search was conducted to identify all studies that compared functional MR imaging with the Wada test for determining hemispheric language dominance prior to brain surgery. Studies meeting predetermined inclusion criteria were selected independently by two radiologists who also assessed their quality using the Quality Assessment of Diagnostic Accuracy Studies tool. Language dominance was classified as typical (left hemispheric language dominance) or atypical (right hemispheric language dominance or bilateral language representation) for each patient. A meta-analysis was then performed by using a bivariate random-effects model to derive estimates of sensitivity and specificity, with Wada as the standard of reference. Subgroup analyses were also performed to compare the different functional MR imaging techniques utilized by the studies. Twenty-three studies, comprising 442 patients, met inclusion criteria. The sensitivity and specificity of functional MR imaging for atypical language dominance (compared with the Wada test) were 83.5% (95% confidence interval: 80.2%, 86.7%) and 88.1% (95% confidence interval: 87.0%, 89.2%), respectively. Functional MR imaging provides an excellent, noninvasive alternative for language lateralization and should be considered for the initial preoperative assessment of hemispheric language dominance. Further research may help determine which functional MR methods are most accurate for specific patient populations. RSNA, 2011

USE OF WEIBULL FUNCTION FOR NON-LINEAR ANALYSIS OF EFFECTS OF LOW LEVELS OF SIMULATED HERBICIDE DRIFT ON PLANTS

EPA Science Inventory

We compared two regression models, which are based on the Weibull and probit functions, for the analysis of pesticide toxicity data from laboratory studies on Illinois crop and native plant species. Both mathematical models are continuous, differentiable, strictly positive, and...

On the Utility of Content Analysis in Author Attribution: "The Federalist."

ERIC Educational Resources Information Center

Martindale, Colin; McKenzie, Dean

1995-01-01

Compares the success of lexical statistics, content analysis, and function words in determining the true author of "The Federalist." The function word approach proved most successful in attributing the papers to James Madison. Lexical statistics contributed nothing, while content analytic measures resulted in some success. (MJP)

Plate fixation versus intramedullary fixation for midshaft clavicle fractures: Meta-analysis of complications and functional outcomes.

PubMed

Xiao, Hao; Gao, Hengbo; Zheng, Tuokang; Zhao, Jianhui; Tian, Yingping

2016-04-01

This analysis critically compares publications discussing complications and functional outcomes of plate fixation (PF) versus intramedullary fixation (IF) for midshaft clavicle fractures. Relevant studies published between January 1990 and October 2014, without language restrictions, were identified in database searches of PubMed®, Medline®, Embase and the Chinese National Knowledge Infrastructure (CNKI). Studies that compared postoperative complications and functional outcomes between PF and IF for midshaft clavicle fractures, and provided sufficient data for analysis, were included in this meta-analysis. After strict evaluation, 12 studies were included in this meta-analysis. Studies encompassed 462 participants in the PF group and 440 in the IF group. Study participants were followed up for ≥1 year. Outcomes were superior with IF compared with PF in terms of shoulder constant score at 6-month follow-up, fewer symptomatic hardware complications, lower rate of refracture after hardware removal and less hypertrophic scarring. In other aspects, such as functional recovery at 12-months and 24-months, Disability of Arm, Shoulder and Hand (DASH) questionnaire results at 12-month follow-up, shoulder motion range, rates of superficial infection, temporary brachial plexus lesion, nonunion, malunion, delayed union, implant failure and need for major revision, both techniques were similar. Findings of this meta-analysis suggest that, in many respects, IF was superior to PF for the management of midshaft clavicle fractures. This finding could aid surgeons in making decisions on the optimum internal fixation pattern for midshaft clavicular fractures. © The Author(s) 2016.

Examination of Variables That May Affect the Relationship Between Cognition and Functional Status in Individuals with Mild Cognitive Impairment: A Meta-Analysis

PubMed Central

Mcalister, Courtney; Schmitter-Edgecombe, Maureen; Lamb, Richard

2016-01-01

The objective of this meta-analysis was to improve understanding of the heterogeneity in the relationship between cognition and functional status in individuals with mild cognitive impairment (MCI). Demographic, clinical, and methodological moderators were examined. Cognition explained an average of 23% of the variance in functional outcomes. Executive function measures explained the largest amount of variance (37%), whereas global cognitive status and processing speed measures explained the least (20%). Short- and long-delayed memory measures accounted for more variance (35% and 31%) than immediate memory measures (18%), and the relationship between cognition and functional outcomes was stronger when assessed with informant-report (28%) compared with self-report (21%). Demographics, sample characteristics, and type of everyday functioning measures (i.e., questionnaire, performance-based) explained relatively little variance compared with cognition. Executive functioning, particularly measured by Trails B, was a strong predictor of everyday functioning in individuals with MCI. A large proportion of variance remained unexplained by cognition. PMID:26743326

Relative contributions of three descriptive methods: implications for behavioral assessment.

PubMed

Pence, Sacha T; Roscoe, Eileen M; Bourret, Jason C; Ahearn, William H

2009-01-01

This study compared the outcomes of three descriptive analysis methods-the ABC method, the conditional probability method, and the conditional and background probability method-to each other and to the results obtained from functional analyses. Six individuals who had been diagnosed with developmental delays and exhibited problem behavior participated. Functional analyses indicated that participants' problem behavior was maintained by social positive reinforcement (n = 2), social negative reinforcement (n = 2), or automatic reinforcement (n = 2). Results showed that for all but 1 participant, descriptive analysis outcomes were similar across methods. In addition, for all but 1 participant, the descriptive analysis outcome differed substantially from the functional analysis outcome. This supports the general finding that descriptive analysis is a poor means of determining functional relations.

A Spiking Neural Network Methodology and System for Learning and Comparative Analysis of EEG Data From Healthy Versus Addiction Treated Versus Addiction Not Treated Subjects.

PubMed

Doborjeh, Maryam Gholami; Wang, Grace Y; Kasabov, Nikola K; Kydd, Robert; Russell, Bruce

2016-09-01

This paper introduces a method utilizing spiking neural networks (SNN) for learning, classification, and comparative analysis of brain data. As a case study, the method was applied to electroencephalography (EEG) data collected during a GO/NOGO cognitive task performed by untreated opiate addicts, those undergoing methadone maintenance treatment (MMT) for opiate dependence and a healthy control group. the method is based on an SNN architecture called NeuCube, trained on spatiotemporal EEG data. NeuCube was used to classify EEG data across subject groups and across GO versus NOGO trials, but also facilitated a deeper comparative analysis of the dynamic brain processes. This analysis results in a better understanding of human brain functioning across subject groups when performing a cognitive task. In terms of the EEG data classification, a NeuCube model obtained better results (the maximum obtained accuracy: 90.91%) when compared with traditional statistical and artificial intelligence methods (the maximum obtained accuracy: 50.55%). more importantly, new information about the effects of MMT on cognitive brain functions is revealed through the analysis of the SNN model connectivity and its dynamics. this paper presented a new method for EEG data modeling and revealed new knowledge on brain functions associated with mental activity which is different from the brain activity observed in a resting state of the same subjects.

Development of a Time-Variant Figure-of-Merit for Use in Analysis of Air Combat Maneuvering Engagements

DTIC Science & Technology

1976-07-16

Influence of Range 10 5 Range Performance Penalty Function II 6 Influence of Closing Velocity 12 7 Energy Influence Function 14 8 Comparison of the...flELtSHAlL, ..E^) RANGE RANGE Figure 7 Energy Influence Function 14 TM 76-1 SA ! PERFORMANCE INDEX COMPARATIVE ANALYSIS Maneuver Conversion Model...hnergy Integral ■’> E s K Energy Influence Function K* Proportionality Constant MT Target Mach Number N Normal Acceleration (load factor) z

Free vibrations and buckling analysis of laminated plates by oscillatory radial basis functions

NASA Astrophysics Data System (ADS)

Neves, A. M. A.; Ferreira, A. J. M.

2015-12-01

In this paper the free vibrations and buckling analysis of laminated plates is performed using a global meshless method. A refined version of Kant's theorie which accounts for transverse normal stress and through-the-thickness deformation is used. The innovation is the use of oscillatory radial basis functions. Numerical examples are performed and results are presented and compared to available references. Such functions proved to be an alternative to the tradicional nonoscillatory radial basis functions.

Brain functional network abnormality extends beyond the sensorimotor network in brachial plexus injury patients.

PubMed

Feng, Jun-Tao; Liu, Han-Qiu; Hua, Xu-Yun; Gu, Yu-Dong; Xu, Jian-Guang; Xu, Wen-Dong

2016-12-01

Brachial plexus injury (BPI) is a type of severe peripheral nerve trauma that leads to central remodeling in the brain, as revealed by functional MRI analysis. However, previously reported remodeling is mostly restricted to sensorimotor areas of the brain. Whether this disturbance in the sensorimotor network leads to larger-scale functional remodeling remains unknown. We sought to explore the higher-level brain functional abnormality pattern of BPI patients from a large-scale network function connectivity dimension in 15 right-handed BPI patients. Resting-state functional MRI data were collected and analyzed using independent component analysis methods. Five components of interest were recognized and compared between patients and healthy subjects. Patients showed significantly altered brain local functional activities in the bilateral fronto-parietal network (FPN), sensorimotor network (SMN), and executive-control network (ECN) compared with healthy subjects. Moreover, functional connectivity between SMN and ECN were significantly less in patients compared with healthy subjects, and connectivity strength between ECN and SMN was negatively correlated with patients' residual function of the affected limb. Functional connectivity between SMN and right FPN were also significantly less than in controls, although connectivity between ECN and default mode network (DMN) was greater than in controls. These data suggested that brain functional disturbance in BPI patients extends beyond the sensorimotor network and cascades serial remodeling in the brain, which significantly correlates with residual hand function of the paralyzed limb. Furthermore, functional remodeling in these higher-level functional networks may lead to cognitive alterations in complex tasks.

Comparative analysis of short - term functional outcomes and quality of life in a prospective series of brachytherapy and Da Vinci robotic prostatectomy

PubMed Central

García-Sánchez, Cristina; Román Martín, Ana A.; Conde-Sánchez, J. Manuel; Congregado-Ruíz, C. Belén; Osman-García, Ignacio; Medina-López, Rafael A.

2017-01-01

ABSTRACT Introduction There is a growing interest in achieving higher survival rates with the lowest morbidity in localized prostate cancer (PC) treatment. Consequently, minimally invasive techniques such as low-dose rate brachytherapy (BT) and robotic-assisted prostatectomy (RALP) have been developed and improved. Comparative analysis of functional outcomes and quality of life in a prospective series of 51BT and 42Da Vinci prostatectomies DV Materials and Methods Comparative analysis of functional outcomes and quality of life in a prospective series of 93 patients with low-risk localized PC diagnosed in 2011. 51patients underwent low-dose rate BT and the other 42 patients RALP. IIEF to assess erectile function, ICIQ to evaluate continence and SF36 test to quality of life wee employed. Results ICIQ at the first revision shows significant differences which favour the BT group, 79% present with continence or mild incontinence, whereas in the DV group 45% show these positive results. Differences disappear after 6 months, with 45 patients (89%) presenting with continence or mild incontinence in the BT group vs. 30 (71%) in the DV group. 65% of patients are potent in the first revision following BT and 39% following DV. Such differences are not significant and cannot be observed after 6 months. No significant differences were found in the comparative analysis of quality of life. Conclusions ICIQ after surgery shows significant differences in favour of BT, which disappear after 6 months. Both procedures have a serious impact on erectile function, being even greater in the DV group. Differences between groups disappear after 6 months. PMID:28128908

Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem.

PubMed

Illeghems, Koen; De Vuyst, Luc; Weckx, Stefan

2013-08-01

Acetobacter pasteurianus 386B, an acetic acid bacterium originating from a spontaneous cocoa bean heap fermentation, proved to be an ideal functional starter culture for coca bean fermentations. It is able to dominate the fermentation process, thereby resisting high acetic acid concentrations and temperatures. However, the molecular mechanisms underlying its metabolic capabilities and niche adaptations are unknown. In this study, whole-genome sequencing and comparative genome analysis was used to investigate this strain's mechanisms to dominate the cocoa bean fermentation process. The genome sequence of A. pasteurianus 386B is composed of a 2.8-Mb chromosome and seven plasmids. The annotation of 2875 protein-coding sequences revealed important characteristics, including several metabolic pathways, the occurrence of strain-specific genes such as an endopolygalacturonase, and the presence of mechanisms involved in tolerance towards various stress conditions. Furthermore, the low number of transposases in the genome and the absence of complete phage genomes indicate that this strain might be more genetically stable compared with other A. pasteurianus strains, which is an important advantage for the use of this strain as a functional starter culture. Comparative genome analysis with other members of the Acetobacteraceae confirmed the functional properties of A. pasteurianus 386B, such as its thermotolerant nature and unique genetic composition. Genome analysis of A. pasteurianus 386B provided detailed insights into the underlying mechanisms of its metabolic features, niche adaptations, and tolerance towards stress conditions. Combination of these data with previous experimental knowledge enabled an integrated, global overview of the functional characteristics of this strain. This knowledge will enable improved fermentation strategies and selection of appropriate acetic acid bacteria strains as functional starter culture for cocoa bean fermentation processes.

Microbial community analysis using MEGAN.

PubMed

Huson, Daniel H; Weber, Nico

2013-01-01

Metagenomics, the study of microbes in the environment using DNA sequencing, depends upon dedicated software tools for processing and analyzing very large sequencing datasets. One such tool is MEGAN (MEtaGenome ANalyzer), which can be used to interactively analyze and compare metagenomic and metatranscriptomic data, both taxonomically and functionally. To perform a taxonomic analysis, the program places the reads onto the NCBI taxonomy, while functional analysis is performed by mapping reads to the SEED, COG, and KEGG classifications. Samples can be compared taxonomically and functionally, using a wide range of different charting and visualization techniques. PCoA analysis and clustering methods allow high-level comparison of large numbers of samples. Different attributes of the samples can be captured and used within analysis. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de. © 2013 Elsevier Inc. All rights reserved.

Delay differential equations via the matrix Lambert W function and bifurcation analysis: application to machine tool chatter.

PubMed

Yi, Sun; Nelson, Patrick W; Ulsoy, A Galip

2007-04-01

In a turning process modeled using delay differential equations (DDEs), we investigate the stability of the regenerative machine tool chatter problem. An approach using the matrix Lambert W function for the analytical solution to systems of delay differential equations is applied to this problem and compared with the result obtained using a bifurcation analysis. The Lambert W function, known to be useful for solving scalar first-order DDEs, has recently been extended to a matrix Lambert W function approach to solve systems of DDEs. The essential advantages of the matrix Lambert W approach are not only the similarity to the concept of the state transition matrix in lin ear ordinary differential equations, enabling its use for general classes of linear delay differential equations, but also the observation that we need only the principal branch among an infinite number of roots to determine the stability of a system of DDEs. The bifurcation method combined with Sturm sequences provides an algorithm for determining the stability of DDEs without restrictive geometric analysis. With this approach, one can obtain the critical values of delay, which determine the stability of a system and hence the preferred operating spindle speed without chatter. We apply both the matrix Lambert W function and the bifurcation analysis approach to the problem of chatter stability in turning, and compare the results obtained to existing methods. The two new approaches show excellent accuracy and certain other advantages, when compared to traditional graphical, computational and approximate methods.

Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes.

PubMed

Illeghems, Koen; De Vuyst, Luc; Weckx, Stefan

2015-10-12

Lactobacillus fermentum 222 and Lactobacillus plantarum 80, isolates from a spontaneous Ghanaian cocoa bean fermentation process, proved to be interesting functional starter culture strains for cocoa bean fermentations. Lactobacillus fermentum 222 is a thermotolerant strain, able to dominate the fermentation process, thereby converting citrate and producing mannitol. Lactobacillus plantarum 80 is an acid-tolerant and facultative heterofermentative strain that is competitive during cocoa bean fermentation processes. In this study, whole-genome sequencing and comparative genome analysis was used to investigate the mechanisms of these strains to dominate the cocoa bean fermentation process. Through functional annotation and analysis of the high-coverage contigs obtained through 454 pyrosequencing, plantaricin production was predicted for L. plantarum 80. For L. fermentum 222, genes encoding a complete arginine deiminase pathway were attributed. Further, in-depth functional analysis revealed the capacities of these strains associated with carbohydrate and amino acid metabolism, such as the ability to use alternative external electron acceptors, the presence of an extended pyruvate metabolism, and the occurrence of several amino acid conversion pathways. A comparative genome sequence analysis using publicly available genome sequences of strains of the species L. plantarum and L. fermentum revealed unique features of both strains studied. Indeed, L. fermentum 222 possessed genes encoding additional citrate transporters and enzymes involved in amino acid conversions, whereas L. plantarum 80 is the only member of this species that harboured a gene cluster involved in uptake and consumption of fructose and/or sorbose. In-depth genome sequence analysis of the candidate functional starter culture strains L. fermentum 222 and L. plantarum 80 revealed their metabolic capacities, niche adaptations and functionalities that enable them to dominate the cocoa bean fermentation process. Further, these results offered insights into the cocoa bean fermentation ecosystem as a whole and will facilitate the selection of appropriate starter culture strains for controlled cocoa bean fermentation processes.

Impact of Renal Hilar Control on Outcomes of Robotic Partial Nephrectomy: Systematic Review and Cumulative Meta-analysis.

PubMed

Cacciamani, Giovanni E; Medina, Luis G; Gill, Tania S; Mendelsohn, Alec; Husain, Fatima; Bhardwaj, Lokesh; Artibani, Walter; Sotelo, Renè; Gill, Inderbir S

2018-02-05

During robotic partial nephrectomy (RPN), various techniques of hilar control have been described, including on-clamp, early unclamping, selective/super-selective clamping, and completely-unclamped RPN. To evaluate the impact of various hilar control techniques on perioperative, functional, and oncological outcomes of RPN for tumors. We conducted a systematic literature review and meta-analysis of all comparative studies on various hilar control techniques during RPN using PubMed, Scopus, and Web of Science according to the Preferred Reporting Items for Systematic Review and Meta-analysis statement, and Methods and Guide for Effectiveness and Comparative Effectiveness Review of the Agency for Healthcare Research and Quality. Cumulative meta-analysis of comparative studies was conducted using Review Manager 5.3. Of 987 RPN publications in the literature, 19 qualified for this analysis. Comparison of off-clamp versus on-clamp RPN (n=9), selective clamping versus on-clamp RPN (n=3), super selective clamping versus on-clamp RPN (n=5), and early unclamped versus on-clamp (n=3) were reported. Patients undergoing RPN using off-clamp, selective/super selective, or early unclamp techniques had higher estimated blood loss compared with on-clamp RPN (weight mean difference [WMD]: 47.83, p=0.000, WMD: 41.06, p=0.02, and WMD: 37.50, p=0.47); however, this did not seem clinically relevant, since transfusion rates were similar (odds ratio [OR]: 0.98, p=0.95, OR: 0.72, p=0.7, and OR: 1.36, p=0.33, respectively). All groups appeared similar with regards to hospital stay, transfusions, overall and major complications, and positive cancer margin rates. Short- and long-term renal functional outcomes appeared superior in the off-clamp and super selective clamp groups compared with the on-clamp RPN cohort. Off-clamp, selective/super selective clamp, and early unclamp hilar control techniques are safe and feasible approaches for RPN surgery, with similar perioperative and oncological outcomes compared with on-clamp RPN. Minimizing global renal ischemia may provide superior renal function preservation. However, higher quality data are necessary for definitive conclusions in this regard. The objective of partial nephrectomy is to treat the cancer while maximizing renal function preservation. Clamping the main vessels is done primarily to reduce the blood loss during partial nephrectomy; however, vascular clamping can compromise kidney function. In order to avoid clamping, various techniques have been described. Our analysis showed that techniques that avoid main renal artery clamping during RPN are associated with better renal function preservation, yet deliver non-inferior perioperative and oncological outcomes as compared with robotic partial nephrectomy procedures that clamp the main vessels. Copyright © 2018 European Association of Urology. Published by Elsevier B.V. All rights reserved.

RELATIVE CONTRIBUTIONS OF THREE DESCRIPTIVE METHODS: IMPLICATIONS FOR BEHAVIORAL ASSESSMENT

PubMed Central

Pence, Sacha T; Roscoe, Eileen M; Bourret, Jason C; Ahearn, William H

2009-01-01

This study compared the outcomes of three descriptive analysis methods—the ABC method, the conditional probability method, and the conditional and background probability method—to each other and to the results obtained from functional analyses. Six individuals who had been diagnosed with developmental delays and exhibited problem behavior participated. Functional analyses indicated that participants' problem behavior was maintained by social positive reinforcement (n  =  2), social negative reinforcement (n  =  2), or automatic reinforcement (n  =  2). Results showed that for all but 1 participant, descriptive analysis outcomes were similar across methods. In addition, for all but 1 participant, the descriptive analysis outcome differed substantially from the functional analysis outcome. This supports the general finding that descriptive analysis is a poor means of determining functional relations. PMID:19949536

Functional outcomes in African-Americans after robot-assisted radical prostatectomy.

PubMed

DeCastro, G Joel; Jayram, Gautam; Razmaria, Aria; Shalhav, Arieh; Zagaja, Gregory P

2012-08-01

Previous studies have demonstrated differences in surgical outcomes after radical prostatectomy based on ethnicity. We compared sexual and urinary outcomes in African-American (AA) patients 6 and 12 months after robot-assisted radical prostatectomy (RARP) with those of non-AA patients. We reviewed our RARP database at our institution for patients with at least 12 months of follow-up. Erectile function was defined using the University of California, Los Angeles Prostate Cancer Index as erections "firm enough for masturbation and foreplay" or "firm enough for intercourse," while urinary continence was defined as being "pad free." Only patients who were potent and pad free preoperatively were included in the analysis. Multivariate logistic regression was used to compare postoperative potency and urinary pad-free status between AA and non-AA patients while controlling for pertinent demographic, clinical, and pathologic variables. In the urinary continence analysis, 140 AA patients and 576 non-AA patients were included, compared with 105 AAs and 500 non-AA patients who were included in the analysis of sexual function. At 12 months postoperatively, a smaller proportion of AA patients were potent compared with non-AA patients (60% vs 76.4%, P=0.001). Similarly, we found a lower incidence of pad-free status for AA patients at 12 months postoperatively (55.7% vs 69.8%, P=0.039). Similar functional results were found at 6 months postoperatively for both analysis groups. AA men appear to have worse urinary and sexual outcomes at 12 months after RARP compared with non-AA patients. At 6 months, there is no statistically significant difference. Further, longer-term studies are needed to validate these results.

Plate fixation versus intramedullary fixation for midshaft clavicle fractures: Meta-analysis of complications and functional outcomes

PubMed Central

Xiao, Hao; Gao, Hengbo; Zheng, Tuokang; Zhao, Jianhui

2016-01-01

Objective This analysis critically compares publications discussing complications and functional outcomes of plate fixation (PF) versus intramedullary fixation (IF) for midshaft clavicle fractures. Methods Relevant studies published between January 1990 and October 2014, without language restrictions, were identified in database searches of PubMed®, Medline®, Embase and the Chinese National Knowledge Infrastructure (CNKI). Studies that compared postoperative complications and functional outcomes between PF and IF for midshaft clavicle fractures, and provided sufficient data for analysis, were included in this meta-analysis. Results After strict evaluation, 12 studies were included in this meta-analysis. Studies encompassed 462 participants in the PF group and 440 in the IF group. Study participants were followed up for ≥1 year. Outcomes were superior with IF compared with PF in terms of shoulder constant score at 6-month follow-up, fewer symptomatic hardware complications, lower rate of refracture after hardware removal and less hypertrophic scarring. In other aspects, such as functional recovery at 12-months and 24-months, Disability of Arm, Shoulder and Hand (DASH) questionnaire results at 12-month follow-up, shoulder motion range, rates of superficial infection, temporary brachial plexus lesion, nonunion, malunion, delayed union, implant failure and need for major revision, both techniques were similar. Conclusions Findings of this meta-analysis suggest that, in many respects, IF was superior to PF for the management of midshaft clavicle fractures. This finding could aid surgeons in making decisions on the optimum internal fixation pattern for midshaft clavicular fractures. PMID:26880791

Variability in the Results of Meta-Analysis as a Function of Comparing Effect Sizes Based on Scores from Noncomparable Measures: A Simulation Study

ERIC Educational Resources Information Center

Nugent, William R.

2017-01-01

Meta-analysis is a significant methodological advance that is increasingly important in research synthesis. Fundamental to meta-analysis is the presumption that effect sizes, such as the standardized mean difference (SMD), based on scores from different measures are comparable. It has been argued that population observed score SMDs based on scores…

Genome-Wide Comparative Analysis of the Phospholipase D Gene Families among Allotetraploid Cotton and Its Diploid Progenitors

PubMed Central

Tang, Kai; Dong, Chun-Juan; Liu, Jin-Yuan

2016-01-01

In this study, 40 phospholipase D (PLD) genes were identified from allotetraploid cotton Gossypium hirsutum, and 20 PLD genes were examined in diploid cotton Gossypium raimondii. Combining with 19 previously identified Gossypium arboreum PLD genes, a comparative analysis was performed among the PLD gene families among allotetraploid and two diploid cottons. Based on the orthologous relationships, we found that almost each G. hirsutum PLD had a corresponding homolog in the G. arboreum and G. raimondii genomes, except for GhPLDβ3A, whose homolog GaPLDβ3 may have been lost during the evolution of G. arboreum after the interspecific hybridization. Phylogenetic analysis showed that all of the cotton PLDs were unevenly classified into six numbered subgroups: α, β/γ, δ, ε, ζ and φ. An N-terminal C2 domain was found in the α, β/γ, δ and ε subgroups, while phox homology (PX) and pleckstrin homology (PH) domains were identified in the ζ subgroup. The subgroup φ possessed a single peptide instead of a functional domain. In each phylogenetic subgroup, the PLDs showed high conservation in gene structure and amino acid sequences in functional domains. The expansion of GhPLD and GrPLD gene families were mainly attributed to segmental duplication and partly attributed to tandem duplication. Furthermore, purifying selection played a critical role in the evolution of PLD genes in cotton. Quantitative RT-PCR documented that allotetraploid cotton PLD genes were broadly expressed and each had a unique spatial and developmental expression pattern, indicating their functional diversification in cotton growth and development. Further analysis of cis-regulatory elements elucidated transcriptional regulations and potential functions. Our comparative analysis provided valuable information for understanding the putative functions of the PLD genes in cotton fiber. PMID:27213891

One-leg hop kinematics 20 years following anterior cruciate ligament rupture: Data revisited using functional data analysis.

PubMed

Hébert-Losier, Kim; Pini, Alessia; Vantini, Simone; Strandberg, Johan; Abramowicz, Konrad; Schelin, Lina; Häger, Charlotte K

2015-12-01

Despite interventions, anterior cruciate ligament ruptures can cause long-term deficits. To assist in identifying and treating deficiencies, 3D-motion analysis is used for objectivizing data. Conventional statistics are commonly employed to analyze kinematics, reducing continuous data series to discrete variables. Conversely, functional data analysis considers the entire data series. Here, we employ functional data analysis to examine and compare the entire time-domain of knee-kinematic curves from one-leg hops between and within three groups. All subjects (n=95) were part of a long-term follow-up study involving anterior cruciate ligament ruptures treated ~20 years ago conservatively with physiotherapy only or with reconstructive surgery and physiotherapy, and matched knee-healthy controls. Between-group differences (injured leg, treated groups; non-dominant leg, controls) were identified during the take-off and landing phases, and in the sagittal (flexion/extension) rather than coronal (abduction/adduction) and transverse (internal/external) planes. Overall, surgical and control groups demonstrated comparable knee-kinematic curves. However, compared to controls, the physiotherapy-only group exhibited less flexion during the take-off (0-55% of the normalized phase) and landing (44-73%) phase. Between-leg differences were absent in controls and the surgically treated group, but observed during the flight (4-22%, injured leg>flexion) and the landing (57-85%, injured leg

Examination of Variables That May Affect the Relationship Between Cognition and Functional Status in Individuals with Mild Cognitive Impairment: A Meta-Analysis.

PubMed

Mcalister, Courtney; Schmitter-Edgecombe, Maureen; Lamb, Richard

2016-03-01

The objective of this meta-analysis was to improve understanding of the heterogeneity in the relationship between cognition and functional status in individuals with mild cognitive impairment (MCI). Demographic, clinical, and methodological moderators were examined. Cognition explained an average of 23% of the variance in functional outcomes. Executive function measures explained the largest amount of variance (37%), whereas global cognitive status and processing speed measures explained the least (20%). Short- and long-delayed memory measures accounted for more variance (35% and 31%) than immediate memory measures (18%), and the relationship between cognition and functional outcomes was stronger when assessed with informant-report (28%) compared with self-report (21%). Demographics, sample characteristics, and type of everyday functioning measures (i.e., questionnaire, performance-based) explained relatively little variance compared with cognition. Executive functioning, particularly measured by Trails B, was a strong predictor of everyday functioning in individuals with MCI. A large proportion of variance remained unexplained by cognition. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Comparative Biochemical and Functional Studies on a Branded Human Recombinant Factor VIIa and a Biosimilar Equivalent Product.

PubMed

Sadeghi, Nasiredin; Kahn, Daniel; Syed, Daneyal; Iqbal, Omer; Abro, Schuharazad; Eshraghi, Reza; Hoppensteadt, Debra; Fareed, Jawed

2014-09-01

Recombinant factor VIIa (rFVIIa; NovoSeven, Novo Nordisk, Copenhagen, Denmark) is used to control bleeding in patients with hemophilia. A generic version of FVIIa was developed by AryoGen (Tehran, Iran). This study compared the composition and functional activities of AryoSeven and NovoSeven. Each product was compared at equigravimetric (1 mg/mL) stock solution for protein content. The proteomic profile was obtained using surface-enhanced laser desorption ionization mass spectrometry. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis was carried out to determine the protein profile and Western blotting was performed using a polyclonal rabbit antihuman FVIIa antibody. The FVIIa-related antigen was also measured using a commercially available enzyme-linked immunosorbent assay method. Functional assay included the prothrombin time correction in FVII-deficient plasma. The protein content was comparable in 2 products and the mass spectra analysis showed a single peak at 50 kDa in all products. The SDS-PAGE and immunoblotting studies were comparable. Both products exhibited similar coagulant properties in different assays. © The Author(s) 2014.

A multicriteria decision analysis of augmentative treatment of upper limbs in persons with tetraplegia.

PubMed

Hummel, J M Marjan; Snoek, Govert J; van Til, Janine A; van Rossum, Wouter; Ijzerman, Maarten J

2005-01-01

This study supported the evaluation by a rehabilitation team of the performance of two treatment options that improve the arm-hand function in subjects with sixth cervical vertebra (C6) level Motor Group 2 tetraplegia. The analytic hierarchy process, a technique for multicriteria decision analysis, was used by a rehabilitation team and potential recipients to quantitatively compare a new technology, Functional Elec trical Stimulation (FES), with conventional surgery. Perform-ance was measured by functional improvement, treatment load, risks, user-friendliness, and social outcomes. Functional improvement after FES was considered better than that after conventional surgery. However, the rehabilitation team's overall rating for conventional surgery was slightly higher than that for FES (57% vs 44%). Compared with the rehabilitation team, potential recipients gave greater weight to burden of treatment and less weight to functional improvement. This study shows that evaluation of new technology must be more comprehensive than the evaluation of functional improvement alone, and that patient preferences may differ from those of the rehabilitation team.

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.

PubMed

Sun, Eric I; Leyn, Semen A; Kazanov, Marat D; Saier, Milton H; Novichkov, Pavel S; Rodionov, Dmitry A

2013-09-02

In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels.An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis. A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations. The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome-wide collection of reference RNA motif regulons is available in the RegPrecise database (http://regprecise.lbl.gov/).

Higher protein intake increases cardiac function parameters in healthy children: metabolic programming by infant nutrition-secondary analysis from a clinical trial.

PubMed

Collell, Rosa; Closa-Monasterolo, Ricardo; Ferré, Natalia; Luque, Veronica; Koletzko, Berthold; Grote, Veit; Janas, Roman; Verduci, Elvira; Escribano, Joaquín

2016-06-01

Protein intake may modulate cardiac structure and function in pathological conditions, but there is a lack of knowledge on potential effects in healthy infants. Secondary analysis of an ongoing randomized clinical trial comparing two groups of infants receiving a higher (HP) or lower (LP) protein content formula in the first year of life, and compared with an observational group of breastfed (BF) infants. Growth and dietary intake were assessed periodically from birth to 2 y. Insulin-like growth factor 1 (IGF-1) axis parameters were analyzed at 6 mo in a blood sample. At 2 y, cardiac mass and function were assessed by echocardiography. HP infants (n = 50) showed a higher BMI z-score at 2 y compared with LP (n = 47) or BF (n = 44). Cardiac function parameters were increased in the HP group compared with the LP and were directly related to the protein intake during the first 6 mo of life. Moreover, there was an increase in free IGF-1 in the HP group at 6 mo. A moderate increase in protein supply during the first year of life is associated with higher cardiac function parameters at 2 y. IGF-1 axis modifications may, at least in part, underlie these effects.

WEBnm@ v2.0: Web server and services for comparing protein flexibility.

PubMed

Tiwari, Sandhya P; Fuglebakk, Edvin; Hollup, Siv M; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn H; Tekle, Kidane M; Reuter, Nathalie

2014-12-30

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

Quality of Life and Aesthetic Plastic Surgery: A Systematic Review and Meta-analysis.

PubMed

Dreher, Rodrigo; Blaya, Carolina; Tenório, Juliana L C; Saltz, Renato; Ely, Pedro B; Ferrão, Ygor A

2016-09-01

Quality of life (QoL) is an important outcome in plastic surgery. However, authors use different scales to address this subject, making it difficult to compare the outcomes. To address this discrepancy, the aim of this study was to perform a systematic review and a random effect meta-analysis. The search was made in two electronic databases (LILACS and PUBMED) using Mesh and non-Mesh terms related to aesthetic plastic surgery and QoL. We performed qualitative and quantitative analyses of the gathered data. We calculated a random effect meta-analysis with Der Simonian and Laird as variance estimator to compare pre- and postoperative QoL standardized mean difference. To check if there is difference between aesthetic surgeries, we compared reduction mammoplasty to other aesthetic surgeries. Of 1,715 identified, 20 studies were included in the qualitative analysis and 16 went through quantitative analysis. The random effect of all aesthetic surgeries shows that QoL improved after surgery. Reduction mammoplasty has improved QoL more than other procedures in social functioning and physical functioning domains. Aesthetic plastic surgery increases QoL. Reduction mammoplasty seems to have better improvement compared with other aesthetic surgeries.

Comparative analysis of numerical simulation techniques for incoherent imaging of extended objects through atmospheric turbulence

NASA Astrophysics Data System (ADS)

Lachinova, Svetlana L.; Vorontsov, Mikhail A.; Filimonov, Grigory A.; LeMaster, Daniel A.; Trippel, Matthew E.

2017-07-01

Computational efficiency and accuracy of wave-optics-based Monte-Carlo and brightness function numerical simulation techniques for incoherent imaging of extended objects through atmospheric turbulence are evaluated. Simulation results are compared with theoretical estimates based on known analytical solutions for the modulation transfer function of an imaging system and the long-exposure image of a Gaussian-shaped incoherent light source. It is shown that the accuracy of both techniques is comparable over the wide range of path lengths and atmospheric turbulence conditions, whereas the brightness function technique is advantageous in terms of the computational speed.

Integrative analysis of environmental sequences using MEGAN4.

PubMed

Huson, Daniel H; Mitra, Suparna; Ruscheweyh, Hans-Joachim; Weber, Nico; Schuster, Stephan C

2011-09-01

A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

Statistical correlation analysis for comparing vibration data from test and analysis

NASA Technical Reports Server (NTRS)

Butler, T. G.; Strang, R. F.; Purves, L. R.; Hershfeld, D. J.

1986-01-01

A theory was developed to compare vibration modes obtained by NASTRAN analysis with those obtained experimentally. Because many more analytical modes can be obtained than experimental modes, the analytical set was treated as expansion functions for putting both sources in comparative form. The dimensional symmetry was developed for three general cases: nonsymmetric whole model compared with a nonsymmetric whole structural test, symmetric analytical portion compared with a symmetric experimental portion, and analytical symmetric portion with a whole experimental test. The theory was coded and a statistical correlation program was installed as a utility. The theory is established with small classical structures.

Functional Evolution of a cis-Regulatory Module

PubMed Central

Palsson, Arnar; Alekseeva, Elena; Bergman, Casey M; Nathan, Janaki; Kreitman, Martin

2005-01-01

Lack of knowledge about how regulatory regions evolve in relation to their structure–function may limit the utility of comparative sequence analysis in deciphering cis-regulatory sequences. To address this we applied reverse genetics to carry out a functional genetic complementation analysis of a eukaryotic cis-regulatory module—the even-skipped stripe 2 enhancer—from four Drosophila species. The evolution of this enhancer is non-clock-like, with important functional differences between closely related species and functional convergence between distantly related species. Functional divergence is attributable to differences in activation levels rather than spatiotemporal control of gene expression. Our findings have implications for understanding enhancer structure–function, mechanisms of speciation and computational identification of regulatory modules. PMID:15757364

Northwestern University Flexible Subischial Vacuum Socket for persons with transfemoral amputation: Part 2 Description and Preliminary evaluation.

PubMed

Fatone, Stefania; Caldwell, Ryan

2017-06-01

Current transfemoral prosthetic sockets are problematic as they restrict function, lack comfort, and cause residual limb problems. Development of a subischial socket with lower proximal trim lines is an appealing way to address this problem and may contribute to improving quality of life of persons with transfemoral amputation. The purpose of this study was to illustrate the use of a new subischial socket in two subjects. Case series. Two unilateral transfemoral prosthesis users participated in preliminary socket evaluations comparing functional performance of the new subischial socket to ischial containment sockets. Testing included gait analysis, socket comfort score, and performance-based clinical outcome measures (Rapid-Sit-To-Stand, Four-Square-Step-Test, and Agility T-Test). For both subjects, comfort was better in the subischial socket, while gait and clinical outcomes were generally comparable between sockets. While these evaluations are promising regarding the ability to function in this new socket design, more definitive evaluation is needed. Clinical relevance Using gait analysis, socket comfort score and performance-based outcome measures, use of the Northwestern University Flexible Subischial Vaccum Socket was evaluated in two transfemoral prosthesis users. Socket comfort improved for both subjects with comparable function compared to ischial containment sockets.

Comparative Analysis of the Clinical Significance of Oscillatory Components in the Rhythmic Structure of Pulse Signal in the Diagnostics of Psychosomatic Disorders in School Age Children.

PubMed

Desova, A A; Dorofeyuk, A A; Anokhin, A M

2017-01-01

We performed a comparative analysis of the types of spectral density typical of various parameters of pulse signal. The experimental material was obtained during the examination of school age children with various psychosomatic disorders. We also performed a typological analysis of the spectral density functions corresponding to the time series of different parameters of a single oscillation of pulse signals; the results of their comparative analysis are presented. We determined the most significant spectral components for two disordersin children: arterial hypertension and mitral valve prolapse.

Computational Methods to Work as First-Pass Filter in Deleterious SNP Analysis of Alkaptonuria

PubMed Central

Magesh, R.; George Priya Doss, C.

2012-01-01

A major challenge in the analysis of human genetic variation is to distinguish functional from nonfunctional SNPs. Discovering these functional SNPs is one of the main goals of modern genetics and genomics studies. There is a need to effectively and efficiently identify functionally important nsSNPs which may be deleterious or disease causing and to identify their molecular effects. The prediction of phenotype of nsSNPs by computational analysis may provide a good way to explore the function of nsSNPs and its relationship with susceptibility to disease. In this context, we surveyed and compared variation databases along with in silico prediction programs to assess the effects of deleterious functional variants on protein functions. In other respects, we attempted these methods to work as first-pass filter to identify the deleterious substitutions worth pursuing for further experimental research. In this analysis, we used the existing computational methods to explore the mutation-structure-function relationship in HGD gene causing alkaptonuria. PMID:22606059

Partnering for functional genomics research conference: Abstracts of poster presentations

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

NONE

1998-06-01

This reports contains abstracts of poster presentations presented at the Functional Genomics Research Conference held April 16--17, 1998 in Oak Ridge, Tennessee. Attention is focused on the following areas: mouse mutagenesis and genomics; phenotype screening; gene expression analysis; DNA analysis technology development; bioinformatics; comparative analyses of mouse, human, and yeast sequences; and pilot projects to evaluate methodologies.

Treatment effects between monotherapy of donepezil versus combination with memantine for Alzheimer disease: A meta-analysis.

PubMed

Chen, Ruey; Chan, Pi-Tuan; Chu, Hsin; Lin, Yu-Cih; Chang, Pi-Chen; Chen, Chien-Yu; Chou, Kuei-Ru

2017-01-01

This is the first meta-analysis to compare the treatment effects and safety of administering donepezil alone versus a combination of memantine and donepezil to treat patients with moderate to severe Alzheimer Disease, particularly regarding cognitive functions, behavioral and psychological symptoms in dementia (BPSD), and global functions. PubMed, Medline, Embase, PsycINFO, and Cochrane databases were used to search for English and non-English articles for inclusion in the meta-analysis to evaluate the effect size and incidence of adverse drug reactions of different treatments. Compared with patients who received donepezil alone, those who received donepezil in combination with memantine exhibited limited improvements in cognitive functions (g = 0.378, p < .001), BPSD (g = -0.878, p < .001) and global functions (g = -0.585, p = .004). Gradual titration of memantine plus a fixed dose and gradual titration of donepezil as well as a fixed dose and gradual titration of memantine resulted in limited improvements in cognitive functions(g = 0.371, p = .005), BPSD(g = -0.913, p = .001), and global functions(g = -0.371, p = .001). Both in the 24th week and at the final evaluation point, the combination of donepezil and memantine led to greater improvement in cognitive functions, BPSD, and global functions than did donepezil alone in patients with moderate to severe Alzheimer Disease.

Cartilage Restoration of the Knee: A Systematic Review and Meta-analysis of Level 1 Studies.

PubMed

Mundi, Raman; Bedi, Asheesh; Chow, Linda; Crouch, Sarah; Simunovic, Nicole; Sibilsky Enselman, Elizabeth; Ayeni, Olufemi R

2016-07-01

Focal cartilage defects of the knee are a substantial cause of pain and disability in active patients. There has been an emergence of randomized controlled trials evaluating surgical techniques to manage such injuries, including marrow stimulation (MS), autologous chondrocyte implantation (ACI), and osteochondral autograft transfer (OAT). A meta-analysis was conducted to determine if any single technique provides superior clinical results at intermediate follow-up. Systematic review and meta-analysis of randomized controlled trials. The MEDLINE, EMBASE, and Cochrane Library databases were systematically searched and supplemented with manual searches of PubMed and reference lists. Eligible studies consisted exclusively of randomized controlled trials comparing MS, ACI, or OAT techniques in patients with focal cartilage defects of the knee. The primary outcome of interest was function (Lysholm score, International Knee Documentation Committee score, Knee Osteoarthritis Outcome Score) and pain at 24 months postoperatively. A meta-analysis using standardized mean differences was performed to provide a pooled estimate of effect comparing treatments. A total of 12 eligible randomized trials with a cumulative sample size of 765 patients (62% males) and a mean (±SD) lesion size of 3.9 ± 1.3 cm(2) were included in this review. There were 5 trials comparing ACI with MS, 3 comparing ACI with OAT, and 3 evaluating different generations of ACI. In a pooled analysis comparing ACI with MS, there was no difference in outcomes at 24-month follow-up for function (standardized mean difference, 0.47 [95% CI, -0.19 to 1.13]; P = .16) or pain (standardized mean difference, -0.13 [95% CI, -0.39 to 0.13]; P = .33). The comparisons of ACI to OAT or between different generations of ACI were not amenable to pooled analysis. Overall, 5 of the 6 trials concluded that there was no significant difference in functional outcomes between ACI and OAT or between generations of ACI. There is no significant difference between MS, ACI, and OAT in improving function and pain at intermediate-term follow-up. Further randomized trials with long-term outcomes are warranted. © 2015 The Author(s).

Early Rehabilitation in Elderly after Arthroplasty versus Internal Fixation for Unstable Intertrochanteric Fractures of Femur: Systematic Review and Meta-Analysis.

PubMed

Yoo, Jun Il; Ha, Yong Chan; Lim, Jae Young; Kang, Hyun; Yoon, Byung Ho; Kim, Hyunho

2017-05-01

The purpose of this study was to compare the outcomes focusing on the functional outcome and clinical results of replacement arthroplasty (AP) vs. internal fixation (IF) for the treatment of unstable intertrochanteric femoral fracture in elderly. Systematic review and meta-analysis were performed on 10 available clinical studies (2 randomized controlled trials and 8 comparative studies). Subgroup analysis was performed by type of methodological quality. Partial weight bearing time in AP group was earlier than that in IF group (SMD = -0.86; 95% CI = -0.42, 1.29; P = 0.050). The overall outcomes such as mortality, reoperation rate, and complication showed no significant diffrence between the 2 groups (AP vs. IF). Therefore, this systematic review demonstrates that AP provides superior functional outcomes especially earlier mobilization, as compared to IF in elderly patients with an unstable intertrochanteric femoral fracture. © 2017 The Korean Academy of Medical Sciences.

Classroom Application of a Trial-Based Functional Analysis

ERIC Educational Resources Information Center

Bloom, Sarah E.; Iwata, Brian A.; Fritz, Jennifer N.; Roscoe, Eileen M.; Carreau, Abbey B.

2011-01-01

We evaluated a trial-based approach to conducting functional analyses in classroom settings. Ten students referred for problem behavior were exposed to a series of assessment trials, which were interspersed among classroom activities throughout the day. Results of these trial-based functional analyses were compared to those of more traditional…

Improving information retrieval in functional analysis.

PubMed

Rodriguez, Juan C; González, Germán A; Fresno, Cristóbal; Llera, Andrea S; Fernández, Elmer A

2016-12-01

Transcriptome analysis is essential to understand the mechanisms regulating key biological processes and functions. The first step usually consists of identifying candidate genes; to find out which pathways are affected by those genes, however, functional analysis (FA) is mandatory. The most frequently used strategies for this purpose are Gene Set and Singular Enrichment Analysis (GSEA and SEA) over Gene Ontology. Several statistical methods have been developed and compared in terms of computational efficiency and/or statistical appropriateness. However, whether their results are similar or complementary, the sensitivity to parameter settings, or possible bias in the analyzed terms has not been addressed so far. Here, two GSEA and four SEA methods and their parameter combinations were evaluated in six datasets by comparing two breast cancer subtypes with well-known differences in genetic background and patient outcomes. We show that GSEA and SEA lead to different results depending on the chosen statistic, model and/or parameters. Both approaches provide complementary results from a biological perspective. Hence, an Integrative Functional Analysis (IFA) tool is proposed to improve information retrieval in FA. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required, since the best SEA/GSEA alternatives are integrated. IFA utility was demonstrated by evaluating four prostate cancer and the TCGA breast cancer microarray datasets, which showed its biological generalization capabilities. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Development of PIPA: An Integrated and Automated Pipeline for Genome-Wide Protein Function Annotation

DTIC Science & Technology

2008-01-25

limitations and plans for improvement Perhaps, one of PIPA’s main limitations is that all of its currently integrated resources to predict protein function...are planning on expending PIPA’s function prediction capabilities by incorporating comparative analysis approaches, e.g., phy- logenetic tree analysis...tools and services. Nucleic Acids Res 2005/12/31 edition. 2006, 34(Database issue):D247-51. 6. Bru C, Courcelle E, Carrere S, Beausse Y, Dalmar S

Variational Methods in Sensitivity Analysis and Optimization for Aerodynamic Applications

NASA Technical Reports Server (NTRS)

Ibrahim, A. H.; Hou, G. J.-W.; Tiwari, S. N. (Principal Investigator)

1996-01-01

Variational methods (VM) sensitivity analysis, which is the continuous alternative to the discrete sensitivity analysis, is employed to derive the costate (adjoint) equations, the transversality conditions, and the functional sensitivity derivatives. In the derivation of the sensitivity equations, the variational methods use the generalized calculus of variations, in which the variable boundary is considered as the design function. The converged solution of the state equations together with the converged solution of the costate equations are integrated along the domain boundary to uniquely determine the functional sensitivity derivatives with respect to the design function. The determination of the sensitivity derivatives of the performance index or functional entails the coupled solutions of the state and costate equations. As the stable and converged numerical solution of the costate equations with their boundary conditions are a priori unknown, numerical stability analysis is performed on both the state and costate equations. Thereafter, based on the amplification factors obtained by solving the generalized eigenvalue equations, the stability behavior of the costate equations is discussed and compared with the state (Euler) equations. The stability analysis of the costate equations suggests that the converged and stable solution of the costate equation is possible only if the computational domain of the costate equations is transformed to take into account the reverse flow nature of the costate equations. The application of the variational methods to aerodynamic shape optimization problems is demonstrated for internal flow problems at supersonic Mach number range. The study shows, that while maintaining the accuracy of the functional sensitivity derivatives within the reasonable range for engineering prediction purposes, the variational methods show a substantial gain in computational efficiency, i.e., computer time and memory, when compared with the finite difference sensitivity analysis.

A Comparative Analysis of the Functional Disability Levels of Adult Day Care, Adult Day Health and ICF-Level Nursing Home Elderly in Hawaii.

ERIC Educational Resources Information Center

Hayashida, Cullen T.

This study compared the functional disability levels of participants in adult day centers with patients in intermediate care facilities (ICFs). A three-page questionnaire measuring demographics, social resources, physical health, mental health, and activities of daily living as assessed by the Activities of Daily Living scale and the Instrumental…

Spatial Assessment of Forest Ecosystem Functions and Services using Human Relating Factors for SDG

NASA Astrophysics Data System (ADS)

Song, C.; Lee, W. K.; Jeon, S. W.; Kim, T.; Lim, C. H.

2015-12-01

Application of ecosystem service concept in environmental related decision making could be numerical and objective standard for policy maker between preserving and developing perspective of environment. However, pursuing maximum benefit from natural capital through ecosystem services caused failure by losing ecosystem functions through its trade-offs. Therefore, difference between ecosystem functions and services were demonstrated and would apply human relating perspectives. Assessment results of ecosystem functions and services can be divided 3 parts. Tree growth per year set as the ecosystem function factor and indicated through so called pure function map. After that, relating functions can be driven such as water conservation, air pollutant purification, climate change regulation, and timber production. Overall process and amount are numerically quantified. These functional results can be transferred to ecosystem services by multiplying economic unit value, so function reflecting service maps can be generated. On the other hand, above services, to implement more reliable human demand, human reflecting service maps are also be developed. As the validation, quantified ecosystem functions are compared with former results through pixel based analysis. Three maps are compared, and through comparing difference between ecosystem function and services and inversed trends in function based and human based service are analysed. In this study, we could find differences in PF, FRS, and HRS in relation to based ecosystem conditions. This study suggests that the differences in PF, FRS, and HRS should be understood in the decision making process for sustainable management of ecosystem services. Although the analysis is based on in sort existing process separation, it is important to consider the possibility of different usage of ecosystem function assessment results and ecosystem service assessment results in SDG policy making. Furthermore, process based functional approach can suggest environmental information which is reflected the other kinds of perspective.

Identifying functional reorganization of spelling networks: an individual peak probability comparison approach

PubMed Central

Purcell, Jeremy J.; Rapp, Brenda

2013-01-01

Previous research has shown that damage to the neural substrates of orthographic processing can lead to functional reorganization during reading (Tsapkini et al., 2011); in this research we ask if the same is true for spelling. To examine the functional reorganization of spelling networks we present a novel three-stage Individual Peak Probability Comparison (IPPC) analysis approach for comparing the activation patterns obtained during fMRI of spelling in a single brain-damaged individual with dysgraphia to those obtained in a set of non-impaired control participants. The first analysis stage characterizes the convergence in activations across non-impaired control participants by applying a technique typically used for characterizing activations across studies: Activation Likelihood Estimate (ALE) (Turkeltaub et al., 2002). This method was used to identify locations that have a high likelihood of yielding activation peaks in the non-impaired participants. The second stage provides a characterization of the degree to which the brain-damaged individual's activations correspond to the group pattern identified in Stage 1. This involves performing a Mahalanobis distance statistics analysis (Tsapkini et al., 2011) that compares each of a control group's peak activation locations to the nearest peak generated by the brain-damaged individual. The third stage evaluates the extent to which the brain-damaged individual's peaks are atypical relative to the range of individual variation among the control participants. This IPPC analysis allows for a quantifiable, statistically sound method for comparing an individual's activation pattern to the patterns observed in a control group and, thus, provides a valuable tool for identifying functional reorganization in a brain-damaged individual with impaired spelling. Furthermore, this approach can be applied more generally to compare any individual's activation pattern with that of a set of other individuals. PMID:24399981

Analyzing coastal environments by means of functional data analysis

NASA Astrophysics Data System (ADS)

Sierra, Carlos; Flor-Blanco, Germán; Ordoñez, Celestino; Flor, Germán; Gallego, José R.

2017-07-01

Here we used Functional Data Analysis (FDA) to examine particle-size distributions (PSDs) in a beach/shallow marine sedimentary environment in Gijón Bay (NW Spain). The work involved both Functional Principal Components Analysis (FPCA) and Functional Cluster Analysis (FCA). The grainsize of the sand samples was characterized by means of laser dispersion spectroscopy. Within this framework, FPCA was used as a dimension reduction technique to explore and uncover patterns in grain-size frequency curves. This procedure proved useful to describe variability in the structure of the data set. Moreover, an alternative approach, FCA, was applied to identify clusters and to interpret their spatial distribution. Results obtained with this latter technique were compared with those obtained by means of two vector approaches that combine PCA with CA (Cluster Analysis). The first method, the point density function (PDF), was employed after adapting a log-normal distribution to each PSD and resuming each of the density functions by its mean, sorting, skewness and kurtosis. The second applied a centered-log-ratio (clr) to the original data. PCA was then applied to the transformed data, and finally CA to the retained principal component scores. The study revealed functional data analysis, specifically FPCA and FCA, as a suitable alternative with considerable advantages over traditional vector analysis techniques in sedimentary geology studies.

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis.

PubMed

Luo, Gang; Fotidis, Ioannis A; Angelidaki, Irini

2016-01-01

Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure. The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors. The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

A SVM-based quantitative fMRI method for resting-state functional network detection.

PubMed

Song, Xiaomu; Chen, Nan-kuei

2014-09-01

Resting-state functional magnetic resonance imaging (fMRI) aims to measure baseline neuronal connectivity independent of specific functional tasks and to capture changes in the connectivity due to neurological diseases. Most existing network detection methods rely on a fixed threshold to identify functionally connected voxels under the resting state. Due to fMRI non-stationarity, the threshold cannot adapt to variation of data characteristics across sessions and subjects, and generates unreliable mapping results. In this study, a new method is presented for resting-state fMRI data analysis. Specifically, the resting-state network mapping is formulated as an outlier detection process that is implemented using one-class support vector machine (SVM). The results are refined by using a spatial-feature domain prototype selection method and two-class SVM reclassification. The final decision on each voxel is made by comparing its probabilities of functionally connected and unconnected instead of a threshold. Multiple features for resting-state analysis were extracted and examined using an SVM-based feature selection method, and the most representative features were identified. The proposed method was evaluated using synthetic and experimental fMRI data. A comparison study was also performed with independent component analysis (ICA) and correlation analysis. The experimental results show that the proposed method can provide comparable or better network detection performance than ICA and correlation analysis. The method is potentially applicable to various resting-state quantitative fMRI studies. Copyright © 2014 Elsevier Inc. All rights reserved.

Sex-Related Differences in Rat Choroid Plexus and Cerebrospinal Fluid: A cDNA Microarray and Proteomic Analysis.

PubMed

Quintela, T; Marcelino, H; Deery, M J; Feret, R; Howard, J; Lilley, K S; Albuquerque, T; Gonçalves, I; Duarte, A C; Santos, C R A

2016-01-01

The choroid plexus (CP) epithelium is a unique structure in the brain that forms an interface between the peripheral blood and the cerebrospinal fluid (CSF), which is mostly produced by the CP itself. Because the CP transcriptome is regulated by the sex hormone background, the present study compared gene/protein expression profiles in the CP and CSF from male and female rats aiming to better understand sex-related differences in CP functions and brain physiology. We used data previously obtained by cDNA microarrays to compare the CP transcriptome between male and female rats, and complemented these data with the proteomic analysis of the CSF of castrated and sham-operated males and females. Microarray analysis showed that 17 128 and 17 002 genes are expressed in the male and female CP, which allowed the functional annotation of 141 and 134 pathways, respectively. Among the most expressed genes, canonical pathways associated with mitochondrial dysfunctions and oxidative phosphorylation were the most prominent, whereas the most relevant molecular and cellular functions annotated were protein synthesis, cellular growth and proliferation, cell death and survival, molecular transport, and protein trafficking. No significant differences were found between males and females regarding these pathways. Seminal functions of the CP differentially regulated between sexes were circadian rhythm signalling, as well as several canonical pathways related to stem cell differentiation, metabolism and the barrier function of the CP. The proteomic analysis identified five down-regulated proteins in the CSF samples from male rats compared to females and seven proteins exhibiting marked variation in the CSF of gonadectomised males compared to sham animals, whereas no differences were found between sham and ovariectomised females. These data clearly show sex-related differences in CP gene expression and CSF protein composition that may impact upon neurological diseases. © 2015 British Society for Neuroendocrinology.

Further analysis of drivers licensed with medical conditions in Utah

DOT National Transportation Integrated Search

2001-03-01

The Utah Driver License Division has implemented a program since 1979 that restricts drivers with medical conditions by functional ability category (medical condition) by assigning them a functional ability level. This study compares the citation, al...

Microarray RNA expression analysis of cerebral white matter lesions reveals changes in multiple functional pathways.

PubMed

Simpson, Julie E; Hosny, Ola; Wharton, Stephen B; Heath, Paul R; Holden, Hazel; Fernando, Malee S; Matthews, Fiona; Forster, Gill; O'Brien, John T; Barber, Robert; Kalaria, Raj N; Brayne, Carol; Shaw, Pamela J; Lewis, Claire E; Ince, Paul G

2009-02-01

White matter lesions (WML) in brain aging are linked to dementia and depression. Ischemia contributes to their pathogenesis but other mechanisms may contribute. We used RNA microarray analysis with functional pathway grouping as an unbiased approach to investigate evidence for additional pathogenetic mechanisms. WML were identified by MRI and pathology in brains donated to the Medical Research Council Cognitive Function and Ageing Study Cognitive Function and Aging Study. RNA was extracted to compare WML with nonlesional white matter samples from cases with lesions (WM[L]), and from cases with no lesions (WM[C]) using RNA microarray and pathway analysis. Functional pathways were validated for selected genes by quantitative real-time polymerase chain reaction and immunocytochemistry. We identified 8 major pathways in which multiple genes showed altered RNA transcription (immune regulation, cell cycle, apoptosis, proteolysis, ion transport, cell structure, electron transport, metabolism) among 502 genes that were differentially expressed in WML compared to WM[C]. In WM[L], 409 genes were altered involving the same pathways. Genes selected to validate this microarray data all showed the expected changes in RNA levels and immunohistochemical expression of protein. WML represent areas with a complex molecular phenotype. From this and previous evidence, WML may arise through tissue ischemia but may also reflect the contribution of additional factors like blood-brain barrier dysfunction. Differential expression of genes in WM[L] compared to WM[C] indicate a "field effect" in the seemingly normal surrounding white matter.

Computed tomographic-based quantification of emphysema and correlation to pulmonary function and mechanics.

PubMed

Washko, George R; Criner, Gerald J; Mohsenifar, Zab; Sciurba, Frank C; Sharafkhaneh, Amir; Make, Barry J; Hoffman, Eric A; Reilly, John J

2008-06-01

Computed tomographic based indices of emphysematous lung destruction may highlight differences in disease pathogenesis and further enable the classification of subjects with Chronic Obstructive Pulmonary Disease. While there are multiple techniques that can be utilized for such radiographic analysis, there is very little published information comparing the performance of these methods in a clinical case series. Our objective was to examine several quantitative and semi-quantitative methods for the assessment of the burden of emphysema apparent on computed tomographic scans and compare their ability to predict lung mechanics and function. Automated densitometric analysis was performed on 1094 computed tomographic scans collected upon enrollment into the National Emphysema Treatment Trial. Trained radiologists performed an additional visual grading of emphysema on high resolution CT scans. Full pulmonary function test results were available for correlation, with a subset of subjects having additional measurements of lung static recoil. There was a wide range of emphysematous lung destruction apparent on the CT scans and univariate correlations to measures of lung function were of modest strength. No single method of CT scan analysis clearly outperformed the rest of the group. Quantification of the burden of emphysematous lung destruction apparent on CT scan is a weak predictor of lung function and mechanics in severe COPD with no uniformly superior method found to perform this analysis. The CT based quantification of emphysema may augment pulmonary function testing in the characterization of COPD by providing complementary phenotypic information.

Dilemmas of Transfer Pricing Comparability Analysis in Manufacturing Entities. Polish-Czech Case Study

NASA Astrophysics Data System (ADS)

Sulik-Górecka, Aleksandra

2018-06-01

Modern manufacturing entities often operate in capital groups, and their role is sometimes limited to the function of cost centers. From the legal point of view, however, they are separate entities obliged to apply transfer pricing regulations. Meeting the requirements of the arm's length principle can be very difficult at this time, given the relationships and conflicts of interest in the capital group. Complexity increases in capital groups operating in different countries, due to differences in tax regulations. The main purpose of the paper is to demonstrate that the need to valuate the sale of finished goods to a manufacturing entity, which is a subject to a different tax jurisdiction, may lead to a problem of compliance with the arm's length principle. In addition, the paper proposes a methodology for comparability analysis that may be used by manufacturing entities to defend conditions of setting transfer pricing. The paper presents the different functional profiles of manufacturing entities and points out the difficulties that they may encounter when preparing the comparability analysis. It has also been noted that there are differences in transfer pricing regulations in different countries, for example by analyzing Polish and Czech regulations. The lack of uniform benchmarking legislation can cause inconsistencies in the selection of comparable data, resulting in differences in transfer pricing. The paper uses the method of legal regulation review and analysis of results of published studies concerning the scope of transfer pricing and comparability analysis. The paper also adopts a case study analysis.

Bragg-cell receiver study

NASA Technical Reports Server (NTRS)

Wilson, Lonnie A.

1987-01-01

Bragg-cell receivers are employed in specialized Electronic Warfare (EW) applications for the measurement of frequency. Bragg-cell receiver characteristics are fully characterized for simple RF emitter signals. This receiver is early in its development cycle when compared to the IFM receiver. Functional mathematical models are derived and presented in this report for the Bragg-cell receiver. Theoretical analysis is presented and digital computer signal processing results are presented for the Bragg-cell receiver. Probability density function analysis are performed for output frequency. Probability density function distributions are observed to depart from assumed distributions for wideband and complex RF signals. This analysis is significant for high resolution and fine grain EW Bragg-cell receiver systems.

[Prematurity: longitudinal analysis of executive functions].

PubMed

Sastre-Riba, S

2009-02-27

Understanding cognitive development requires an interdisciplinary and neuropsychological approach. Executive functions facilitates cognitive activity and they are related to progressive cerebral configuration during pregnancy and infancy. One of the aims of the actual neuropsychology is the ontogeny of executive functions and their capacity to explain differential and normative developmental trends, specially because of its consequences on mental flexibility, monitoring, planning and cognitive control; they are also essential for good performance at school. The incidence of developmental risk factors as prematurity could affect long-term executive functioning expressed in learning difficulties or behavioral control. We studied, comparatively and longitudinally, the individual activity on objects displayed by typical babies (n = 25), and preterm babies (n = 10) from 1.5 to 2 years-old. Applying systematic observational methodology, spontaneous babies' activity is registered. Double intra and inter-group analysis compare the data from the resolution of a non-verbal task through a multifaceted design. Results obtained show us differential pattern of early executive functioning among the groups studied. The growth of executive functioning is showed, too, through the ages studied for every group.

Multivariate Analysis of Schools and Educational Policy.

ERIC Educational Resources Information Center

Kiesling, Herbert J.

This report describes a multivariate analysis technique that approaches the problems of educational production function analysis by (1) using comparable measures of output across large experiments, (2) accounting systematically for differences in socioeconomic background, and (3) treating the school as a complete system in which different…

Quality of life after open or robotic prostatectomy, cryoablation or brachytherapy for localized prostate cancer.

PubMed

Malcolm, John B; Fabrizio, Michael D; Barone, Bethany B; Given, Robert W; Lance, Raymond S; Lynch, Donald F; Davis, John W; Shaves, Mark E; Schellhammer, Paul F

2010-05-01

Health related quality of life concerns factor prominently in prostate cancer management. We describe health related quality of life impact and recovery profiles of 4 commonly used operative treatments for localized prostate cancer. Beginning in February 2000 all patients treated with open radical prostatectomy, robot assisted laparoscopic prostatectomy, brachytherapy or cryotherapy were asked to complete the UCLA-PCI questionnaire before treatment, and at 3, 6, 12, 18, 24, 30 and 36 months after treatment. Outcomes were compared across treatment types with statistical analysis using univariate and multivariate models. A total of 785 patients treated between February 2000 and December 2008 were included in the analysis with a mean followup of 24 months. All health related quality of life domains were adversely affected by all treatments and recovery profiles varied significantly by treatment type. Overall urinary function and bother outcomes scored significantly higher after brachytherapy and cryotherapy compared to open radical prostatectomy and robotic assisted laparoscopic radical prostatectomy. Brachytherapy and cryotherapy had a 3-fold higher rate of return to baseline urinary function compared to open radical prostatectomy and robotic assisted laparoscopic radical prostatectomy. Sexual function and bother scores were highest after brachytherapy, with a 5-fold higher rate of return to baseline function compared to cryotherapy, open radical prostatectomy and robotic assisted laparoscopic radical prostatectomy. All 4 treatments were associated with relatively transient and less pronounced impact on bowel function and bother. In a study of sequential health related quality of life assessments brachytherapy and cryotherapy were associated with higher urinary function and bother scores compared to open radical prostatectomy and da Vinci prostatectomy. Brachytherapy was associated with higher sexual function and bother scores compared to open radical prostatectomy, robotic assisted laparoscopic radical prostatectomy and cryotherapy. 2010 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Wastewater-Based Epidemiology of Stimulant Drugs: Functional Data Analysis Compared to Traditional Statistical Methods.

PubMed

Salvatore, Stefania; Bramness, Jørgen Gustav; Reid, Malcolm J; Thomas, Kevin Victor; Harman, Christopher; Røislien, Jo

2015-01-01

Wastewater-based epidemiology (WBE) is a new methodology for estimating the drug load in a population. Simple summary statistics and specification tests have typically been used to analyze WBE data, comparing differences between weekday and weekend loads. Such standard statistical methods may, however, overlook important nuanced information in the data. In this study, we apply functional data analysis (FDA) to WBE data and compare the results to those obtained from more traditional summary measures. We analysed temporal WBE data from 42 European cities, using sewage samples collected daily for one week in March 2013. For each city, the main temporal features of two selected drugs were extracted using functional principal component (FPC) analysis, along with simpler measures such as the area under the curve (AUC). The individual cities' scores on each of the temporal FPCs were then used as outcome variables in multiple linear regression analysis with various city and country characteristics as predictors. The results were compared to those of functional analysis of variance (FANOVA). The three first FPCs explained more than 99% of the temporal variation. The first component (FPC1) represented the level of the drug load, while the second and third temporal components represented the level and the timing of a weekend peak. AUC was highly correlated with FPC1, but other temporal characteristic were not captured by the simple summary measures. FANOVA was less flexible than the FPCA-based regression, and even showed concordance results. Geographical location was the main predictor for the general level of the drug load. FDA of WBE data extracts more detailed information about drug load patterns during the week which are not identified by more traditional statistical methods. Results also suggest that regression based on FPC results is a valuable addition to FANOVA for estimating associations between temporal patterns and covariate information.

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains.

PubMed

Bhattacharyya, Anamitra; Stilwagen, Stephanie; Ivanova, Natalia; D'Souza, Mark; Bernal, Axel; Lykidis, Athanasios; Kapatral, Vinayak; Anderson, Iain; Larsen, Niels; Los, Tamara; Reznik, Gary; Selkov, Eugene; Walunas, Theresa L; Feil, Helene; Feil, William S; Purcell, Alexander; Lassez, Jean-Louis; Hawkins, Trevor L; Haselkorn, Robert; Overbeek, Ross; Predki, Paul F; Kyrpides, Nikos C

2002-09-17

Xylella fastidiosa (Xf) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander, which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two "gapped" Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an "in silico" cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their conjugative transfer machinery, identification of potential differences in their adhesion mechanisms, and highlighting of the absence of a classical quorum-sensing mechanism. This study demonstrates the effectiveness of comparative analysis strategies in the interpretation of genomes that are closely related.

Transactive System: Part II: Analysis of Two Pilot Transactive Systems using Foundational Theory and Metrics

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

Lian, Jianming; Sun, Y.; Kalsi, Karanjit

This document is the second of a two-part report. Part 1 reviewed several demonstrations of transactive control and compared them in terms of their payoff functions, control decisions, information privacy, and mathematical solution concepts. It was suggested in Part 1 that these four listed components should be adopted for meaningful comparison and design of future transactive systems. Part 2 proposes qualitative and quantitative metrics that will be needed to compare alternative transactive systems. It then uses the analysis and design principles from Part 1 while conducting more in-depth analysis of two transactive demonstrations: the American Electric Power (AEP) gridSMART Demonstration,more » which used a double –auction market mechanism, and a consensus method like that used in the Pacific Northwest Smart Grid Demonstration. Ultimately, metrics must be devised and used to meaningfully compare alternative transactive systems. One significant contribution of this report is an observation that the decision function used for thermostat control in the AEP gridSMART Demonstration has superior performance if its decision function is recast to more accurately reflect the power that will be used under for thermostatic control under alternative market outcomes.« less

The Neglect of Monotone Comparative Statics Methods

ERIC Educational Resources Information Center

Tremblay, Carol Horton; Tremblay, Victor J.

2010-01-01

Monotone methods enable comparative static analysis without the restrictive assumptions of the implicit-function theorem. Ease of use and flexibility in solving comparative static and game-theory problems have made monotone methods popular in the economics literature and in graduate courses, but they are still absent from undergraduate…

Nuclear PDF for neutrino and charged lepton data

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

Kovarik, K.

2011-10-06

Neutrino Deep Inelastic Scattering (DIS) on nuclei is an essential process to constrain the strange quark parton distribution functions (PDF) in the proton. The critical component on the way to using the neutrino DIS data in a proton PDF analysis is understanding the nuclear effects in parton distribution functions. We parametrize these effects by nuclear parton distribution functions (NPDF). Here we compare results from two analysis of NPDF both done at next-to-leading order in QCD. The first uses neutral current charged-lepton (l{sup {+-}A}) Deeply Inelastic Scattering (DIS) and Drell-Yan data for several nuclear targets and the second uses neutrino-nucleon DISmore » data. We compare the nuclear corrections factors (F{sub 2}{sup Fe}/F{sub 2}{sup D}) for the charged-lepton data with other results from the literature. In particular, we compare and contrast fits based upon the charged-lepton DIS data with those using neutrino-nucleon DIS data.« less

Comparison of tricuspid annular plane systolic excursion with fractional area change for the evaluation of right ventricular systolic function: a meta-analysis

PubMed Central

Low, See-Wei; Pasha, Ahmed K; Howe, Carol L; Lee, Kwan S; Suryanarayana, Prakash G

2018-01-01

Background Accurate determination of right ventricular ejection fraction (RVEF) is challenging because of the unique geometry of the right ventricle. Tricuspidannular plane systolic excursion (TAPSE) and fractional area change (FAC) are commonly used echocardiographic quantitative estimates of RV function. Cardiac MRI (CMRI) has emerged as the gold standard for assessment of RVEF. We sought to summarise the available data on correlation of TAPSE and FAC with CMRI-derived RVEF and to compare their accuracy. Methods We searched PubMed, EMBASE, Web of Science, CINAHL, ClinicalTrials.gov and the Cochrane Library databases for studies that assessed the correlation of TAPSE or FAC with CMRI-derived RVEF. Data from each study selected were pooled and analysed to compare the correlation coefficient of TAPSE and FAC with CMRI-derived RVEF. Subgroup analysis was performed on patients with pulmonary hypertension. Results Analysis of data from 17 studies with a total of 1280 patients revealed that FAC had a higher correlation with CMRI-derived RVEF compared with TAPSE (0.56vs0.40, P=0.018). In patients with pulmonary hypertension, there was no statistical difference in the mean correlation coefficient of FAC and TAPSE to CMR (0.57vs0.46, P=0.16). Conclusions FAC provides a more accurate estimate of RV systolic function (RVSF) compared with TAPSE. Adoption of FAC as a routine tool for the assessment of RVSF should be considered, especially since it is also an independent predictor of morbidity and mortality. Further studies will be needed to compare other methods of echocardiographic measurement of RV function. PMID:29387425

Northwestern University Flexible Subischial Vacuum Socket for persons with transfemoral amputation: Part 2 Description and Preliminary evaluation

PubMed Central

Fatone, Stefania; Caldwell, Ryan

2017-01-01

Background: Current transfemoral prosthetic sockets are problematic as they restrict function, lack comfort, and cause residual limb problems. Development of a subischial socket with lower proximal trim lines is an appealing way to address this problem and may contribute to improving quality of life of persons with transfemoral amputation. Objectives: The purpose of this study was to illustrate the use of a new subischial socket in two subjects. Study design: Case series. Methods: Two unilateral transfemoral prosthesis users participated in preliminary socket evaluations comparing functional performance of the new subischial socket to ischial containment sockets. Testing included gait analysis, socket comfort score, and performance-based clinical outcome measures (Rapid-Sit-To-Stand, Four-Square-Step-Test, and Agility T-Test). Results: For both subjects, comfort was better in the subischial socket, while gait and clinical outcomes were generally comparable between sockets. Conclusion: While these evaluations are promising regarding the ability to function in this new socket design, more definitive evaluation is needed. Clinical relevance Using gait analysis, socket comfort score and performance-based outcome measures, use of the Northwestern University Flexible Subischial Vaccum Socket was evaluated in two transfemoral prosthesis users. Socket comfort improved for both subjects with comparable function compared to ischial containment sockets. PMID:28132589

Accuracy of Presurgical Functional MR Imaging for Language Mapping of Brain Tumors: A Systematic Review and Meta-Analysis.

PubMed

Weng, Hsu-Huei; Noll, Kyle R; Johnson, Jason M; Prabhu, Sujit S; Tsai, Yuan-Hsiung; Chang, Sheng-Wei; Huang, Yen-Chu; Lee, Jiann-Der; Yang, Jen-Tsung; Yang, Cheng-Ta; Tsai, Ying-Huang; Yang, Chun-Yuh; Hazle, John D; Schomer, Donald F; Liu, Ho-Ling

2018-02-01

Purpose To compare functional magnetic resonance (MR) imaging for language mapping (hereafter, language functional MR imaging) with direct cortical stimulation (DCS) in patients with brain tumors and to assess factors associated with its accuracy. Materials and Methods PubMed/MEDLINE and related databases were searched for research articles published between January 2000 and September 2016. Findings were pooled by using bivariate random-effects and hierarchic summary receiver operating characteristic curve models. Meta-regression and subgroup analyses were performed to evaluate whether publication year, functional MR imaging paradigm, magnetic field strength, statistical threshold, and analysis software affected classification accuracy. Results Ten articles with a total of 214 patients were included in the analysis. On a per-patient basis, the pooled sensitivity and specificity of functional MR imaging was 44% (95% confidence interval [CI]: 14%, 78%) and 80% (95% CI: 54%, 93%), respectively. On a per-tag basis (ie, each DCS stimulation site or "tag" was considered a separate data point across all patients), the pooled sensitivity and specificity were 67% (95% CI: 51%, 80%) and 55% (95% CI: 25%, 82%), respectively. The per-tag analysis showed significantly higher sensitivity for studies with shorter functional MR imaging session times (P = .03) and relaxed statistical threshold (P = .05). Significantly higher specificity was found when expressive language task (P = .02), longer functional MR imaging session times (P < .01), visual presentation of stimuli (P = .04), and stringent statistical threshold (P = .01) were used. Conclusion Results of this study showed moderate accuracy of language functional MR imaging when compared with intraoperative DCS, and the included studies displayed significant methodologic heterogeneity. © RSNA, 2017 Online supplemental material is available for this article.

A comparative analysis of alternative approaches for quantifying nonlinear dynamics in cardiovascular system.

PubMed

Chen, Yun; Yang, Hui

2013-01-01

Heart rate variability (HRV) analysis has emerged as an important research topic to evaluate autonomic cardiac function. However, traditional time and frequency-domain analysis characterizes and quantify only linear and stationary phenomena. In the present investigation, we made a comparative analysis of three alternative approaches (i.e., wavelet multifractal analysis, Lyapunov exponents and multiscale entropy analysis) for quantifying nonlinear dynamics in heart rate time series. Note that these extracted nonlinear features provide information about nonlinear scaling behaviors and the complexity of cardiac systems. To evaluate the performance, we used 24-hour HRV recordings from 54 healthy subjects and 29 heart failure patients, available in PhysioNet. Three nonlinear methods are evaluated not only individually but also in combination using three classification algorithms, i.e., linear discriminate analysis, quadratic discriminate analysis and k-nearest neighbors. Experimental results show that three nonlinear methods capture nonlinear dynamics from different perspectives and the combined feature set achieves the best performance, i.e., sensitivity 97.7% and specificity 91.5%. Collectively, nonlinear HRV features are shown to have the promise to identify the disorders in autonomic cardiovascular function.

GEAR: genomic enrichment analysis of regional DNA copy number changes.

PubMed

Kim, Tae-Min; Jung, Yu-Chae; Rhyu, Mun-Gan; Jung, Myeong Ho; Chung, Yeun-Jun

2008-02-01

We developed an algorithm named GEAR (genomic enrichment analysis of regional DNA copy number changes) for functional interpretation of genome-wide DNA copy number changes identified by array-based comparative genomic hybridization. GEAR selects two types of chromosomal alterations with potential biological relevance, i.e. recurrent and phenotype-specific alterations. Then it performs functional enrichment analysis using a priori selected functional gene sets to identify primary and clinical genomic signatures. The genomic signatures identified by GEAR represent functionally coordinated genomic changes, which can provide clues on the underlying molecular mechanisms related to the phenotypes of interest. GEAR can help the identification of key molecular functions that are activated or repressed in the tumor genomes leading to the improved understanding on the tumor biology. GEAR software is available with online manual in the website, http://www.systemsbiology.co.kr/GEAR/.

Combining Multiobjective Optimization and Cluster Analysis to Study Vocal Fold Functional Morphology

PubMed Central

Palaparthi, Anil; Riede, Tobias

2017-01-01

Morphological design and the relationship between form and function have great influence on the functionality of a biological organ. However, the simultaneous investigation of morphological diversity and function is difficult in complex natural systems. We have developed a multiobjective optimization (MOO) approach in association with cluster analysis to study the form-function relation in vocal folds. An evolutionary algorithm (NSGA-II) was used to integrate MOO with an existing finite element model of the laryngeal sound source. Vocal fold morphology parameters served as decision variables and acoustic requirements (fundamental frequency, sound pressure level) as objective functions. A two-layer and a three-layer vocal fold configuration were explored to produce the targeted acoustic requirements. The mutation and crossover parameters of the NSGA-II algorithm were chosen to maximize a hypervolume indicator. The results were expressed using cluster analysis and were validated against a brute force method. Results from the MOO and the brute force approaches were comparable. The MOO approach demonstrated greater resolution in the exploration of the morphological space. In association with cluster analysis, MOO can efficiently explore vocal fold functional morphology. PMID:24771563

Atlas-Based Ventricular Shape Analysis for Understanding Congenital Heart Disease.

PubMed

Farrar, Genevieve; Suinesiaputra, Avan; Gilbert, Kathleen; Perry, James C; Hegde, Sanjeet; Marsden, Alison; Young, Alistair A; Omens, Jeffrey H; McCulloch, Andrew D

2016-12-01

Congenital heart disease is associated with abnormal ventricular shape that can affect wall mechanics and may be predictive of long-term adverse outcomes. Atlas-based parametric shape analysis was used to analyze ventricular geometries of eight adolescent or adult single-ventricle CHD patients with tricuspid atresia and Fontans. These patients were compared with an "atlas" of non-congenital asymptomatic volunteers, resulting in a set of z-scores which quantify deviations from the control population distribution on a patient-by-patient basis. We examined the potential of these scores to: (1) quantify abnormalities of ventricular geometry in single ventricle physiologies relative to the normal population; (2) comprehensively quantify wall motion in CHD patients; and (3) identify possible relationships between ventricular shape and wall motion that may reflect underlying functional defects or remodeling in CHD patients. CHD ventricular geometries at end-diastole and end-systole were individually compared with statistical shape properties of an asymptomatic population from the Cardiac Atlas Project. Shape analysis-derived model properties, and myocardial wall motions between end-diastole and end-systole, were compared with physician observations of clinical functional parameters. Relationships between altered shape and altered function were evaluated via correlations between atlas-based shape and wall motion scores. Atlas-based shape analysis identified a diverse set of specific quantifiable abnormalities in ventricular geometry or myocardial wall motion in all subjects. Moreover, this initial cohort displayed significant relationships between specific shape abnormalities such as increased ventricular sphericity and functional defects in myocardial deformation, such as decreased long-axis wall motion. These findings suggest that atlas-based ventricular shape analysis may be a useful new tool in the management of patients with CHD who are at risk of impaired ventricular wall mechanics and chamber remodeling.

IMAGING OF BRAIN FUNCTION BASED ON THE ANALYSIS OF FUNCTIONAL CONNECTIVITY - IMAGING ANALYSIS OF BRAIN FUNCTION BY FMRI AFTER ACUPUNCTURE AT LR3 IN HEALTHY INDIVIDUALS.

PubMed

Zheng, Yu; Wang, Yuying; Lan, Yujun; Qu, Xiaodong; Lin, Kelin; Zhang, Jiping; Qu, Shanshan; Wang, Yanjie; Tang, Chunzhi; Huang, Yong

2016-01-01

This Study observed the relevant brain areas activated by acupuncture at the Taichong acupoint (LR3) and analyzed the functional connectivity among brain areas using resting state functional magnetic resonance imaging (fMRI) to explore the acupoint specificity of the Taichong acupoint. A total of 45 healthy subjects were randomly divided into the Taichong (LR3) group, sham acupuncture group and sham acupoint group. Subjects received resting state fMRI before acupuncture, after true (sham) acupuncture in each group. Analysis of changes in connectivity among the brain areas was performed using the brain functional connectivity method. The right cerebrum temporal lobe was selected as the seed point to analyze the functional connectivity. It had a functional connectivity with right cerebrum superior frontal gyrus, limbic lobe cingulate gyrus and left cerebrum inferior temporal gyrus (BA 37), inferior parietal lobule compared by before vs. after acupuncture at LR3, and right cerebrum sub-lobar insula and left cerebrum middle frontal gyrus, medial frontal gyrus compared by true vs. sham acupuncture at LR3, and right cerebrum occipital lobe cuneus, occipital lobe sub-gyral, parietal lobe precuneus and left cerebellum anterior lobe culmen by acupuncture at LR3 vs. sham acupoint. Acupuncture at LR3 mainly specifically activated the brain functional network that participates in visual function, associative function, and emotion cognition, which are similar to the features on LR3 in tradition Chinese medicine. These brain areas constituted a neural network structure with specific functions that had specific reference values for the interpretation of the acupoint specificity of the Taichong acupoint.

Comparative sequence analysis of Sordaria macrospora and Neurospora crassa as a means to improve genome annotation.

PubMed

Nowrousian, Minou; Würtz, Christian; Pöggeler, Stefanie; Kück, Ulrich

2004-03-01

One of the most challenging parts of large scale sequencing projects is the identification of functional elements encoded in a genome. Recently, studies of genomes of up to six different Saccharomyces species have demonstrated that a comparative analysis of genome sequences from closely related species is a powerful approach to identify open reading frames and other functional regions within genomes [Science 301 (2003) 71, Nature 423 (2003) 241]. Here, we present a comparison of selected sequences from Sordaria macrospora to their corresponding Neurospora crassa orthologous regions. Our analysis indicates that due to the high degree of sequence similarity and conservation of overall genomic organization, S. macrospora sequence information can be used to simplify the annotation of the N. crassa genome.

Lipophilic versus hydrophilic statin therapy for heart failure: a protocol for an adjusted indirect comparison meta-analysis

PubMed Central

2013-01-01

Background Statins are known to reduce cardiovascular morbidity and mortality in primary and secondary prevention studies. Subsequently, a number of nonrandomised studies have shown statins improve clinical outcomes in patients with heart failure (HF). Small randomised controlled trials (RCT) also show improved cardiac function, reduced inflammation and mortality with statins in HF. However, the findings of two large RCTs do not support the evidence provided by previous studies and suggest statins lack beneficial effects in HF. Two meta-analyses have shown statins do not improve survival, whereas two others showed improved cardiac function and reduced inflammation in HF. It appears lipophilic statins produce better survival and other outcome benefits compared to hydrophilic statins. But the two types have not been compared in direct comparison trials in HF. Methods/design We will conduct a systematic review and meta-analysis of lipophilic and hydrophilic statin therapy in patients with HF. Our objectives are: 1. To determine the effects of lipophilic statins on (1) mortality, (2) hospitalisation for worsening HF, (3) cardiac function and (4) inflammation. 2. To determine the effects of hydrophilic statins on (1) mortality, (2) hospitalisation for worsening HF, (3) cardiac function and (4) inflammation. 3. To compare the efficacy of lipophilic and hydrophilic statins on HF outcomes with an adjusted indirect comparison meta-analysis. We will conduct an electronic search of databases for RCTs that evaluate statins in patients with HF. The reference lists of all identified studies will be reviewed. Two independent reviewers will conduct the search. The inclusion criteria include: 1. RCTs comparing statins with placebo or no statin in patients with symptomatic HF. 2. RCTs that employed the intention-to-treat (ITT) principle in data analysis. 3. Symptomatic HF patients of all aetiologies and on standard treatment. 4. Statin of any dose as intervention. 5. Placebo or no statin arm as control. The exclusion criteria include: 1. RCTs involving cerivastatin in HF patients. 2. RCTs with less than 4 weeks of follow-up. Discussion We will perform an adjusted indirect comparison meta-analysis of lipophilic versus hydrophilic statins in patients with HF using placebo or no statin arm as common comparator. PMID:23618535

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PubMed

Lovelock, Paul K; Spurdle, Amanda B; Mok, Myth T S; Farrugia, Daniel J; Lakhani, Sunil R; Healey, Sue; Arnold, Stephen; Buchanan, Daniel; Couch, Fergus J; Henderson, Beric R; Goldgar, David E; Tavtigian, Sean V; Chenevix-Trench, Georgia; Brown, Melissa A

2007-01-01

Many of the DNA sequence variants identified in the breast cancer susceptibility gene BRCA1 remain unclassified in terms of their potential pathogenicity. Both multifactorial likelihood analysis and functional approaches have been proposed as a means to elucidate likely clinical significance of such variants, but analysis of the comparative value of these methods for classifying all sequence variants has been limited. We have compared the results from multifactorial likelihood analysis with those from several functional analyses for the four BRCA1 sequence variants A1708E, G1738R, R1699Q, and A1708V. Our results show that multifactorial likelihood analysis, which incorporates sequence conservation, co-inheritance, segregation, and tumour immunohistochemical analysis, may improve classification of variants. For A1708E, previously shown to be functionally compromised, analysis of oestrogen receptor, cytokeratin 5/6, and cytokeratin 14 tumour expression data significantly strengthened the prediction of pathogenicity, giving a posterior probability of pathogenicity of 99%. For G1738R, shown to be functionally defective in this study, immunohistochemistry analysis confirmed previous findings of inconsistent 'BRCA1-like' phenotypes for the two tumours studied, and the posterior probability for this variant was 96%. The posterior probabilities of R1699Q and A1708V were 54% and 69%, respectively, only moderately suggestive of increased risk. Interestingly, results from functional analyses suggest that both of these variants have only partial functional activity. R1699Q was defective in foci formation in response to DNA damage and displayed intermediate transcriptional transactivation activity but showed no evidence for centrosome amplification. In contrast, A1708V displayed an intermediate transcriptional transactivation activity and a normal foci formation response in response to DNA damage but induced centrosome amplification. These data highlight the need for a range of functional studies to be performed in order to identify variants with partially compromised function. The results also raise the possibility that A1708V and R1699Q may be associated with a low or moderate risk of cancer. While data pooling strategies may provide more information for multifactorial analysis to improve the interpretation of the clinical significance of these variants, it is likely that the development of current multifactorial likelihood approaches and the consideration of alternative statistical approaches will be needed to determine whether these individually rare variants do confer a low or moderate risk of breast cancer.

The effect of balneotherapy on pain relief, stiffness, and physical function in patients with osteoarthritis of the knee: a meta-analysis.

PubMed

Matsumoto, Hiromi; Hagino, Hiroshi; Hayashi, Kunihiko; Ideno, Yuki; Wada, Takashi; Ogata, Toru; Akai, Masami; Seichi, Atsushi; Iwaya, Tsutomu

2017-08-01

This meta-analysis was performed to determine the effect of balneotherapy on relieving pain and stiffness and improving physical function, compared to controls, among patients with knee osteoarthritis. We searched electronic databases for eligible studies published from 2004 to December 31, 2016, with language restrictions of English or Japanese. We screened publications in Medline, Embase, Cochrane library, and the Japan Medical Abstracts Society Database using two approaches, MeSH terms and free words. Studies that examined the effect of balneotherapy for treating knee osteoarthritis of a ≥2-week duration were included. Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores were used as the outcome measure. A total of 102 publications were assessed according to the exclusion criteria of the study; eight clinical trial studies, which comprised a total of 359 cases and 375 controls, were included in this meta-analysis. The meta-analysis analyzed improvement in WOMAC score at the final follow-up visit, which varied from 2 to 12 months post-intervention. Our meta-analysis indicates that balneotherapy was clinically effective in relieving pain and stiffness, and improving function, as assessed by WOMAC score, compared to controls. However, there was high heterogeneity (88 to 93%). It is possible that balneotherapy may reduce pain and stiffness, and improve function, in individuals with knee osteoarthritis, although the quality of current publications contributes to the heterogeneity observed in this meta-analysis.

Local-global alignment for finding 3D similarities in protein structures

DOEpatents

Zemla, Adam T [Brentwood, CA

2011-09-20

A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

Measurement of myocardial blood flow by cardiovascular magnetic resonance perfusion: comparison of distributed parameter and Fermi models with single and dual bolus.

PubMed

Papanastasiou, Giorgos; Williams, Michelle C; Kershaw, Lucy E; Dweck, Marc R; Alam, Shirjel; Mirsadraee, Saeed; Connell, Martin; Gray, Calum; MacGillivray, Tom; Newby, David E; Semple, Scott Ik

2015-02-17

Mathematical modeling of cardiovascular magnetic resonance perfusion data allows absolute quantification of myocardial blood flow. Saturation of left ventricle signal during standard contrast administration can compromise the input function used when applying these models. This saturation effect is evident during application of standard Fermi models in single bolus perfusion data. Dual bolus injection protocols have been suggested to eliminate saturation but are much less practical in the clinical setting. The distributed parameter model can also be used for absolute quantification but has not been applied in patients with coronary artery disease. We assessed whether distributed parameter modeling might be less dependent on arterial input function saturation than Fermi modeling in healthy volunteers. We validated the accuracy of each model in detecting reduced myocardial blood flow in stenotic vessels versus gold-standard invasive methods. Eight healthy subjects were scanned using a dual bolus cardiac perfusion protocol at 3T. We performed both single and dual bolus analysis of these data using the distributed parameter and Fermi models. For the dual bolus analysis, a scaled pre-bolus arterial input function was used. In single bolus analysis, the arterial input function was extracted from the main bolus. We also performed analysis using both models of single bolus data obtained from five patients with coronary artery disease and findings were compared against independent invasive coronary angiography and fractional flow reserve. Statistical significance was defined as two-sided P value < 0.05. Fermi models overestimated myocardial blood flow in healthy volunteers due to arterial input function saturation in single bolus analysis compared to dual bolus analysis (P < 0.05). No difference was observed in these volunteers when applying distributed parameter-myocardial blood flow between single and dual bolus analysis. In patients, distributed parameter modeling was able to detect reduced myocardial blood flow at stress (<2.5 mL/min/mL of tissue) in all 12 stenotic vessels compared to only 9 for Fermi modeling. Comparison of single bolus versus dual bolus values suggests that distributed parameter modeling is less dependent on arterial input function saturation than Fermi modeling. Distributed parameter modeling showed excellent accuracy in detecting reduced myocardial blood flow in all stenotic vessels.

SOME PROBLEMS OF EDUCATIONAL ORGANIZATION IN COMPARATIVE PERSPECTIVE.

ERIC Educational Resources Information Center

HILLS, JEAN

A COMPARATIVE ANALYSIS OF EDUCATIONAL ORGANIZATION WAS MADE WITHIN A THEORETICAL FRAMEWORK INVOLVING SOCIAL SYSTEM TERMS. ATTENTION WAS FOCUSED ON DIFFERENCES AMONG ORGANIZATIONS IN TERMS OF FUNCTIONS PERFORMED FOR SOCIETY. FOUR MAJOR COMPONENTS OF ACTION SYSTEMS USED TO COMPARE SEVERAL ORGANIZATIONS WERE IDENTIFIED AS FOLLOWS--(1) THE ORIENTATION…

Identification of segregated regions in the functional brain connectome of autistic patients by a combination of fuzzy spectral clustering and entropy analysis

PubMed Central

Sato, João Ricardo; Balardin, Joana; Vidal, Maciel Calebe; Fujita, André

2016-01-01

Background Several neuroimaging studies support the model of abnormal development of brain connectivity in patients with autism-spectrum disorders (ASD). In this study, we aimed to test the hypothesis of reduced functional network segregation in autistic patients compared with controls. Methods Functional MRI data from children acquired under a resting-state protocol (Autism Brain Imaging Data Exchange [ABIDE]) were submitted to both fuzzy spectral clustering (FSC) with entropy analysis and graph modularity analysis. Results We included data from 814 children in our analysis. We identified 5 regions of interest comprising the motor, temporal and occipito-temporal cortices with increased entropy (p < 0.05) in the clustering structure (i.e., more segregation in the controls). Moreover, we noticed a statistically reduced modularity (p < 0.001) in the autistic patients compared with the controls. Significantly reduced eigenvector centrality values (p < 0.05) in the patients were observed in the same regions that were identified in the FSC analysis. Limitations There is considerable heterogeneity in the fMRI acquisition protocols among the sites that contributed to the ABIDE data set (e.g., scanner type, pulse sequence, duration of scan and resting-state protocol). Moreover, the sites differed in many variables related to sample characterization (e.g., age, IQ and ASD diagnostic criteria). Therefore, we cannot rule out the possibility that additional differences in functional network organization would be found in a more homogeneous data sample of individuals with ASD. Conclusion Our results suggest that the organization of the whole-brain functional network in patients with ASD is different from that observed in controls, which implies a reduced modularity of the brain functional networks involved in sensorimotor, social, affective and cognitive processing. PMID:26505141

Large-Scale Network Analysis of Whole-Brain Resting-State Functional Connectivity in Spinal Cord Injury: A Comparative Study.

PubMed

Kaushal, Mayank; Oni-Orisan, Akinwunmi; Chen, Gang; Li, Wenjun; Leschke, Jack; Ward, Doug; Kalinosky, Benjamin; Budde, Matthew; Schmit, Brian; Li, Shi-Jiang; Muqeet, Vaishnavi; Kurpad, Shekar

2017-09-01

Network analysis based on graph theory depicts the brain as a complex network that allows inspection of overall brain connectivity pattern and calculation of quantifiable network metrics. To date, large-scale network analysis has not been applied to resting-state functional networks in complete spinal cord injury (SCI) patients. To characterize modular reorganization of whole brain into constituent nodes and compare network metrics between SCI and control subjects, fifteen subjects with chronic complete cervical SCI and 15 neurologically intact controls were scanned. The data were preprocessed followed by parcellation of the brain into 116 regions of interest (ROI). Correlation analysis was performed between every ROI pair to construct connectivity matrices and ROIs were categorized into distinct modules. Subsequently, local efficiency (LE) and global efficiency (GE) network metrics were calculated at incremental cost thresholds. The application of a modularity algorithm organized the whole-brain resting-state functional network of the SCI and the control subjects into nine and seven modules, respectively. The individual modules differed across groups in terms of the number and the composition of constituent nodes. LE demonstrated statistically significant decrease at multiple cost levels in SCI subjects. GE did not differ significantly between the two groups. The demonstration of modular architecture in both groups highlights the applicability of large-scale network analysis in studying complex brain networks. Comparing modules across groups revealed differences in number and membership of constituent nodes, indicating modular reorganization due to neural plasticity.

Altered functional connectivity of amygdala underlying the neuromechanism of migraine pathogenesis.

PubMed

Chen, Zhiye; Chen, Xiaoyan; Liu, Mengqi; Dong, Zhao; Ma, Lin; Yu, Shengyuan

2017-12-01

The amygdala is a large grey matter complex in the limbic system, and it may contribute in the neurolimbic pain network in migraine. However, the detailed neuromechanism remained to be elucidated. The objective of this study is to investigate the amygdala structural and functional changes in migraine and to elucidate the mechanism of neurolimbic pain-modulating in the migraine pathogenesis. Conventional MRI, 3D structure images and resting state functional MRI were performed in 18 normal controls (NC), 18 patients with episodic migraine (EM), and 16 patients with chronic migraine (CM). The amygdala volume was measured using FreeSurfer software and the functional connectivity (FC) of bilateral amygdala was computed over the whole brain. Analysis of covariance was performed on the individual FC maps among groups. The increased FC of left amygdala was observed in EM compared with NC, and the decreased of right amygdala was revealed in CM compared with NC. The increased FC of bilateral amygdala was observed in CM compared with EM. The correlation analysis showed a negative correlation between the score of sleep quality (0, normal; 1, mild sleep disturbance; 2, moderate sleep disturbance; 3, serious sleep disturbance) and the increased FC strength of left amygdala in EM compared with NC, and a positive correlation between the score of sleep quality and the increased FC strength of left amygdala in CM compared with EM, and other clinical variables showed no significant correlation with altered FC of amygdala. The altered functional connectivity of amygdala demonstrated that neurolimbic pain network contribute in the EM pathogenesis and CM chronicization.

Functional Role of Tyr12 in the Catalytic Activity of Novel Zeta-like Glutathione S-transferase from Acidovorax sp. KKS102.

PubMed

Shehu, Dayyabu; Alias, Zazali

2018-05-19

Glutathione S-transferases (GSTs) are a family of enzymes that function in the detoxification of variety of electrophilic substrates. In the present work, we report a novel zeta-like GST (designated as KKSG9) from the biphenyl/polychlorobiphenyl degrading organism Acidovorax sp. KKS102. KKSG9 possessed low sequence similarity but similar biochemical properties to zeta class GSTs. Functional analysis showed that the enzyme exhibits wider substrate specificity compared to most zeta class GSTs by reacting with 1-chloro-2,4-dinitrobenzene (CDNB), p-nitrobenzyl chloride (NBC), ethacrynic acid (EA), hydrogen peroxide, and cumene hydroperoxide. The enzyme also displayed dehalogenation function against dichloroacetate, permethrin, and dieldrin. The functional role of Tyr12 was also investigated by site-directed mutagenesis. The mutant (Y12C) displayed low catalytic activity and dehalogenation function against all the substrates when compared with the wild type. Kinetic analysis using NBC and GSH as substrates showed that the mutant (Y12C) displayed a higher affinity for NBC when compared with the wild type, however, no significant change in GSH affinity was observed. These findings suggest that the presence of tyrosine residue in the motif might represent an evolutionary trend toward improving the catalytic activity of the enzyme. The enzyme as well could be useful in the bioremediation of various types of organochlorine pollutants.

An Analysis of the Correspondence between Imagined Interaction Attributes and Functions

ERIC Educational Resources Information Center

Bodie, Graham D.; Honeycutt, James M.; Vickery, Andrea J.

2013-01-01

Imagined interaction (II) theory has been productive for communication and social cognition scholarship. There is, however, a yet untested assumption within II theory that the 8 attributes are related to all 6 functions and that II functions can be compared and contrasted in terms of II attributes. In addition, there is little research exploring…

OBSERVER RATING VERSUS THREE-DIMENSIONAL MOTION ANALYSIS OF LOWER EXTREMITY KINEMATICS DURING FUNCTIONAL SCREENING TESTS: A SYSTEMATIC REVIEW.

PubMed

Maclachlan, Liam; White, Steven G; Reid, Duncan

2015-08-01

Functional assessments are conducted in both clinical and athletic settings in an attempt to identify those individuals who exhibit movement patterns that may increase their risk of non-contact injury. In place of highly sophisticated three-dimensional motion analysis, functional testing can be completed through observation. To evaluate the validity of movement observation assessments by summarizing the results of articles comparing human observation in real-time or video play-back and three-dimensional motion analysis of lower extremity kinematics during functional screening tests. Systematic review. A computerized systematic search was conducted through Medline, SPORTSdiscus, Scopus, Cinhal, and Cochrane health databases between February and April of 2014. Validity studies comparing human observation (real-time or video play-back) to three-dimensional motion analysis of functional tasks were selected. Only studies comprising uninjured, healthy subjects conducting lower extremity functional assessments were appropriate for review. Eligible observers were certified health practitioners or qualified members of sports and athletic training teams that conduct athlete screening. The Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) was used to appraise the literature. Results are presented in terms of functional tasks. Six studies met the inclusion criteria. Across these studies, two-legged squats, single-leg squats, drop-jumps, and running and cutting manoeuvres were the functional tasks analysed. When compared to three-dimensional motion analysis, observer ratings of lower extremity kinematics, such as knee position in relation to the foot, demonstrated mixed results. Single-leg squats achieved target sensitivity values (≥ 80%) but not specificity values (≥ 50%>%). Drop-jump task agreement ranged from poor (< 50%) to excellent (> 80%). Two-legged squats achieved 88% sensitivity and 85% specificity. Mean underestimations as large as 198 (peak knee flexion) were found in the results of those assessing running and side-step cutting manoeuvres. Variables such as the speed of movement, the methods of rating, the profiles of participants and the experience levels of observers may have influenced the outcomes of functional testing. The small number of studies used limits generalizability. Furthermore, this review used two dimensional video-playback for the majority of observations. If the movements had been rated in real-time three dimensional video, the results may have been different. Slower, speed controlled movements using dichotomous ratings reach target sensitivity and demonstrate higher overall levels of agreement. As a result, their utilization in functional screening is advocated. 1A.

The effects of whole body vibration on mobility and balance in children with cerebral palsy: a systematic review with meta-analysis.

PubMed

Saquetto, M; Carvalho, V; Silva, C; Conceição, C; Gomes-Neto, M

2015-06-01

We performed a meta-analysis to evaluate the effects of whole-body vibration on physiologic and functional measurements in children with cerebral palsy. We searched MEDLINE, Cochrane Controlled Trials Register, EMBASE, Scielo, CINAHL (from the earliest date available to November 2014) for randomized controlled trials, that aimed to investigate the effects of whole-body vibration versus exercise and/or versus control on physiologic and functional measurements in children with cerebral palsy. Two reviewers independently selected the studies. Weighted mean differences (WMDs) and 95% confidence intervals (CIs) were calculated. Six studies with 176 patients comparing whole-body vibration to exercise and/or control were included. Whole-body vibration resulted in improvement in: gait speed WMDs (0.13 95% CI: 0.05 to 0.20); gross motor function dimension E WMDs (2.97 95% CI: 0.07 to 5.86) and femur bone density (1.32 95% CI: 0.28 to 2.36). The meta-analysis also showed a nonsignificant difference in muscle strength and gross motor function dimension D for participants in the whole-body vibration compared with control group. No serious adverse events were reported. Whole-body vibration may improve gait speed and standing function in children with cerebral palsy and could be considered for inclusion in rehabilitation programs.

Outcome assessment of lingual and labial appliances compared with cephalometric analysis, peer assessment rating, and objective grading system in Angle Class II extraction cases.

PubMed

Deguchi, Toru; Terao, Fumie; Aonuma, Tomo; Kataoka, Tomoki; Sugawara, Yasuyo; Yamashiro, Takashi; Takano-Yamamoto, Teruko

2015-05-01

To validate our hypothesis that there would be significant differences in treatment outcomes, including cephalometric values, degree of root resorption, occlusal indices, and functional aspect, between cases treated with labial and lingual appliances. Twenty-four consecutively treated Class II cases with extractions and lingual appliance were compared with 25 matched cases treated with extraction and labial appliance. Orthodontic treatment outcomes were evaluated by cephalometric analysis, peer assessment rating, and an objective grading system (OGS). Additionally, functional analysis was also performed in both groups after orthodontic treatment. Statistical comparison was performed using the Wilcoxon signed rank test within the groups, and the Mann-Whitney U-test was used to compare between the labial and lingual groups. The only significant difference between the groups was that the interincisal angle was larger in the lingual group than in the labial group. OGS evaluation showed that control over root angulation was significantly worse in the lingual group than in the labial group. There was no significant difference between groups in the amount of root resorption or in functional evaluation. Generally, lingual appliances offer comparable treatment results to those obtained with labial appliances. However, care should be taken with lingual appliances because they are more prone to produce uprighted incisors and root angulation.

Comparative analysis of gut microbiota associated with body mass index in a large Korean cohort.

PubMed

Yun, Yeojun; Kim, Han-Na; Kim, Song E; Heo, Seong Gu; Chang, Yoosoo; Ryu, Seungho; Shin, Hocheol; Kim, Hyung-Lae

2017-07-04

Gut microbiota plays an important role in the harvesting, storage, and expenditure of energy obtained from one's diet. Our cross-sectional study aimed to identify differences in gut microbiota according to body mass index (BMI) in a Korean population. 16S rRNA gene sequence data from 1463 subjects were categorized by BMI into normal, overweight, and obese groups. Fecal microbiotas were compared to determine differences in diversity and functional inference analysis related with BMI. The correlation between genus-level microbiota and BMI was tested using zero-inflated Gaussian mixture models, with or without covariate adjustment of nutrient intake. We confirmed differences between 16Sr RNA gene sequencing data of each BMI group, with decreasing diversity in the obese compared with the normal group. According to analysis of inferred metagenomic functional content using PICRUSt algorithm, a highly significant discrepancy in metabolism and immune functions (P < 0.0001) was predicted in the obese group. Differential taxonomic components in each BMI group were greatly affected by nutrient adjustment, whereas signature bacteria were not influenced by nutrients in the obese compared with the overweight group. We found highly significant statistical differences between normal, overweight and obese groups using a large sample size with or without diet confounding factors. Our informative dataset sheds light on the epidemiological study on population microbiome.

Transdiagnostic differences in the resting-state functional connectivity of the prefrontal cortex in depression and schizophrenia.

PubMed

Chen, Xi; Liu, Chang; He, Hui; Chang, Xin; Jiang, Yuchao; Li, Yingjia; Duan, Mingjun; Li, Jianfu; Luo, Cheng; Yao, Dezhong

2017-08-01

Depression and schizophrenia are two of the most serious psychiatric disorders. They share similar symptoms but the pathology-specific commonalities and differences remain unknown. This study was conducted to acquire a full picture of the functional alterations in schizophrenia and depression patients. The resting-state fMRI data from 20 patients with schizophrenia, 20 patients with depression and 20 healthy control subjects were collected. A data-driven approach that included local functional connectivity density (FCD) analysis combined with multivariate pattern analysis (MVPA) was used to compare the three groups. Based on the results of the MVPA, the local FCD value in the orbitofrontal cortex (OFC) can differentiate depression patients from schizophrenia patients. The patients with depression had a higher local FCD value in the medial and anterior parts of the OFC than the subjects in the other two groups, which suggested altered abstract and reward reinforces processing in depression patients. Subsequent functional connectivity analysis indicated that the connection in the prefrontal cortex was significantly lower in people with schizophrenia compared to people with depression and healthy controls. The systematically different medications for schizophrenia and depression may have different effects on functional connectivity. These results suggested that the resting-state functional connectivity pattern in the prefrontal cortex may be a transdiagnostic difference between depression and schizophrenia patients. Copyright © 2017 Elsevier B.V. All rights reserved.

A novel method for calculating relative free energy of similar molecules in two environments

NASA Astrophysics Data System (ADS)

Farhi, Asaf; Singh, Bipin

2017-03-01

Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy, simple implementation, robustness and efficiency, which prevent the calculations from being automated and limit their use. Here we present an exact and complete decoupling analysis in which the partition functions of the compared systems decompose into the partition functions of the common and different subsystems. This decoupling analysis is applicable to submolecules with coupled degrees of freedom such as the methyl group and to any potential function (including the typical dihedral potentials), enabling to remove less terms in the transformation which results in a more efficient calculation. Then we show mathematically, in the context of partition function decoupling, that the two compared systems can be simulated separately, eliminating the need to design a composite system. We demonstrate the decoupling analysis and the separate transformations in a relative free energy calculation using MD simulations for a general force field and compare to another calculation and to experimental results. We present a unified soft-core technique that ensures the monotonicity of the numerically integrated function (analytical proof) which is important for the selection of intermediates. We show mathematically that in this soft-core technique the numerically integrated function can be non-steep only when we transform the systems separately, which can simplify the numerical integration. Finally, we show that when the systems have rugged energy landscape they can be equilibrated without introducing another sampling dimension which can also enable to use the simulation results for other free energy calculations.

Test Cases for Modeling and Validation of Structures with Piezoelectric Actuators

NASA Technical Reports Server (NTRS)

Reaves, Mercedes C.; Horta, Lucas G.

2001-01-01

A set of benchmark test articles were developed to validate techniques for modeling structures containing piezoelectric actuators using commercially available finite element analysis packages. The paper presents the development, modeling, and testing of two structures: an aluminum plate with surface mounted patch actuators and a composite box beam with surface mounted actuators. Three approaches for modeling structures containing piezoelectric actuators using the commercially available packages: MSC/NASTRAN and ANSYS are presented. The approaches, applications, and limitations are discussed. Data for both test articles are compared in terms of frequency response functions from deflection and strain data to input voltage to the actuator. Frequency response function results using the three different analysis approaches provided comparable test/analysis results. It is shown that global versus local behavior of the analytical model and test article must be considered when comparing different approaches. Also, improper bonding of actuators greatly reduces the electrical to mechanical effectiveness of the actuators producing anti-resonance errors.

Dcode.org anthology of comparative genomic tools.

PubMed

Loots, Gabriela G; Ovcharenko, Ivan

2005-07-01

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical application of comparative sequence analysis to genetics and genomics, we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools, zPicture and Mulan; a phylogenetic shadowing tool, eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools, rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, Creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ website.

Idiopathic Pulmonary Fibrosis: Data-driven Textural Analysis of Extent of Fibrosis at Baseline and 15-Month Follow-up.

PubMed

Humphries, Stephen M; Yagihashi, Kunihiro; Huckleberry, Jason; Rho, Byung-Hak; Schroeder, Joyce D; Strand, Matthew; Schwarz, Marvin I; Flaherty, Kevin R; Kazerooni, Ella A; van Beek, Edwin J R; Lynch, David A

2017-10-01

Purpose To evaluate associations between pulmonary function and both quantitative analysis and visual assessment of thin-section computed tomography (CT) images at baseline and at 15-month follow-up in subjects with idiopathic pulmonary fibrosis (IPF). Materials and Methods This retrospective analysis of preexisting anonymized data, collected prospectively between 2007 and 2013 in a HIPAA-compliant study, was exempt from additional institutional review board approval. The extent of lung fibrosis at baseline inspiratory chest CT in 280 subjects enrolled in the IPF Network was evaluated. Visual analysis was performed by using a semiquantitative scoring system. Computer-based quantitative analysis included CT histogram-based measurements and a data-driven textural analysis (DTA). Follow-up CT images in 72 of these subjects were also analyzed. Univariate comparisons were performed by using Spearman rank correlation. Multivariate and longitudinal analyses were performed by using a linear mixed model approach, in which models were compared by using asymptotic χ 2 tests. Results At baseline, all CT-derived measures showed moderate significant correlation (P < .001) with pulmonary function. At follow-up CT, changes in DTA scores showed significant correlation with changes in both forced vital capacity percentage predicted (ρ = -0.41, P < .001) and diffusing capacity for carbon monoxide percentage predicted (ρ = -0.40, P < .001). Asymptotic χ 2 tests showed that inclusion of DTA score significantly improved fit of both baseline and longitudinal linear mixed models in the prediction of pulmonary function (P < .001 for both). Conclusion When compared with semiquantitative visual assessment and CT histogram-based measurements, DTA score provides additional information that can be used to predict diminished function. Automatic quantification of lung fibrosis at CT yields an index of severity that correlates with visual assessment and functional change in subjects with IPF. © RSNA, 2017.

DFT Study of Small Gold Clusters, Au n (2≤ n ≤ 6): Stability and Charge Distribution Using M08-SO Functional

NASA Astrophysics Data System (ADS)

Carvalho, F. S.; Braga, J. P.

2018-05-01

We have investigated the more stable structures for small gold clusters, Aun (2≤ n ≤ 6), using the density functional theory method. Two functionals used in the literature, the well-known B3LYP and M06-L, were compared with the one that has not been used for this system yet, M08-SO, and the results for dimer were compared with experimental data. It was found that M08-SO gives the best results for the effective core potential and basis set tested. Therefore, the functional M08-SO was used for other structures. The planar geometries were found to have the lowest energies. After the geometry optimization, Mulliken populational analysis (MPA) and natural populational analysis (NPA) were carried out and the results for charge distribution in gold trimer and tetramer were compared with data found in literature. The MPA calculation does not give results in agreement with the literature. On the other hand, the NPA calculation gives coherent data. The results showed that the charge distribution will not always predict the more favorable site of interaction.

An NCME Instructional Module on Latent DIF Analysis Using Mixture Item Response Models

ERIC Educational Resources Information Center

Cho, Sun-Joo; Suh, Youngsuk; Lee, Woo-yeol

2016-01-01

The purpose of this ITEMS module is to provide an introduction to differential item functioning (DIF) analysis using mixture item response models. The mixture item response models for DIF analysis involve comparing item profiles across latent groups, instead of manifest groups. First, an overview of DIF analysis based on latent groups, called…

Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map.

PubMed

Smith, Ian; Greenside, Peyton G; Natoli, Ted; Lahr, David L; Wadden, David; Tirosh, Itay; Narayan, Rajiv; Root, David E; Golub, Todd R; Subramanian, Aravind; Doench, John G

2017-11-01

The application of RNA interference (RNAi) to mammalian cells has provided the means to perform phenotypic screens to determine the functions of genes. Although RNAi has revolutionized loss-of-function genetic experiments, it has been difficult to systematically assess the prevalence and consequences of off-target effects. The Connectivity Map (CMAP) represents an unprecedented resource to study the gene expression consequences of expressing short hairpin RNAs (shRNAs). Analysis of signatures for over 13,000 shRNAs applied in 9 cell lines revealed that microRNA (miRNA)-like off-target effects of RNAi are far stronger and more pervasive than generally appreciated. We show that mitigating off-target effects is feasible in these datasets via computational methodologies to produce a consensus gene signature (CGS). In addition, we compared RNAi technology to clustered regularly interspaced short palindromic repeat (CRISPR)-based knockout by analysis of 373 single guide RNAs (sgRNAs) in 6 cells lines and show that the on-target efficacies are comparable, but CRISPR technology is far less susceptible to systematic off-target effects. These results will help guide the proper use and analysis of loss-of-function reagents for the determination of gene function.

Symptoms, visual function, and mucin expression of eyes with tear film instability.

PubMed

Shimazaki-Den, Seika; Dogru, Murat; Higa, Kazunari; Shimazaki, Jun

2013-09-01

We examined symptoms, tear stability, visual function, and conjunctival cytology in eyes with an unstable tear film (UTF), expressed as a short tear film breakup time without epithelial damage or low tear secretion, and compared the results with those from eyes with aqueous deficiency (AD) associated with epithelial damage, and healthy eyes. We divided the patients with ocular discomfort into 2 groups according to the breakup time, Schirmer value, and epithelial staining score: UTF group (≤5 seconds, >5 mm, and <3 points; 21 eyes of 21 patients) and AD group (≤5 seconds, ≤5 mm, and ≥3 points; 21 eyes of 21 patients). We examined all patients and 17 healthy subjects for symptoms, tear functions, tear film stability by tear film lipid layer interferometry and tear film analysis system, and functional visual acuity. Conjunctival impression cytology was performed to investigate changes in goblet cell density, squamous metaplasia, and messenger RNA expression of MUC5AC and MUC16. The symptom scores, tear film analysis system index, and functional visual acuity testing were significantly worse in the UTF and AD groups compared with those in the control group (P < 0.05). The messenger RNA expression levels of MUC5AC and MUC16 were significantly lower in UTF and AD eyes compared with those in the control eyes (P < 0.0001). An UTF itself can cause dry eye symptoms and visual disturbance comparable with those of AD dry eyes.

Global analysis of bacterial transcription factors to predict cellular target processes.

PubMed

Doerks, Tobias; Andrade, Miguel A; Lathe, Warren; von Mering, Christian; Bork, Peer

2004-03-01

Whole-genome sequences are now available for >100 bacterial species, giving unprecedented power to comparative genomics approaches. We have applied genome-context methods to predict target processes that are regulated by transcription factors (TFs). Of 128 orthologous groups of proteins annotated as TFs, to date, 36 are functionally uncharacterized; in our analysis we predict a probable cellular target process or biochemical pathway for half of these functionally uncharacterized TFs.

Network analysis of mesoscale optical recordings to assess regional, functional connectivity.

PubMed

Lim, Diana H; LeDue, Jeffrey M; Murphy, Timothy H

2015-10-01

With modern optical imaging methods, it is possible to map structural and functional connectivity. Optical imaging studies that aim to describe large-scale neural connectivity often need to handle large and complex datasets. In order to interpret these datasets, new methods for analyzing structural and functional connectivity are being developed. Recently, network analysis, based on graph theory, has been used to describe and quantify brain connectivity in both experimental and clinical studies. We outline how to apply regional, functional network analysis to mesoscale optical imaging using voltage-sensitive-dye imaging and channelrhodopsin-2 stimulation in a mouse model. We include links to sample datasets and an analysis script. The analyses we employ can be applied to other types of fluorescence wide-field imaging, including genetically encoded calcium indicators, to assess network properties. We discuss the benefits and limitations of using network analysis for interpreting optical imaging data and define network properties that may be used to compare across preparations or other manipulations such as animal models of disease.

Dual-echo ASL based assessment of motor networks: a feasibility study

NASA Astrophysics Data System (ADS)

Storti, Silvia Francesca; Boscolo Galazzo, Ilaria; Pizzini, Francesca B.; Menegaz, Gloria

2018-04-01

Objective. Dual-echo arterial spin labeling (DE-ASL) technique has been recently proposed for the simultaneous acquisition of ASL and blood-oxygenation-level-dependent (BOLD)-functional magnetic resonance imaging (fMRI) data. The assessment of this technique in detecting functional connectivity at rest or during motor and motor imagery tasks is still unexplored both per-se and in comparison with conventional methods. The purpose is to quantify the sensitivity of the DE-ASL sequence with respect to the conventional fMRI sequence (cvBOLD) in detecting brain activations, and to assess and compare the relevance of node features in decoding the network structure. Approach. Thirteen volunteers were scanned acquiring a pseudo-continuous DE-ASL sequence from which the concomitant BOLD (ccBOLD) simultaneously to the ASL can be extracted. The approach consists of two steps: (i) model-based analyses for assessing brain activations at individual and group levels, followed by statistical analysis for comparing the activation elicited by the three sequences under two conditions (motor and motor imagery), respectively; (ii) brain connectivity graph-theoretical analysis for assessing and comparing the network models properties. Main results. Our results suggest that cvBOLD and ccBOLD have comparable sensitivity in detecting the regions involved in the active task, whereas ASL offers a higher degree of co-localization with smaller activation volumes. The connectivity results and the comparative analysis of node features across sequences revealed that there are no strong changes between rest and tasks and that the differences between the sequences are limited to few connections. Significance. Considering the comparable sensitivity of the ccBOLD and cvBOLD sequences in detecting activated brain regions, the results demonstrate that DE-ASL can be successfully applied in functional studies allowing to obtain both ASL and BOLD information within a single sequence. Further, DE-ASL is a powerful technique for research and clinical applications allowing to perform quantitative comparisons as well as to characterize functional connectivity.

Variational Methods in Design Optimization and Sensitivity Analysis for Two-Dimensional Euler Equations

NASA Technical Reports Server (NTRS)

Ibrahim, A. H.; Tiwari, S. N.; Smith, R. E.

1997-01-01

Variational methods (VM) sensitivity analysis employed to derive the costate (adjoint) equations, the transversality conditions, and the functional sensitivity derivatives. In the derivation of the sensitivity equations, the variational methods use the generalized calculus of variations, in which the variable boundary is considered as the design function. The converged solution of the state equations together with the converged solution of the costate equations are integrated along the domain boundary to uniquely determine the functional sensitivity derivatives with respect to the design function. The application of the variational methods to aerodynamic shape optimization problems is demonstrated for internal flow problems at supersonic Mach number range. The study shows, that while maintaining the accuracy of the functional sensitivity derivatives within the reasonable range for engineering prediction purposes, the variational methods show a substantial gain in computational efficiency, i.e., computer time and memory, when compared with the finite difference sensitivity analysis.

The Convergent Validity of the Questions about Behavioral Function Scale and Functional Analysis for Problem Behavior Displayed by Individuals with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Watkins, Nicholas; Rapp, John T.

2013-01-01

Only a few studies have compared the convergent validity of the Questions About Behavioral Function (QABF) scale to the results of functional analyses (FA). In the current study, six participants who emitted problem behaviors participated in either a brief, or a no-interaction-series FA, while each participant's parent completed the QABF. The…

Comparative Analysis of Membership Function on Mamdani Fuzzy Inference System for Decision Making

NASA Astrophysics Data System (ADS)

harliana, Putri; Rahim, Robbi

2017-12-01

Membership function is a curve that shows mapping the input data points into the value or degree of membership which has an interval between 0 and 1. One way to get membership value is through a function approach. There are some membership functions can be used on mamdani fuzzy inference system. They are triangular, trapezoid, singleton, sigmoid, Gaussian, etc. In this paper only discuss three membership functions, are triangular, trapezoid and Gaussian. These three membership functions will be compared to see the difference in parameter values and results obtained. For case study in this paper is admission of students at popular school. There are three variable can be used, they are students’ report, IQ score and parents’ income. Which will then be created if-then rules.

The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity

PubMed Central

Stein, Matthias; Pilli, Manohar; Bernauer, Sabine; Habermann, Bianca H.; Zerial, Marino; Wade, Rebecca C.

2012-01-01

Background Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying molecular recognition motifs, binding partner preferences and selectivities are not well understood. Methodology/Principal Findings Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic molecular interaction fields of 62 human Rab proteins revealed a wide range of binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics. Conclusions/Significance We have analysed conservation of sequence and of molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their binding partner selectivity. PMID:22523562

Association of presence/absence and on/off patterns of Helicobacter pylori oipA gene with peptic ulcer disease and gastric cancer risks: a meta-analysis.

PubMed

Liu, Jingwei; He, Caiyun; Chen, Moye; Wang, Zhenning; Xing, Chengzhong; Yuan, Yuan

2013-11-20

There are increasing studies examining the relationship between the status of H. pylori oipA gene and peptic ulcer disease (PUD) and gastric cancer (GC) but the results turn out to be controversial. We attempted to clarify whether oipA gene status is linked with PUD and/or GC risks. A systematically literature search was performed through four electronic databases. According to the specific inclusion and exclusion criteria, seven articles were ultimately available for the meta-analysis of oipA presence/absence with PUD and GC, and eleven articles were included for the meta-analysis of oipA on/off status with PUD and GC. For the on/off functional status analysis of oipA gene, the "on" status showed significant associations with increased risks of PUD (OR = 3.97, 95% CI: 2.89, 5.45; P < 0.001) and GC (OR = 2.43, 95% CI: 1.45, 4.07; P = 0.001) compared with gastritis and functional dyspepsia controls. Results of the homogeneity test indicated different effects of oipA "on" status on PUD risk between children and adult subgroups and on GC risk between PCR-sequencing and immunoblot subgroups. For the presence/absence analysis of oipA gene, we found null association of the presence of oipA gene with the risks of PUD (OR = 1.93, 95% CI: 0.60, 6.25; P = 0.278) and GC (OR = 2.09, 95% CI: 0.51, 8.66; P = 0.308) compared with gastritis and functional dyspepsia controls. To be concluded, when oipA exists, the functional "on" status of this gene showed association with increased risks for PUD and GC compared with gastritis and FD controls. However, merely investigating the presence/absence of oipA would overlook the importance of its functional on/off status and would not be reliable to predict risks of PUD and GC. Further large-scale and well-designed studies concerning on/off status of oipA are required to confirm our meta-analysis results.

Functional Magnetic Resonance Imaging of Working Memory and Executive Dysfunction in Systemic Lupus Erythematosus and Antiphospholipid Antibody-Positive Patients.

PubMed

Kozora, E; Uluğ, A M; Erkan, D; Vo, A; Filley, C M; Ramon, G; Burleson, A; Zimmerman, R; Lockshin, M D

2016-11-01

Standardized cognitive tests and functional magnetic resonance imaging (fMRI) studies of systemic lupus erythematosus (SLE) patients demonstrate deficits in working memory and executive function. These neurobehavioral abnormalities are not well studied in antiphospholipid syndrome, which may occur independently of or together with SLE. This study compares an fMRI paradigm involving motor skills, working memory, and executive function in SLE patients without antiphospholipid antibody (aPL) (the SLE group), aPL-positive non-SLE patients (the aPL-positive group), and controls. Brain MRI, fMRI, and standardized cognitive assessment results were obtained from 20 SLE, 20 aPL-positive, and 10 healthy female subjects with no history of neuropsychiatric abnormality. Analysis of fMRI data showed no differences in performance across groups on bilateral motor tasks. When analysis of variance was used, significant group differences were found in 2 executive function tasks (word generation and word rhyming) and in a working memory task (N-Back). Patients positive for aPL demonstrated higher activation in bilateral frontal, temporal, and parietal cortices compared to controls during working memory and executive function tasks. SLE patients also demonstrated bilateral frontal and temporal activation during working memory and executive function tasks. Compared to controls, both aPL-positive and SLE patients had elevated cortical activation, primarily in the frontal lobes, during tasks involving working memory and executive function. These findings are consistent with cortical overactivation as a compensatory mechanism for early white matter neuropathology in these disorders. © 2016, American College of Rheumatology.

Psychological and functional effect of different primary treatments for prostate cancer: A comparative prospective analysis.

PubMed

Sciarra, Alessandro; Gentilucci, Alessandro; Salciccia, Stefano; Von Heland, Magnus; Ricciuti, Giam Piero; Marzio, Vittorio; Pierella, Federico; Musio, Daniela; Tombolini, Vincenzo; Frantellizzi, Viviana; Pasquini, Massimo; Maraone, Annalisa; Guandalini, Alessio; Maggi, Martina

2018-04-26

The aim of the study was to comparatively evaluate the psychological and functional effect of different primary treatments in patients with prostate cancer. We conducted a single-center prospective non randomized study in a real-life setting using functional and psychological questionnaires in prostate cancer cases submitted to radical prostatectomy, external radiotherapy, or active surveillance. Totally, 220 cases were evaluated at baseline and during the follow-up at 1-, 3-, 6-, and 12-month interval after therapy. Patients self-completed questionnaires on urinary symptoms and incontinence, erectile and bowel function, psychological distress (PD), anxiety, and depression. Several significant differences among the three groups of treatment were found regarding the total score of the functional questionnaires. Regarding PD, cases submitted to radical prostatectomy showed stable scores during all the 12 months of follow-up whereas cases submitted to radiotherapy showed a rapid significant worsening of scores at 1-month interval and persistent also at 6- and 12-month interval. Cases submitted to active surveillance showed a slight and slow worsening of scores only at 12-month interval. PD and depression resulted to be more associated with urinary symptoms than sexual function worsening whereas anxiety resulted to be associated either with urinary symptoms or sexual function worsening. The results of our comparative and prospective analysis could be used to better inform treatment decision-making. Patients and their teams might wish to know how functional and psychological aspects may differently be influenced by treatment choice. Copyright © 2018 Elsevier Inc. All rights reserved.

[Comparative analysis on the biological basis of blood stasis syndrome induced by qi-stagnation and qi-deficiency in patients with unstable angina pectoris].

PubMed

Ren, Jian-xun; Liu, Jian-xun; Lin, Cheng-ren

2010-04-01

To comparatively analyse the objective characteristics of different syndrome types of qi-disturbance-induced blood stasis syndrome (QDBS) in the pathogenetic evolution of unstable angina coronary heart disease (UA-CHD). Seventy-eight patients with UA-CHD of QDBS were differentiated into 2 groups: 55 in the qi-deficiency-induced blood-stasis syndrome group (A) and 23 in the qi-stagnation-induced blood-stasis syndrome group (B). The comparative analysis on them was carried out through comparing their blood pressure, glucose and lipid metabolisms, coagulation function, thyroid function and inflammation reaction changes, etc. In the pathogenetic process of qi-disturbance induced blood stasis, the initiating age, levels of HbA1c, TSH, PT and APTT between the two groups were significantly different (P < 0.05). Levels of TNF-alpha and LN were higher and levels of sIgA lower in patients than those in healthy subjects (P < 0.05). Inflammation immune reaction may play an important role in the pathogenetic process of blood-stasis syndrome, and the functional disturbance of hypothalamus, pituitary and endocrinal secretion induced by emotional stress is possibly the essence of qi-stagnation induced blood stasis syndrome.

Functional Connectivity Parcellation of the Human Thalamus by Independent Component Analysis.

PubMed

Zhang, Sheng; Li, Chiang-Shan R

2017-11-01

As a key structure to relay and integrate information, the thalamus supports multiple cognitive and affective functions through the connectivity between its subnuclei and cortical and subcortical regions. Although extant studies have largely described thalamic regional functions in anatomical terms, evidence accumulates to suggest a more complex picture of subareal activities and connectivities of the thalamus. In this study, we aimed to parcellate the thalamus and examine whole-brain connectivity of its functional clusters. With resting state functional magnetic resonance imaging data from 96 adults, we used independent component analysis (ICA) to parcellate the thalamus into 10 components. On the basis of the independence assumption, ICA helps to identify how subclusters overlap spatially. Whole brain functional connectivity of each subdivision was computed for independent component's time course (ICtc), which is a unique time series to represent an IC. For comparison, we computed seed-region-based functional connectivity using the averaged time course across all voxels within a thalamic subdivision. The results showed that, at p < 10 -6 , corrected, 49% of voxels on average overlapped among subdivisions. Compared with seed-region analysis, ICtc analysis revealed patterns of connectivity that were more distinguished between thalamic clusters. ICtc analysis demonstrated thalamic connectivity to the primary motor cortex, which has eluded the analysis as well as previous studies based on averaged time series, and clarified thalamic connectivity to the hippocampus, caudate nucleus, and precuneus. The new findings elucidate functional organization of the thalamus and suggest that ICA clustering in combination with ICtc rather than seed-region analysis better distinguishes whole-brain connectivities among functional clusters of a brain region.

Comparing renal function preservation after laparoscopic radio frequency ablation assisted tumor enucleation and laparoscopic partial nephrectomy for clinical T1a renal tumor: using a 3D parenchyma measurement system.

PubMed

Zhu, Liangsong; Wu, Guangyu; Huang, Jiwei; Wang, Jianfeng; Zhang, Ruiyun; Kong, Wen; Xue, Wei; Huang, Yiran; Chen, Yonghui; Zhang, Jin

2017-05-01

To compare the renal function preservation between laparoscopic radio frequency ablation assisted tumor enucleation and laparoscopic partial nephrectomy. Data were analyzed from 246 patients who underwent laparoscopic radio frequency ablation assisted tumor enucleation and laparoscopic partial nephrectomy for solitary cT1a renal cell carcinoma from January 2013 to July 2015. To reduce the intergroup difference, we used a 1:1 propensity matching analysis. The functional renal parenchyma volume preservation were measured preoperative and 12 months after surgery. The total renal function recovery and spilt GFR was compared. Multivariable logistic analysis was used for predictive factors for renal function decline. After 1:1 propensity matching, each group including 100 patients. Patients in the laparoscopic radio frequency ablation assisted tumor enucleation had a smaller decrease in estimate glomerular filtration rate at 1 day (-7.88 vs -20.01%, p < 0.001), 3 months (-2.31 vs -10.39%, p < 0.001), 6 months (-2.16 vs -7.99%, p = 0.015), 12 months (-3.26 vs -8.03%, p = 0.012) and latest test (-3.24 vs -8.02%, p = 0.040), also had better functional renal parenchyma volume preservation (89.19 vs 84.27%, p < 0.001), lower decrease of the spilt glomerular filtration rate (-9.41 vs -17.13%, p < 0.001) at 12 months. The functional renal parenchyma volume preservation, warm ischemia time and baseline renal function were the important independent factors in determining long-term functional recovery. The laparoscopic radio frequency ablation assisted tumor enucleation technology has unique advantage and potential in preserving renal parenchyma without ischemia damage compared to conventional laparoscopic partial nephrectomy, and had a better outcome, thus we recommend this technique in selected T1a patients.

Analysis and selection of optimal function implementations in massively parallel computer

DOEpatents

Archer, Charles Jens [Rochester, MN; Peters, Amanda [Rochester, MN; Ratterman, Joseph D [Rochester, MN

2011-05-31

An apparatus, program product and method optimize the operation of a parallel computer system by, in part, collecting performance data for a set of implementations of a function capable of being executed on the parallel computer system based upon the execution of the set of implementations under varying input parameters in a plurality of input dimensions. The collected performance data may be used to generate selection program code that is configured to call selected implementations of the function in response to a call to the function under varying input parameters. The collected performance data may be used to perform more detailed analysis to ascertain the comparative performance of the set of implementations of the function under the varying input parameters.

APOE polymorphism as a potential determinant of functional fitness in the elderly regardless of nutritional status.

PubMed

Snejdrlova, Michaela; Kalvach, Zdenek; Topinkova, Eva; Vrablik, Michal; Prochazkova, Renata; Kvasilova, Marie; Lanska, Vera; Zlatohlavek, Lukas; Prusikova, Martina; Ceska, Richard

2011-01-01

Life expectancy is determined by a combination of genetic predisposition (~25%) and environmental influences (~75%). Nevertheless a stronger genetic influence is anticipated in long-living individuals. Apolipoprotein E (APOE) gene belongs among the most studied candidate genes of longevity. We evaluated the relation of APOE polymorphism and fitness status in the elderly. We examined a total number of 128 subjects, over 80 years of age. Using a battery of functional tests their fitness status was assessed and the subjects were stratified into 5 functional categories according to Spirduso´s classification. Biochemistry analysis was performed by enzymatic method using automated analyzers. APOE gene polymorphism was analysed performed using PCR-RFLP. APOE4 allele carriers had significantly worse fitness status compared to non-carriers (p=0.025). Multiple logistic regression analysis showed the APOE4 carriers had higher risk (p=0.05) of functional unfitness compared to APOE2/E3 individuals. APOE gene polymorphism seems be an important genetic contributor to frailty development in the elderly. While APOE2 carriers tend to remain functionally fit till higher age, the functional status of APOE4 carriers deteriorates more rapidly. © 2011 Neuroendocrinology Letters

Functional approach to high-throughput plant growth analysis

PubMed Central

2013-01-01

Method Taking advantage of the current rapid development in imaging systems and computer vision algorithms, we present HPGA, a high-throughput phenotyping platform for plant growth modeling and functional analysis, which produces better understanding of energy distribution in regards of the balance between growth and defense. HPGA has two components, PAE (Plant Area Estimation) and GMA (Growth Modeling and Analysis). In PAE, by taking the complex leaf overlap problem into consideration, the area of every plant is measured from top-view images in four steps. Given the abundant measurements obtained with PAE, in the second module GMA, a nonlinear growth model is applied to generate growth curves, followed by functional data analysis. Results Experimental results on model plant Arabidopsis thaliana show that, compared to an existing approach, HPGA reduces the error rate of measuring plant area by half. The application of HPGA on the cfq mutant plants under fluctuating light reveals the correlation between low photosynthetic rates and small plant area (compared to wild type), which raises a hypothesis that knocking out cfq changes the sensitivity of the energy distribution under fluctuating light conditions to repress leaf growth. Availability HPGA is available at http://www.msu.edu/~jinchen/HPGA. PMID:24565437

Functions of behavior change interventions when implementing multi-professional teamwork at an emergency department: a comparative case study

PubMed Central

2014-01-01

Background While there is strong support for the benefits of working in multi-professional teams in health care, the implementation of multi-professional teamwork is reported to be complex and challenging. Implementation strategies combining multiple behavior change interventions are recommended, but the understanding of how and why the behavior change interventions influence staff behavior is limited. There is a lack of studies focusing on the functions of different behavior change interventions and the mechanisms driving behavior change. In this study, applied behavior analysis is used to analyze the function and impact of different behavior change interventions when implementing multi-professional teamwork. Methods A comparative case study design was applied. Two sections of an emergency department implemented multi-professional teamwork involving changes in work processes, aimed at increasing inter-professional collaboration. Behavior change interventions and staff behavior change were studied using observations, interviews and document analysis. Using a hybrid thematic analysis, the behavior change interventions were categorized according to the DCOM® model. The functions of the behavior change interventions were then analyzed using applied behavior analysis. Results The two sections used different behavior change interventions, resulting in a large difference in the degree of staff behavior change. The successful section enabled staff performance of teamwork behaviors with a strategy based on ongoing problem-solving and frequent clarification of directions. Managerial feedback initially played an important role in motivating teamwork behaviors. Gradually, as staff started to experience positive outcomes of the intervention, motivation for teamwork behaviors was replaced by positive task-generated feedback. Conclusions The functional perspective of applied behavior analysis offers insight into the behavioral mechanisms that describe how and why behavior change interventions influence staff behavior. The analysis demonstrates how enabling behavior change interventions, managerial feedback and task-related feedback interact in their influence on behavior and have complementary functions during different stages of implementation. PMID:24885212

Structure-Function Correlation Using Confocal Laser Ophthalmoscope in Primary Open-Angle Glaucoma and Pseudoexfoliative Glaucoma.

PubMed

Pappas, Theofanis; Founti, Panayiota; Yin, Xiang Jun; Koskosas, Archimidis; Anastasopoulos, Eleftherios; Salonikiou, Angeliki; Kilintzis, Vasilios; Antoniadis, Antonios; Ziakas, Nikolaos; Topouzis, Fotis

2016-04-01

To compare Heidelberg Retina Tomograph (HRT) optic disc parameters and structure-function correlation between primary open-angle glaucoma (POAG) and pseudoexfoliative glaucoma (PEXG). Prospective, observation case series. A total of 54 POAG and 33 PEXG cases, consecutively recruited from a University Glaucoma Service, underwent a comprehensive ophthalmic examination, including HRT optic disc imaging. Glaucoma definition required the presence of both structural and functional damage. One eye per subject was included in the analysis. T test, Mann-Whitney U test, and analysis of covariance were used to compare HRT parameters between POAG and PEXG, adjusting for age, mean deviation (MD) in the visual field, intraocular pressure, and disc area. The correlation between HRT and MD was assessed in each group. Cup area (P=0.048), height variation contour (P=0.016), and cup/disc area ratio (P=0.023) were higher in POAG, whereas the mean retinal nerve fiber layer thickness (P=0.048), retinal nerve fiber layer cross-section area (P=0.044), and rim area (P=0.048) were lower in POAG, compared with PEXG. The correlation of HRT parameters with MD was significant only in the POAG group. At a similar level of functional damage, POAG subjects presented with more pronounced structural damage than PEXG subjects. The correlation between HRT and visual field parameters was more evident in POAG, compared with PEXG.

Gene Network Construction from Microarray Data Identifies a Key Network Module and Several Candidate Hub Genes in Age-Associated Spatial Learning Impairment

PubMed Central

Uddin, Raihan; Singh, Shiva M.

2017-01-01

As humans age many suffer from a decrease in normal brain functions including spatial learning impairments. This study aimed to better understand the molecular mechanisms in age-associated spatial learning impairment (ASLI). We used a mathematical modeling approach implemented in Weighted Gene Co-expression Network Analysis (WGCNA) to create and compare gene network models of young (learning unimpaired) and aged (predominantly learning impaired) brains from a set of exploratory datasets in rats in the context of ASLI. The major goal was to overcome some of the limitations previously observed in the traditional meta- and pathway analysis using these data, and identify novel ASLI related genes and their networks based on co-expression relationship of genes. This analysis identified a set of network modules in the young, each of which is highly enriched with genes functioning in broad but distinct GO functional categories or biological pathways. Interestingly, the analysis pointed to a single module that was highly enriched with genes functioning in “learning and memory” related functions and pathways. Subsequent differential network analysis of this “learning and memory” module in the aged (predominantly learning impaired) rats compared to the young learning unimpaired rats allowed us to identify a set of novel ASLI candidate hub genes. Some of these genes show significant repeatability in networks generated from independent young and aged validation datasets. These hub genes are highly co-expressed with other genes in the network, which not only show differential expression but also differential co-expression and differential connectivity across age and learning impairment. The known function of these hub genes indicate that they play key roles in critical pathways, including kinase and phosphatase signaling, in functions related to various ion channels, and in maintaining neuronal integrity relating to synaptic plasticity and memory formation. Taken together, they provide a new insight and generate new hypotheses into the molecular mechanisms responsible for age associated learning impairment, including spatial learning. PMID:29066959

Gene Network Construction from Microarray Data Identifies a Key Network Module and Several Candidate Hub Genes in Age-Associated Spatial Learning Impairment.

PubMed

Uddin, Raihan; Singh, Shiva M

2017-01-01

As humans age many suffer from a decrease in normal brain functions including spatial learning impairments. This study aimed to better understand the molecular mechanisms in age-associated spatial learning impairment (ASLI). We used a mathematical modeling approach implemented in Weighted Gene Co-expression Network Analysis (WGCNA) to create and compare gene network models of young (learning unimpaired) and aged (predominantly learning impaired) brains from a set of exploratory datasets in rats in the context of ASLI. The major goal was to overcome some of the limitations previously observed in the traditional meta- and pathway analysis using these data, and identify novel ASLI related genes and their networks based on co-expression relationship of genes. This analysis identified a set of network modules in the young, each of which is highly enriched with genes functioning in broad but distinct GO functional categories or biological pathways. Interestingly, the analysis pointed to a single module that was highly enriched with genes functioning in "learning and memory" related functions and pathways. Subsequent differential network analysis of this "learning and memory" module in the aged (predominantly learning impaired) rats compared to the young learning unimpaired rats allowed us to identify a set of novel ASLI candidate hub genes. Some of these genes show significant repeatability in networks generated from independent young and aged validation datasets. These hub genes are highly co-expressed with other genes in the network, which not only show differential expression but also differential co-expression and differential connectivity across age and learning impairment. The known function of these hub genes indicate that they play key roles in critical pathways, including kinase and phosphatase signaling, in functions related to various ion channels, and in maintaining neuronal integrity relating to synaptic plasticity and memory formation. Taken together, they provide a new insight and generate new hypotheses into the molecular mechanisms responsible for age associated learning impairment, including spatial learning.

Meta-Analysis of Structured Triglyceride versus Physical Mixture Medium- and Long-Chain Triglycerides for PN in Liver Resection Patients.

PubMed

Zhao, Yajie; Wang, Chengfeng

2017-01-01

The use of total parenteral nutrition can affect liver function, causing a series of problems such as cholestasis. The aim of this meta-analysis was to compare structured triglyceride- (STG-) based lipid emulsions with physical medium-chain triglyceride (MCT)/long-chain triglyceride (LCT) mixtures in patients who had undergone liver surgery to identify any differences between these two types of parenteral nutrition. We searched the databases of PubMed, the Cochrane Library, Web of Science, EMBASE, and Chinese Biomedicine Database from January 2007 to March 2017 and included studies that compared STG-based lipid emulsions with physical MCT/LCT mixtures for surgical patients with liver disease. The STG was more beneficial than physical MCT/LCT on recovery of liver function and immune function. Therefore, STGs may represent a promising alternative to other types of lipid emulsions for hepatic surgery patients.

Do tasks make a difference? Accounting for heterogeneity of performance of children with reading difficulties on tasks of executive function: findings from a meta-analysis.

PubMed

Booth, Josephine N; Boyle, James M E; Kelly, Steve W

2010-03-01

Research studies have implicated executive functions in reading difficulties (RD). But while some studies have found children with RD to be impaired on tasks of executive function other studies report unimpaired performance. A meta-analysis was carried out to determine whether these discrepant findings can be accounted for by differences in the tasks of executive function that are utilized. A total of 48 studies comparing the performance on tasks of executive function of children with RD with their typically developing peers were included in the meta-analysis, yielding 180 effect sizes. An overall effect size of 0.57 (SE .03) was obtained, indicating that children with RD have impairments on tasks of executive function. However, effect sizes varied considerably suggesting that the impairment is not uniform. Moderator analysis revealed that task modality and IQ-achievement discrepancy definitions of RD influenced the magnitude of effect; however, the age and gender of participants and the nature of the RD did not have an influence. While the children's RD were associated with executive function impairments, variation in effect size is a product of the assessment task employed, underlying task demands, and definitional criteria.

Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins.

PubMed

Zhang, Yu-Juan; Yang, Chun-Lin; Hao, You-Jin; Li, Ying; Chen, Bin; Wen, Jian-Fan

2014-01-25

To fully explore the trends of atomic composition during the macroevolution from prokaryote to eukaryote, five atoms (oxygen, sulfur, nitrogen, carbon, hydrogen) and related functional groups in prokaryotic and eukaryotic proteins were surveyed and compared. Genome-wide analysis showed that eukaryotic proteins have more oxygen, sulfur and nitrogen atoms than prokaryotes do. Clusters of Orthologous Groups (COG) analysis revealed that oxygen, sulfur, carbon and hydrogen frequencies are higher in eukaryotic proteins than in their prokaryotic orthologs. Furthermore, functional group analysis demonstrated that eukaryotic proteins tend to have higher proportions of sulfhydryl, hydroxyl and acylamino, but lower of sulfide and carboxyl. Taken together, an apparent trend of increase was observed for oxygen and sulfur atoms in the macroevolution; the variation of oxygen and sulfur compositions and their related functional groups in macroevolution made eukaryotic proteins carry more useful functional groups. These results will be helpful for better understanding the functional significances of atomic composition evolution. Copyright © 2013 Elsevier B.V. All rights reserved.

Linearised and non-linearised isotherm models optimization analysis by error functions and statistical means

PubMed Central

2014-01-01

In adsorption study, to describe sorption process and evaluation of best-fitting isotherm model is a key analysis to investigate the theoretical hypothesis. Hence, numerous statistically analysis have been extensively used to estimate validity of the experimental equilibrium adsorption values with the predicted equilibrium values. Several statistical error analysis were carried out. In the present study, the following statistical analysis were carried out to evaluate the adsorption isotherm model fitness, like the Pearson correlation, the coefficient of determination and the Chi-square test, have been used. The ANOVA test was carried out for evaluating significance of various error functions and also coefficient of dispersion were evaluated for linearised and non-linearised models. The adsorption of phenol onto natural soil (Local name Kalathur soil) was carried out, in batch mode at 30 ± 20 C. For estimating the isotherm parameters, to get a holistic view of the analysis the models were compared between linear and non-linear isotherm models. The result reveled that, among above mentioned error functions and statistical functions were designed to determine the best fitting isotherm. PMID:25018878

Text Mining Improves Prediction of Protein Functional Sites

PubMed Central

Cohn, Judith D.; Ravikumar, Komandur E.

2012-01-01

We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions. PMID:22393388

A contour for the entanglement entropies in harmonic lattices

NASA Astrophysics Data System (ADS)

Coser, Andrea; De Nobili, Cristiano; Tonni, Erik

2017-08-01

We construct a contour function for the entanglement entropies in generic harmonic lattices. In one spatial dimension, numerical analysis are performed by considering harmonic chains with either periodic or Dirichlet boundary conditions. In the massless regime and for some configurations where the subsystem is a single interval, the numerical results for the contour function are compared to the inverse of the local weight function which multiplies the energy-momentum tensor in the corresponding entanglement hamiltonian, found through conformal field theory methods, and a good agreement is observed. A numerical analysis of the contour function for the entanglement entropy is performed also in a massless harmonic chain for a subsystem made by two disjoint intervals.

Discriminant analysis for fast multiclass data classification through regularized kernel function approximation.

PubMed

Ghorai, Santanu; Mukherjee, Anirban; Dutta, Pranab K

2010-06-01

In this brief we have proposed the multiclass data classification by computationally inexpensive discriminant analysis through vector-valued regularized kernel function approximation (VVRKFA). VVRKFA being an extension of fast regularized kernel function approximation (FRKFA), provides the vector-valued response at single step. The VVRKFA finds a linear operator and a bias vector by using a reduced kernel that maps a pattern from feature space into the low dimensional label space. The classification of patterns is carried out in this low dimensional label subspace. A test pattern is classified depending on its proximity to class centroids. The effectiveness of the proposed method is experimentally verified and compared with multiclass support vector machine (SVM) on several benchmark data sets as well as on gene microarray data for multi-category cancer classification. The results indicate the significant improvement in both training and testing time compared to that of multiclass SVM with comparable testing accuracy principally in large data sets. Experiments in this brief also serve as comparison of performance of VVRKFA with stratified random sampling and sub-sampling.

Creation and characterization of an airway epithelial cell line for stable expression of CFTR variants

PubMed Central

Gottschalk, Laura B.; Vecchio-Pagan, Briana; Sharma, Neeraj; Han, Sangwoo T.; Franca, Arianna; Wohler, Elizabeth S.; Batista, Denise A.S.; Goff, Loyal A.; Cutting, Garry R.

2016-01-01

Background Analysis of the functional consequences and treatment response of rare CFTR variants is challenging due to the limited availability of primary airways cells. Methods A Flp recombination target (FRT) site for stable expression of CFTR was incorporated into an immortalized CF bronchial epithelial cell line (CFBE41o−). CFTR cDNA was integrated into the FRT site. Expression was evaluated by western blotting and confocal microscopy and function measured by short circuit current. RNA sequencing was used to compare the transcriptional profile of the resulting CF8Flp cell line to primary cells and tissues. Results Functional CFTR was expressed from integrated cDNA at the FRT site of the CF8Flp cell line at levels comparable to that seen in native airway cells. CF8Flp cells expressing WT-CFTR have a stable transcriptome comparable to that of primary cultured airway epithelial cells, including genes that play key roles in CFTR pathways. Conclusion CF8Flp cells provide a viable substitute for primary CF airway cells for the analysis of CFTR variants in a native context. PMID:26694805

More with less: A comparative kinematical analysis of Django Reinhardt's adaptations to hand injury.

PubMed

Wininger, Michael; Williams, David J

2015-06-01

At the age of 18 years, jazz guitarist Django Reinhardt (1910-1953) sustained significant burns to his left-hand ring and little fingers; yet, subsequently, he relearned to play and achieved international fame, despite his injuries. Archive film footage and novel motion analysis software were used to compare movements of Django's fretting hand with that of six other guitarists of the same genre. Django employed greater abduction of index and middle fingers (-9.11 ± 6.52° vs -5.78 ± 2.41°; p < 0.001) and more parallel alignment of fingers to the guitar neck (157.7 ± 3.37° vs 150.59 ± 2.67°; p < 0.001) compared to controls. In response to debilitating hand injury, Django developed quantifiable compensatory adaptation of function of his remaining functional fingers by developing an original playing technique. Hand function following injury may be optimized by maximizing latent degrees of freedom in remaining digits, rather than through extensive surgical reconstruction or complex prostheses. Further study of adaptation strategies may inform prosthesis design. © The International Society for Prosthetics and Orthotics 2014.

Effect of exercise on cognitive function in chronic disease patients: a meta-analysis and systematic review of randomized controlled trials.

PubMed

Cai, Hong; Li, Guichen; Hua, Shanshan; Liu, Yufei; Chen, Li

2017-01-01

The purpose of this study was to conduct a meta-analysis and systematic review to assess the effect of exercise on cognitive function in people with chronic diseases. PubMed, Web of Science, Embase, the Cochrane Library, CINAHL, PsycINFO, and three Chinese databases were electronically searched for papers that were published until September 2016. This meta-analysis and systematic review included randomized controlled trials that evaluated the effect of exercise on cognitive function compared with control group for people with chronic diseases. Totally, 35 studies met the inclusion criteria, with 3,113 participants. The main analysis revealed a positive overall random effect of exercise intervention on cognitive function in patients with chronic diseases. The secondary analysis revealed that aerobic exercise interventions and aerobic included exercise interventions had a positive effect on cognition in patients with chronic diseases. The intervention offering low frequency had a positive effect on cognitive function in patients with chronic diseases. Finally, we found that interventions offered at both low exercise intensity and moderate exercise intensity had a positive effect on cognitive function in patients with chronic diseases. The secondary analysis also revealed that exercise interventions were beneficial in Alzheimer's disease patients when grouped by disease type. This meta-analysis and systematic review suggests that exercise interventions positively influence cognitive function in patients with chronic diseases. Beneficial effect was independent of the type of disease, type of exercise, frequency, and the intensity of the exercise intervention.

Image-derived input function with factor analysis and a-priori information.

PubMed

Simončič, Urban; Zanotti-Fregonara, Paolo

2015-02-01

Quantitative PET studies often require the cumbersome and invasive procedure of arterial cannulation to measure the input function. This study sought to minimize the number of necessary blood samples by developing a factor-analysis-based image-derived input function (IDIF) methodology for dynamic PET brain studies. IDIF estimation was performed as follows: (a) carotid and background regions were segmented manually on an early PET time frame; (b) blood-weighted and tissue-weighted time-activity curves (TACs) were extracted with factor analysis; (c) factor analysis results were denoised and scaled using the voxels with the highest blood signal; (d) using population data and one blood sample at 40 min, whole-blood TAC was estimated from postprocessed factor analysis results; and (e) the parent concentration was finally estimated by correcting the whole-blood curve with measured radiometabolite concentrations. The methodology was tested using data from 10 healthy individuals imaged with [(11)C](R)-rolipram. The accuracy of IDIFs was assessed against full arterial sampling by comparing the area under the curve of the input functions and by calculating the total distribution volume (VT). The shape of the image-derived whole-blood TAC matched the reference arterial curves well, and the whole-blood area under the curves were accurately estimated (mean error 1.0±4.3%). The relative Logan-V(T) error was -4.1±6.4%. Compartmental modeling and spectral analysis gave less accurate V(T) results compared with Logan. A factor-analysis-based IDIF for [(11)C](R)-rolipram brain PET studies that relies on a single blood sample and population data can be used for accurate quantification of Logan-V(T) values.

Lung function in type 2 diabetes: the Normative Aging Study.

PubMed

Litonjua, Augusto A; Lazarus, Ross; Sparrow, David; Demolles, Debbie; Weiss, Scott T

2005-12-01

Cross-sectional studies have noted that subjects with diabetes have lower lung function than non-diabetic subjects. We conducted this analysis to determine whether diabetic subjects have different rates of lung function change compared with non-diabetic subjects. We conducted a nested case-control analysis in 352 men who developed diabetes and 352 non-diabetic subjects in a longitudinal observational study of aging in men. We assessed lung function among cases and controls at three time points: Time0, prior to meeting the definition of diabetes; Time1, the point when the definition of diabetes was met; and Time2, the most recent follow-up exam. Cases had lower forced expiratory volume in 1s (FEV1) and forced vital capacity (FVC) at all time points, even with adjustment for age, height, weight, and smoking. In multiple linear regression models adjusting for relevant covariates, there were no differences in rates of FEV1 or FVC change over time between cases and controls. Men who are predisposed to develop diabetes have decreased lung function many years prior to the diagnosis, compared with men who do not develop diabetes. This decrement in lung function remains after the development of diabetes. We postulate that mechanisms involved in the insulin resistant state contribute to the diminished lung function observed in our subjects.

Clinical benefit of drugs targeting mitochondrial function as an adjunct to reperfusion in ST-segment elevation myocardial infarction: A meta-analysis of randomized clinical trials.

PubMed

Campo, Gianluca; Pavasini, Rita; Morciano, Giampaolo; Lincoff, A Michael; Gibson, C Michael; Kitakaze, Masafumi; Lonborg, Jacob; Ahluwalia, Amrita; Ishii, Hideki; Frenneaux, Michael; Ovize, Michel; Galvani, Marcello; Atar, Dan; Ibanez, Borja; Cerisano, Giampaolo; Biscaglia, Simone; Neil, Brandon J; Asakura, Masanori; Engstrom, Thomas; Jones, Daniel A; Dawson, Dana; Ferrari, Roberto; Pinton, Paolo; Ottani, Filippo

2017-10-01

To perform a systematic review and meta-analysis of randomized clinical trials (RCT) comparing the effectiveness of drugs targeting mitochondrial function vs. placebo in patients with ST-segment elevation myocardial infarction (STEMI) undergoing mechanical coronary reperfusion. Inclusion criteria: RCTs enrolling STEMI patients treated with primary percutaneous coronary intervention (PCI) and comparing drugs targeting mitochondrial function vs. placebo. Odds ratios (OR) were computed from individual studies and pooled with random-effect meta-analysis. Fifteen studies were identified involving 5680 patients. When compared with placebo, drugs targeting mitochondrial component/pathway were not associated with significant reduction of cardiovascular and all-cause mortality (OR 0.9, 95% CI 0.7-1.17 and OR 0.92, 95% CI 0.69-1.23, respectively). However, these agents significantly reduced hospital admission for heart failure (HF) (OR 0.64; 95% CI 0.45-0.92) and increased left ventricular ejection fraction (LVEF) (OR 1.44; 95% CI 1.15-1.82). After analysis for subgroups according to the mechanism of action, drugs with direct/selective action did not reduce any outcome. Conversely, those with indirect/unspecific action showed a significant effect on cardiovascular mortality (0.65, 95% CI 0.46-0.92), all-cause mortality (OR 0.69, 95% CI 0.52-0.92), hospital readmission for HF (OR 0.41, 95% CI 0.28-0.6) and LVEF (OR 1.49, 95% CI 1.09-2.05). Administration of drugs targeting mitochondrial function in STEMI patients undergoing primary PCI appear to have no effect on mortality, but may reduce hospital readmission for HF. The drugs with a broad-spectrum mechanism of action seem to be more effective in reducing adverse events. Copyright © 2017 Elsevier B.V. All rights reserved.

The Position as Regards Functional Literacy Pilot Projects. Summary.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Paris (France).

A comparative analysis was made of Experimental World Literacy Program projects in 17 nations (Algeria, Brazil, Chile, Equador, Ethiopia, Guinea, India, Iran, Mali, Jamaica, Madagascar, Nigeria, Sudan, Syria, Tanzania, Tunisia, and Venezuela) after 18 months of operation. Included were functional literacy projects in 10 nations, literacy programs…

Comparing Accessibility Auditing Methods for Ebooks: Crowdsourced, Functionality-Led Versus Web Content Methodologies.

PubMed

James, Abi; Draffan, E A; Wald, Mike

2017-01-01

This paper presents a gap analysis between crowdsourced functional accessibility evaluations of ebooks conducted by non-experts and the technical accessibility standards employed by developers. It also illustrates how combining these approaches can provide more appropriate information for a wider group of users with print impairments.

Comparative Analysis of Alternative Spectral Bands of CO2 and O2 for the Sensing of CO2 Mixing Ratios

NASA Technical Reports Server (NTRS)

Pliutau, Denis; Prasad, Narasimha S.

2013-01-01

We performed comparative studies to establish favorable spectral regions and measurement wavelength combinations in alternative bands of CO2 and O2, for the sensing of CO2 mixing ratios (XCO2) in missions such as ASCENDS. The analysis employed several simulation approaches including separate layers calculations based on pre-analyzed atmospheric data from the modern-era retrospective analysis for research and applications (MERRA), and the line-byline radiative transfer model (LBLRTM) to obtain achievable accuracy estimates as a function of altitude and for the total path over an annual span of variations in atmospheric parameters. Separate layer error estimates also allowed investigation of the uncertainties in the weighting functions at varying altitudes and atmospheric conditions. The parameters influencing the measurement accuracy were analyzed independently and included temperature sensitivity, water vapor interferences, selection of favorable weighting functions, excitations wavelength stabilities and other factors. The results were used to identify favorable spectral regions and combinations of on / off line wavelengths leading to reductions in interferences and the improved total accuracy.

Analysis of the respirogram phase of Korean wrestling athletes compared with nonathletes for sports physiotherapy research.

PubMed

Shin, Yong-Sub; Yang, Seung-Min; Kim, Mee-Young; Lee, Lim-Kyu; Park, Byoung-Sun; Lee, Won-Deok; Noh, Ji-Woong; Kim, Ju-Hyun; Lee, Jeong-Uk; Kwak, Taek-Yong; Lee, Tae-Hyun; Kim, Ju-Young; Park, Jaehong; Kim, Junghwan

2016-01-01

[Purpose] Respiratory function is important for patients including athletes who require physical therapy for respiratory dysfunction. The purpose of the present study was to analyze the differences in the respirograms between Korean wrestling athletes and nonathletes according to phase for the study of sports physiotherapy. [Subjects and Methods] Respiratory function was measured using spirometry in both the athletes and nonathletes while they were in a sitting position. [Results] Spirometry parameters in the athletes were significantly higher than in the nonathletes. In respirogram phasic analysis, the expiratory area and total area of forced vital capacity were significantly increased in the athletes compared with the nonathletes. The slopes of the forced vital capacity for athletes at slopes 1, 2, and 3 of the A area were significantly increased. In correlative analysis, chest circumference was significantly correlated with slope 3 of the A area of the forced vital capacity. [Conclusion] The results suggest that the differences in changes in the phases of the respirogram between the Korean wrestling athletes and nonathletes may in part contribute to our understanding of respiratory function in sports physiotherapy research.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PubMed Central

Lovelock, Paul K; Spurdle, Amanda B; Mok, Myth TS; Farrugia, Daniel J; Lakhani, Sunil R; Healey, Sue; Arnold, Stephen; Buchanan, Daniel; Investigators, kConFab; Couch, Fergus J; Henderson, Beric R; Goldgar, David E; Tavtigian, Sean V; Chenevix-Trench, Georgia; Brown, Melissa A

2007-01-01

Introduction Many of the DNA sequence variants identified in the breast cancer susceptibility gene BRCA1 remain unclassified in terms of their potential pathogenicity. Both multifactorial likelihood analysis and functional approaches have been proposed as a means to elucidate likely clinical significance of such variants, but analysis of the comparative value of these methods for classifying all sequence variants has been limited. Methods We have compared the results from multifactorial likelihood analysis with those from several functional analyses for the four BRCA1 sequence variants A1708E, G1738R, R1699Q, and A1708V. Results Our results show that multifactorial likelihood analysis, which incorporates sequence conservation, co-inheritance, segregation, and tumour immunohistochemical analysis, may improve classification of variants. For A1708E, previously shown to be functionally compromised, analysis of oestrogen receptor, cytokeratin 5/6, and cytokeratin 14 tumour expression data significantly strengthened the prediction of pathogenicity, giving a posterior probability of pathogenicity of 99%. For G1738R, shown to be functionally defective in this study, immunohistochemistry analysis confirmed previous findings of inconsistent 'BRCA1-like' phenotypes for the two tumours studied, and the posterior probability for this variant was 96%. The posterior probabilities of R1699Q and A1708V were 54% and 69%, respectively, only moderately suggestive of increased risk. Interestingly, results from functional analyses suggest that both of these variants have only partial functional activity. R1699Q was defective in foci formation in response to DNA damage and displayed intermediate transcriptional transactivation activity but showed no evidence for centrosome amplification. In contrast, A1708V displayed an intermediate transcriptional transactivation activity and a normal foci formation response in response to DNA damage but induced centrosome amplification. Conclusion These data highlight the need for a range of functional studies to be performed in order to identify variants with partially compromised function. The results also raise the possibility that A1708V and R1699Q may be associated with a low or moderate risk of cancer. While data pooling strategies may provide more information for multifactorial analysis to improve the interpretation of the clinical significance of these variants, it is likely that the development of current multifactorial likelihood approaches and the consideration of alternative statistical approaches will be needed to determine whether these individually rare variants do confer a low or moderate risk of breast cancer. PMID:18036263

Relationship between Speech Production and Perception in People Who Stutter.

PubMed

Lu, Chunming; Long, Yuhang; Zheng, Lifen; Shi, Guang; Liu, Li; Ding, Guosheng; Howell, Peter

2016-01-01

Speech production difficulties are apparent in people who stutter (PWS). PWS also have difficulties in speech perception compared to controls. It is unclear whether the speech perception difficulties in PWS are independent of, or related to, their speech production difficulties. To investigate this issue, functional MRI data were collected on 13 PWS and 13 controls whilst the participants performed a speech production task and a speech perception task. PWS performed poorer than controls in the perception task and the poorer performance was associated with a functional activity difference in the left anterior insula (part of the speech motor area) compared to controls. PWS also showed a functional activity difference in this and the surrounding area [left inferior frontal cortex (IFC)/anterior insula] in the production task compared to controls. Conjunction analysis showed that the functional activity differences between PWS and controls in the left IFC/anterior insula coincided across the perception and production tasks. Furthermore, Granger Causality Analysis on the resting-state fMRI data of the participants showed that the causal connection from the left IFC/anterior insula to an area in the left primary auditory cortex (Heschl's gyrus) differed significantly between PWS and controls. The strength of this connection correlated significantly with performance in the perception task. These results suggest that speech perception difficulties in PWS are associated with anomalous functional activity in the speech motor area, and the altered functional connectivity from this area to the auditory area plays a role in the speech perception difficulties of PWS.

A Comparative Analysis for Wilderness User Fee Policy.

ERIC Educational Resources Information Center

Leuschner, William A.; And Others

1987-01-01

Two similar wilderness areas, one of which charges user fees, were sampled in order to compare user characteristics, trip characteristics, and travel cost demand functions. The purpose was to examine the effect fees had on user behavior and choices of area. Results are presented. (MT)

Does Functional Connectivity Provide a Marker for Cognitive Rehabilitation Effects in Alzheimer's Disease? An Interventional Study.

PubMed

Ochmann, Sina; Dyrba, Martin; Grothe, Michel J; Kasper, Elisabeth; Webel, Steffi; Hauenstein, Karlheinz; Teipel, Stefan J

2017-01-01

Cognitive rehabilitation (CR) is a cognitive intervention for patients with Alzheimer's disease (AD) that aims to maintain everyday competences. The analysis of functional connectivity (FC) in resting-state functional MRI has been used to investigate the effects of cognitive interventions. We evaluated the effect of CR on the default mode network FC in a group of patients with mild AD, compared to an active control group. We performed a three-month interventional study including 16 patients with a diagnosis of AD. The intervention group (IG) consisted of eight patients, performing twelve sessions of CR. The active control group (CG) performed a standardized cognitive training. We used a seed region placed in the posterior cingulate cortex (PCC) for FC analysis, comparing scans acquired before and after the intervention. Effects were thresholded at a significance of p < 0.001 (uncorrected) and a minimal cluster size of 50 voxels. The interaction of group by time showed a higher increase of PCC connectivity in IG compared to CG in the bilateral cerebellar cortex. CG revealed widespread, smaller clusters of higher FC increase compared with IG. Across all participants, an increase in quality of life was associated with connectivity increase over time in the bilateral precuneus. CR showed an effect on the FC of the DMN in the IG. These effects need further study in larger samples to confirm if FC analysis may suit as a surrogate marker for the effect of cognitive interventions in AD.

Evaluating Cellular Polyfunctionality with a Novel Polyfunctionality Index

PubMed Central

Larsen, Martin; Sauce, Delphine; Arnaud, Laurent; Fastenackels, Solène; Appay, Victor; Gorochov, Guy

2012-01-01

Functional evaluation of naturally occurring or vaccination-induced T cell responses in mice, men and monkeys has in recent years advanced from single-parameter (e.g. IFN-γ-secretion) to much more complex multidimensional measurements. Co-secretion of multiple functional molecules (such as cytokines and chemokines) at the single-cell level is now measurable due primarily to major advances in multiparametric flow cytometry. The very extensive and complex datasets generated by this technology raise the demand for proper analytical tools that enable the analysis of combinatorial functional properties of T cells, hence polyfunctionality. Presently, multidimensional functional measures are analysed either by evaluating all combinations of parameters individually or by summing frequencies of combinations that include the same number of simultaneous functions. Often these evaluations are visualized as pie charts. Whereas pie charts effectively represent and compare average polyfunctionality profiles of particular T cell subsets or patient groups, they do not document the degree or variation of polyfunctionality within a group nor does it allow more sophisticated statistical analysis. Here we propose a novel polyfunctionality index that numerically evaluates the degree and variation of polyfuntionality, and enable comparative and correlative parametric and non-parametric statistical tests. Moreover, it allows the usage of more advanced statistical approaches, such as cluster analysis. We believe that the polyfunctionality index will render polyfunctionality an appropriate end-point measure in future studies of T cell responsiveness. PMID:22860124

The effects of whole body vibration on mobility and balance in children with cerebral palsy: a systematic review with meta-analysis

PubMed Central

Saquetto, M.; Carvalho, V.; Silva, C.; Conceição, C.; Gomes-Neto, M.

2015-01-01

Objective: We performed a meta-analysis to evaluate the effects of whole-body vibration on physiologic and functional measurements in children with cerebral palsy. Design and methods: We searched MEDLINE, Cochrane Controlled Trials Register, EMBASE, Scielo, CINAHL (from the earliest date available to November 2014) for randomized controlled trials, that aimed to investigate the effects of whole-body vibration versus exercise and/or versus control on physiologic and functional measurements in children with cerebral palsy. Two reviewers independently selected the studies. Weighted mean differences (WMDs) and 95% confidence intervals (CIs) were calculated. Results: Six studies with 176 patients comparing whole-body vibration to exercise and/or control were included. Whole-body vibration resulted in improvement in: gait speed WMDs (0.13 95% CI:0.05 to 0.20); gross motor function dimension E WMDs (2.97 95% CI:0.07 to 5.86) and femur bone density (1.32 95% CI:0.28 to 2.36). The meta-analysis also showed a nonsignificant difference in muscle strength and gross motor function dimension D for participants in the whole-body vibration compared with control group. No serious adverse events were reported. Conclusions: Whole-body vibration may improve gait speed and standing function in children with cerebral palsy and could be considered for inclusion in rehabilitation programs. PMID:26032205

Testing hypotheses of bat baculum function with 3D models derived from microCT

PubMed Central

Herdina, Anna Nele; Kelly, Diane A; Jahelková, Helena; Lina, Peter H C; Horáček, Ivan; Metscher, Brian D

2015-01-01

The baculum (os penis) has been extensively studied as a taxon-specific character in bats and other mammals but its mechanical function is still unclear. There is a wide consensus in the literature that the baculum is probably a sexually selected character. Using a novel approach combining postmortem manipulation and three-dimensional (3D) imaging, we tested two functional hypotheses in the common noctule bat Nyctalus noctula, the common pipistrelle Pipistrellus pipistrellus, and Nathusius’ pipistrelle Pipistrellus nathusii: (i) whether the baculum can protect the distal urethra and urethral opening from compression during erection and copulation; and (ii) whether the baculum and corpora cavernosa form a functional unit to support both the penile shaft and the more distal glans tip. In freshly dead or frozen and thawed bats, we compared flaccid penises with artificially ‘erect’ penises that were inflated with 10% formalin. Penises were stained with alcoholic iodine and imaged with a lab-based high-resolution x-ray microtomography system. Analysis of the 3D images enabled us to compare the changes in relative positions of the baculum, corpora cavernosa, urethra, and corpus spongiosum with one another between flaccid and ‘erect’ penises. Our results support both functional hypotheses, indicating that the baculum probably performs two different roles during erection. Our approach should prove valuable for comparing and testing the functions of different baculum morphologies in bats and other mammals. Moreover, we have validated an essential component of the groundwork necessary to extend this approach with finite element analysis for quantitative 3D biomechanical modeling of penis function. PMID:25655647

Comparative Transcriptome Analysis between the Cytoplasmic Male Sterile Line NJCMS1A and Its Maintainer NJCMS1B in Soybean (Glycine max (L.) Merr.)

PubMed Central

Li, Jiajia; Han, Shaohuai; Ding, Xianlong; He, Tingting; Dai, Jinying; Yang, Shouping; Gai, Junyi

2015-01-01

Background The utilization of soybean heterosis is probably one of the potential approaches in future yield breakthrough as was the situation in rice breeding in China. Cytoplasmic male sterility (CMS) plays an important role in the production of hybrid seeds. However, the molecular mechanism of CMS in soybean remains unclear. Results The comparative transcriptome analysis between cytoplasmic male sterile line NJCMS1A and its near-isogenic maintainer NJCMS1B in soybean was conducted using Illumina sequencing technology. A total of 88,643 transcripts were produced in Illumina sequencing. Then 56,044 genes were obtained matching soybean reference genome. Three hundred and sixty five differentially expressed genes (DEGs) between NJCMS1A and NJCMS1B were screened by threshold, among which, 339 down-regulated and 26 up-regulated in NJCMS1A compared to in NJCMS1B. Gene Ontology (GO) annotation showed that 242 DEGs were annotated to 19 functional categories. Clusters of Orthologous Groups of proteins (COG) annotation showed that 265 DEGs were classified into 19 categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 46 DEGs were assigned to 33 metabolic pathways. According to functional and metabolic pathway analysis combined with reported literatures, the relations between some key DEGs and the male sterility of NJCMS1A were discussed. qRT-PCR analysis validated that the gene expression pattern in RNA-Seq was reliable. Finally, enzyme activity assay showed that energy supply was decreased in NJCMS1A compared to in NJCMS1B. Conclusions We concluded that the male sterility of NJCMS1A might be related to the disturbed functions and metabolism pathways of some key DEGs, such as DEGs involved in carbohydrate and energy metabolism, transcription factors, regulation of pollen development, elimination of reactive oxygen species (ROS), cellular signal transduction, and programmed cell death (PCD) etc. Future research will focus on cloning and transgenic function validation of possible candidate genes associated with soybean CMS. PMID:25985300

Modified Gaussian influence function of deformable mirror actuators.

PubMed

Huang, Linhai; Rao, Changhui; Jiang, Wenhan

2008-01-07

A new deformable mirror influence function based on a Gaussian function is introduced to analyze the fitting capability of a deformable mirror. The modified expressions for both azimuthal and radial directions are presented based on the analysis of the residual error between a measured influence function and a Gaussian influence function. With a simplex search method, we further compare the fitting capability of our proposed influence function to fit the data produced by a Zygo interferometer with that of a Gaussian influence function. The result indicates that the modified Gaussian influence function provides much better performance in data fitting.

Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG.

PubMed

Uchiyama, Ikuo

2017-01-01

Comparative genomics is becoming an essential approach for identification of genes associated with a specific function or phenotype. Here, we introduce the microbial genome database for comparative analysis (MBGD), which is a comprehensive ortholog database among the microbial genomes available so far. MBGD contains several precomputed ortholog tables including the standard ortholog table covering the entire taxonomic range and taxon-specific ortholog tables for various major taxa. In addition, MBGD allows the users to create an ortholog table within any specified set of genomes through dynamic calculations. In particular, MBGD has a "My MBGD" mode where users can upload their original genome sequences and incorporate them into orthology analysis. The created ortholog table can serve as the basis for various comparative analyses. Here, we describe the use of MBGD and briefly explain how to utilize the orthology information during comparative genome analysis in combination with the stand-alone comparative genomics software RECOG, focusing on the application to comparison of closely related microbial genomes.

[Kidney allotransplantation from the AB0-incompatible donors].

PubMed

Goriaĭnov, V A; Kaabak, M M; Babenko, N N; Shishlo, L A; Morozova, M M; Ragimov, A A; Dazhkova, N G; Salimov, E L

2013-01-01

The experience of 28 kidney allotransplantations from the AB0-incompatible donors was analyzed. The comparative group consisted of 38 patients, who received the AB0-compatible organ. The results were assessed using the following parameters: renal function, morphology of the biopsy samples of the transplanted kidney and actuary survival of the recipients with functioning transplants in both groups. The comparative analysis showed no significant difference between the two groups, giving the right to consider the kidney allotransplantation from the AB0-incompatible donors safe and effective.

Surgical Versus Conservative Intervention for Acute Achilles Tendon Rupture: A PRISMA-Compliant Systematic Review of Overlapping Meta-Analyses.

PubMed

Zhang, Hao; Tang, Hao; He, Qianyun; Wei, Qiang; Tong, Dake; Wang, Chuangfeng; Wu, Dajiang; Wang, Guangchao; Zhang, Xin; Ding, Wenbin; Li, Di; Ding, Chen; Liu, Kang; Ji, Fang

2015-11-01

Although many meta-analyses comparing surgical intervention with conservative treatment have been conducted for acute Achilles tendon rupture, discordant conclusions are shown. This study systematically reviewed the overlapping meta-analyses relating to surgical versus conservative intervention of acute Achilles tendon rupture to assist decision makers select among conflicting meta-analyses, and to offer intervention recommendations based on the currently best evidence.Multiple databases were comprehensively searched for meta-analyses comparing surgical with conservative treatment of acute Achilles tendon rupture. Meta-analyses only comprising randomized controlled trials (RCTs) were included. Two authors independently evaluated the meta-analysis quality and extracted data. The Jadad decision algorithm was applied to ascertain which meta-analysis offered the best evidence.A total of 9 meta-analyses were included. Only RCTs were determined as Level-II evidence. The scores of Assessment of Multiple Systematic Reviews (AMSTAR) ranged from 5 to 10 (median 7). A high-quality meta-analysis with more RCTs was selected according to the Jadad decision algorithm. This study found that when functional rehabilitation was used, conservative intervention was equal to surgical treatment regarding the incidence of rerupture, range of motion, calf circumference, and functional outcomes, while reducing the incidence of other complications. Where functional rehabilitation was not performed, conservative intervention could significantly increase rerupture rate.Conservative intervention may be preferred for acute Achilles tendon rupture at centers offering functional rehabilitation, because it shows a similar rerupture rate with a lower risk of other complications when compared with surgical treatment. However, surgical treatment should be considered at centers without functional rehabilitation as this can reduce the incidence of rerupture.

Mixed kernel function support vector regression for global sensitivity analysis

NASA Astrophysics Data System (ADS)

Cheng, Kai; Lu, Zhenzhou; Wei, Yuhao; Shi, Yan; Zhou, Yicheng

2017-11-01

Global sensitivity analysis (GSA) plays an important role in exploring the respective effects of input variables on an assigned output response. Amongst the wide sensitivity analyses in literature, the Sobol indices have attracted much attention since they can provide accurate information for most models. In this paper, a mixed kernel function (MKF) based support vector regression (SVR) model is employed to evaluate the Sobol indices at low computational cost. By the proposed derivation, the estimation of the Sobol indices can be obtained by post-processing the coefficients of the SVR meta-model. The MKF is constituted by the orthogonal polynomials kernel function and Gaussian radial basis kernel function, thus the MKF possesses both the global characteristic advantage of the polynomials kernel function and the local characteristic advantage of the Gaussian radial basis kernel function. The proposed approach is suitable for high-dimensional and non-linear problems. Performance of the proposed approach is validated by various analytical functions and compared with the popular polynomial chaos expansion (PCE). Results demonstrate that the proposed approach is an efficient method for global sensitivity analysis.

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

PubMed

Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

2016-01-12

Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of reference genomes can impact comprehensive annotation of metatranscriptomes. Consequently, beyond the application of standardized pipelines, additional caution must be taken when interpreting their output and performing downstream, microbiome-specific, analyses. The pipeline used in these analyses along with a tutorial has been made freely available for download from our project website: http://www.compsysbio.org/microbiome .

Longitudinal structure function from logarithmic slopes of F2 at low x

NASA Astrophysics Data System (ADS)

Boroun, G. R.

2018-01-01

Using Laplace transform techniques, I calculate the longitudinal structure function FL(x ,Q2) from the scaling violations of the proton structure function F2(x ,Q2) and make a critical study of this relationship between the structure functions at leading order (LO) up to next-to-next-to leading order (NNLO) analysis at small x . Furthermore, I consider heavy quark contributions to the relation between the structure functions, which leads to compact formula for Nf=3 +Heavy . The nonlinear corrections to the longitudinal structure function at LO up to NNLO analysis are shown in the Nf=4 (light quark flavor) based on the nonlinear corrections at R =2 and R =4 GeV-1 . The results are compared with experimental data of the longitudinal proton structure function FL in the range of 6.5 ≤Q2≤800 GeV2 .

Goal direction and effectiveness, emotional maturity, and nuclear family functioning.

PubMed

Klever, Phillip

2009-07-01

Differentiation of self, a cornerstone concept in Bowen theory, has a profound influence over time on the functioning of the individual and his or her family unit. This 5-year longitudinal study tested this hypothesis with 50 developing nuclear families. The dimensions of differentiation of self that were examined were goal direction and effectiveness and emotional maturity. A qualitative analysis of participants' goals demonstrated that couples with higher functioning developing nuclear families, when compared with couples with lower functioning families, placed more emphasis on family goals, had more balance between family and personal goals, and pursued more goals over the 5 years. The quantitative analysis supported the hypothesis that goal effectiveness and emotional maturity influenced variation in nuclear family functioning. In addition, couple goal effectiveness and emotional maturity were associated with nuclear family functioning more strongly than individual goal effectiveness and emotional maturity were associated with individual functioning.

Treatment of Farm Families under Need Analysis for Student Aid. Final Report.

ERIC Educational Resources Information Center

National Computer Systems, Inc., Arlington, VA.

In response to Congressional request, this report compares the treatment of student financial aid applicants from farm families and non-farm families under two need-analysis formulae. Both the need-analysis methodology for Pell Grants and the Congressional Methodology (CM) for other federal aid calculate ability to pay as a function of income and…

A Factor Analysis of Functional Independence and Functional Assessment Measure Scores Among Focal and Diffuse Brain Injury Patients: The Importance of Bifactor Models.

PubMed

Gunn, Sarah; Burgess, Gerald H; Maltby, John

2018-04-30

To explore the factor structure of the UK Functional Independence Measure and Functional Assessment Measure (FIM+FAM) among focal and diffuse acquired brain injury patients. Criterion standard. A National Health Service acute acquired brain injury inpatient rehabilitation hospital. Referred sample of N=447 adults admitted for inpatient treatment following an acquired brain injury significant enough to justify intensive inpatient neurorehabilitation INTERVENTION: Not applicable. Functional Independence Measure and Functional Assessment Measure. Exploratory factor analysis suggested a 2-factor structure to FIM+FAM scores, among both focal-proximate and diffuse-proximate acquired brain injury aetiologies. Confirmatory factor analysis suggested a 3-factor bifactor structure presented the best fit of the FIM+FAM score data across both aetiologies. However, across both analyses, a convergence was found towards a general factor, demonstrated by high correlations between factors in the exploratory factor analysis, and by a general factor explaining the majority of the variance in scores on confirmatory factor analysis. Our findings suggested that although factors describing specific functional domains can be derived from FIM+FAM item scores, there is a convergence towards a single factor describing overall functioning. This single factor informs the specific group factors (eg, motor, psychosocial, and communication function) after brain injury. Further research into the comparative value of the general and group factors as evaluative/prognostic measures is indicated. Copyright © 2018 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Objective function analysis for electric soundings (VES), transient electromagnetic soundings (TEM) and joint inversion VES/TEM

NASA Astrophysics Data System (ADS)

Bortolozo, Cassiano Antonio; Bokhonok, Oleg; Porsani, Jorge Luís; Monteiro dos Santos, Fernando Acácio; Diogo, Liliana Alcazar; Slob, Evert

2017-11-01

Ambiguities in geophysical inversion results are always present. How these ambiguities appear in most cases open to interpretation. It is interesting to investigate ambiguities with regard to the parameters of the models under study. Residual Function Dispersion Map (RFDM) can be used to differentiate between global ambiguities and local minima in the objective function. We apply RFDM to Vertical Electrical Sounding (VES) and TEM Sounding inversion results. Through topographic analysis of the objective function we evaluate the advantages and limitations of electrical sounding data compared with TEM sounding data, and the benefits of joint inversion in comparison with the individual methods. The RFDM analysis proved to be a very interesting tool for understanding the joint inversion method of VES/TEM. Also the advantage of the applicability of the RFDM analyses in real data is explored in this paper to demonstrate not only how the objective function of real data behaves but the applicability of the RFDM approach in real cases. With the analysis of the results, it is possible to understand how the joint inversion can reduce the ambiguity of the methods.

Structural and Phylogenetic Analysis of a Conserved Actinobacteria-Specific Protein (ASP1; SCO1997) from Streptomyces Coelicolor

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

Gao, B.; Sugiman-Marangos, S; Junop, M

2009-01-01

The Actinobacteria phylum represents one of the largest and most diverse groups of bacteria, encompassing many important and well-characterized organisms including Streptomyces, Bifidobacterium, Corynebacterium and Mycobacterium. Members of this phylum are remarkably diverse in terms of life cycle, morphology, physiology and ecology. Recent comparative genomic analysis of 19 actinobacterial species determined that only 5 genes of unknown function uniquely define this large phylum [1]. The cellular functions of these actinobacteria-specific proteins (ASP) are not known.

Can Automated Facial Expression Analysis Show Differences Between Autism and Typical Functioning?

PubMed

Borsos, Zsófia; Gyori, Miklos

2017-01-01

Exploratory analyses of emotional expressions using a commercially available facial expression recognition software are reported, from the context of a serious game for screening purposes. Our results are based on a comparative analysis of two matched groups of kindergarten-age children (high-functioning children with autism spectrum condition: n=13; typically developing children: n=13). Results indicate that this technology has the potential to identify autism-specific emotion expression features, and may play a role in affective diagnostic and assistive technologies.

[Structural analysis of the functional status of the brain as affected by bemethyl using pattern recognition theory].

PubMed

Bobkov, Iu G; Machula, A I; Morozov, Iu I; Dvalishvili, E G

1987-11-01

Evoked visual potentials in associated, parietal and second somatosensory zones of the neocortex were analysed in trained cats using implanted electrodes. The influence of bemethyl on the structure of behavioral reactions was analysed using theoretical methods of perceptual images, particularly the method of cluster analysis. Bemethyl was shown to increase the level of interaction between the functional elements of the system, leading to a more stable resolution of problems facing the system, as compared to the initial state.

Microbial genome analysis: the COG approach.

PubMed

Galperin, Michael Y; Kristensen, David M; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2017-09-14

For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Analysis/forecast experiments with a flow-dependent correlation function using FGGE data

NASA Technical Reports Server (NTRS)

Baker, W. E.; Bloom, S. C.; Carus, H.; Nestler, M. S.

1986-01-01

The use of a flow-dependent correlation function to improve the accuracy of an optimum interpolation (OI) scheme is examined. The development of the correlation function for the OI analysis scheme used for numerical weather prediction is described. The scheme uses a multivariate surface analysis over the oceans to model the pressure-wind error cross-correlation and it has the ability to use an error correlation function that is flow- and geographically-dependent. A series of four-day data assimilation experiments, conducted from January 5-9, 1979, were used to investigate the effect of the different features of the OI scheme (error correlation) on forecast skill for the barotropic lows and highs. The skill of the OI was compared with that of a successive correlation method (SCM) of analysis. It is observed that the largest difference in the correlation statistics occurred in barotropic and baroclinic lows and highs. The comparison reveals that the OI forecasts were more accurate than the SCM forecasts.

Comparing the effects of the second-and third-generation oral contraceptives on sexual functioning.

PubMed

Shahnazi, Mahnaz; Bayatipayan, Somaye; Khalili, Azizeh Farshbaf; Kochaksaraei, Fatemeh Ranjbar; Jafarabadi, Mohammad Asghari; Banoi, Kamala Gaza; Nahaee, Jila

2015-01-01

The aim of this study was to compare the effects of the second- and third-generation oral contraceptives on women's reproductive sexual function. This randomized, double-blind, placebo-controlled clinical trial was conducted on 82 married women of reproductive age in Tehran. Samples were randomized into the groups receiving second- and third-generation oral contraceptive pills. Female Sexual Function Index (FSFI) tool was used before the intervention and 2 and 4 months after the intervention. Data analysis was carried out using analysis of variance (ANOVA) within repeated measures and P < 0.05 were considered significant. There was a statistically significant difference in the positive and negative moods between the experimental and control groups before the intervention in the second and fourth months. The second-generation pills caused a decrease in sexual function in the second month and an increase in sexual function in the fourth month, but the third-generation pills led to an increase in sexual function in the second and fourth months. The increase in sexual function that resulted from using the third-generation pills was significantly higher than that resulted on using the second-generation pills. According to the results of this study, sexual functioning decreased in the second month of using the second-generation pills and sexual performance was significantly more on using the third-generation pills compared to second-generation pills. The most common type of oral contraceptive used in Iran is the second-generation oral contraceptive LD™ (low-dose estrogen), which is freely distributed in health centers. Therefore, it is necessary for women who wish to use these contraceptive methods to be educated and consulted before they start using them. The third-generation contraceptive pills can be recommended to women who wish to use oral contraceptives.

Renal function changes after percutaneous nephrolithotomy in patients with renal calculi with a solitary kidney compared to bilateral kidneys.

PubMed

Shi, Xiaolei; Peng, Yonghan; Li, Ling; Li, Xiao; Wang, Qi; Zhang, Wei; Dong, Hao; Shen, Rong; Lu, Chaoyue; Liu, Min; Gao, Xiaofeng; Sun, Yinghao

2018-05-26

To evaluate renal function changes and risk factors for acute kidney injury (AKI) after percutaneous nephrolithotomy (PCNL) in patients with renal calculi with a solitary kidney (SK) or normal bilateral kidneys (BKs). Between 2012 and 2016, 859 patients undergoing PCNL were retrospectively reviewed at Changhai Hospital. In all, 53 patients with a SK were paired with 53 patients with normal BKs via a propensity score-matched analysis. Data for the following variables were collected: age, sex, body mass index, stone size, distribution, operation time, perioperative outcomes, and complications. The complications were graded according to the modified Clavien-Dindo system. Univariable and multivariable logistic regression models were constructed to evaluate risk factors for predicting AKI. The SK and BKs groups were comparable in terms of age, sex ratio, stone size, stone location distribution, comorbidities, and American Society of Anesthesiologists Physical Status classification. The initial and final stone-free rates were comparable between the SK and BKs groups (initial: 52.83% vs 58.49%, P = 0.696; final: 84.91% vs 92.45%, P = 0.359). There was no difference between the two groups for complications, according to the Clavien-Dindo grades. The estimated glomerular filtration rate (eGFR) increased dramatically after the stone burden was immediately relieved, and during the 6-month follow-up eGFR was lower in the SK group compared with the BKs group. We found a modest improvement in renal function immediately after PCNL in the BKs group, and renal function gain was delayed in the SK group. Through logistic regression analysis, we discovered that a SK, preoperative creatinine and diabetes were independent risk factors for predicting AKI after PCNL. Considering the overall complication rates, PCNL is generally a safe procedure for treating renal calculi amongst patients with a SK or normal BKs. Follow-up renal function analysis showed a modest improvement in patients of both groups. Compared to patients with normal BKs, patients with a SK were more likely to develop AKI after PCNL. © 2018 The Authors BJU International © 2018 BJU International Published by John Wiley & Sons Ltd.

Social and economic sustainability of urban systems: comparative analysis of metropolitan statistical areas in Ohio, USA

EPA Science Inventory

This article presents a general and versatile methodology for assessing sustainability with Fisher Information as a function of dynamic changes in urban systems. Using robust statistical methods, six Metropolitan Statistical Areas (MSAs) in Ohio were evaluated to comparatively as...

Left ventricular early diastolic inflow velocity and atrial ventricular plane downward velocity: useful parameters to test diastolic function in clinical practice? Diastolic parameters tested in a clinical setting.

PubMed

Winter, R; Gudmundsson, P; Ericsson, G; Willenheimer, R

2001-06-01

To study the clinical value of the colour-M-mode slope of the early diastolic left ventricular filling phase (Vp) and the early diastolic downward M-mode slope of the left atrioventricular plane displacement (EDS), compared with diastolic function assessed by traditional Doppler evaluation. In 65 consecutive patients EDS and Vp were compared with a four-degree traditional diastolic function classification, based on pulsed Doppler assessment of the early to atrial transmitral flow ratio (E/A), the E-wave deceleration time (Edt), and the systolic to diastolic (S/D) pulmonary venous inflow ratio. Vp (P=0.006) and EDS (P=0.045) were related to traditional diastolic function (Kruskal--Wallis analysis). EDS showed a trend brake between the moderate and severe diastolic dysfunction groups by traditional Doppler evaluation. Vp and EDS correlated weakly in simple linear regression analysis (r=0.33). Vp and EDS discriminated poorly between normal and highly abnormal diastolic function. Vp and EDS were significantly related to diastolic function by traditional Doppler evaluation. They were, however, not useful as single parameters of left ventricular diastolic function due to a small difference between normal and highly abnormal values, allowing for little between-measurement variability. Consequently, these methods for the evaluation of left ventricular diastolic function do not add significantly to traditional Doppler evaluation.

Resting-state theta band connectivity and graph analysis in generalized social anxiety disorder.

PubMed

Xing, Mengqi; Tadayonnejad, Reza; MacNamara, Annmarie; Ajilore, Olusola; DiGangi, Julia; Phan, K Luan; Leow, Alex; Klumpp, Heide

2017-01-01

Functional magnetic resonance imaging (fMRI) resting-state studies show generalized social anxiety disorder (gSAD) is associated with disturbances in networks involved in emotion regulation, emotion processing, and perceptual functions, suggesting a network framework is integral to elucidating the pathophysiology of gSAD. However, fMRI does not measure the fast dynamic interconnections of functional networks. Therefore, we examined whole-brain functional connectomics with electroencephalogram (EEG) during resting-state. Resting-state EEG data was recorded for 32 patients with gSAD and 32 demographically-matched healthy controls (HC). Sensor-level connectivity analysis was applied on EEG data by using Weighted Phase Lag Index (WPLI) and graph analysis based on WPLI was used to determine clustering coefficient and characteristic path length to estimate local integration and global segregation of networks. WPLI results showed increased oscillatory midline coherence in the theta frequency band indicating higher connectivity in the gSAD relative to HC group during rest. Additionally, WPLI values positively correlated with state anxiety levels within the gSAD group but not the HC group. Our graph theory based connectomics analysis demonstrated increased clustering coefficient and decreased characteristic path length in theta-based whole brain functional organization in subjects with gSAD compared to HC. Theta-dependent interconnectivity was associated with state anxiety in gSAD and an increase in information processing efficiency in gSAD (compared to controls). Results may represent enhanced baseline self-focused attention, which is consistent with cognitive models of gSAD and fMRI studies implicating emotion dysregulation and disturbances in task negative networks (e.g., default mode network) in gSAD.

[Analysis of virulence factors of Porphyromonas endodontalis based on comparative proteomics technique].

PubMed

Li, H; Ji, H; Wu, S S; Hou, B X

2016-12-09

Objective: To analyze the protein expression profile and the potential virulence factors of Porphyromonas endodontalis (Pe) via comparison with that of two strains of Porphyromonas gingivalis (Pg) with high and low virulences, respectively. Methods: Whole cell comparative proteomics of Pe ATCC35406 was examined and compared with that of high virulent strain Pg W83 andlow virulent strain Pg ATCC33277, respectively. Isobaric tags for relative and absolute quantitation (iTRAQ) combined with nano liquid chromatography-tandem mass spectrometry (Nano-LC-MS/MS) were adopted to identify and quantitate the proteins of Pe and two strains of Pg with various virulences by using the methods of isotopically labeled peptides, mass spectrometric detection and bioinformatics analysis. The biological functions of similar proteins expressed by Pe ATCC35406 and two strains of Pg were quantified and analyzed. Results: Totally 1 210 proteins were identified while Pe compared with Pg W83. There were 130 proteins (10.74% of the total proteins) expressed similarly, including 89 known functional proteins and 41 proteins of unknown functions. Totally 1 223 proteins were identified when Pe compared with Pg ATCC33277. There were 110 proteins (8.99% of the total proteins) expressed similarly, including 72 known functional proteins and 38 proteins of unknown functions. The similarly expressed proteins in Pe and Pg strains with various virulences mainly focused on catalytic activity and binding function, including recombination activation gene (RagA), lipoprotein, chaperonin Dnak, Clp family proteins (ClpC and ClpX) and various iron-binding proteins. They were involved in metabolism and cellular processes. In addition, the type and number of similar virulence proteins between Pe and high virulence Pg were higher than those between Pe and low virulence Pg. Conclusions: Lipoprotein, oxygen resistance protein, iron binding protein were probably the potential virulence factors of Pe ATCC35406. It was speculated that pathogenicity of Pe was more similar to high virulence Pg than that to low virulence strain.

Reduction of Interhemispheric Functional Brain Connectivity in Early Blindness: A Resting-State fMRI Study

PubMed Central

2017-01-01

Objective The purpose of this study was to investigate the resting-state interhemispheric functional connectivity in early blindness by using voxel-mirrored homotopic connectivity (VMHC). Materials and Methods Sixteen early blind patients (EB group) and sixteen age- and gender-matched sighted control volunteers (SC group) were recruited in this study. We used VMHC to identify brain areas with significant differences in functional connectivity between different groups and used voxel-based morphometry (VBM) to calculate the individual gray matter volume (GMV). Results VMHC analysis showed a significantly lower connectivity in primary visual cortex, visual association cortex, and somatosensory association cortex in EB group compared to sighted controls. Additionally, VBM analysis revealed that GMV was reduced in the left lateral calcarine cortices in EB group compared to sighted controls, while it was increased in the left lateral middle occipital gyri. Statistical analysis showed the duration of blindness negatively correlated with VMHC in the bilateral middle frontal gyri, middle temporal gyri, and inferior temporal gyri. Conclusions Our findings help elucidate the pathophysiological mechanisms of EB. The interhemispheric functional connectivity was impaired in EB patients. Additionally, the middle frontal gyri, middle temporal gyri, and inferior temporal gyri may be potential target regions for rehabilitation. PMID:28656145

Structure and function of the abductors in patients with hip osteoarthritis: Systematic review and meta-analysis.

PubMed

Marshall, Amelia Rose; Noronha, Marcos de; Zacharias, Anita; Kapakoulakis, Theo; Green, Rodney

2016-04-27

Hip osteoarthritis (OA) is a major cause of morbidity. Rehabilitation for this population focuses on strengthening the hip muscles, particularly the abductors, however the deficit in function of these muscles is unclear. To review the evidence for the differences in structure and function of hip abductors (gluteus medius and minimus and tensor fascia lata) in hip OA. A systematic review was conducted using MEDLINE, AMED, CINAHL and SportDISCUS, from the earliest date to September 2013. Studies that compared hip OA patients with controls, or the unaffected contralateral hip were included. Studies needed to report data on an outcome related to gross gluteal muscle function. An initial yield of 141 studies was reduced to 22 after application of inclusion/exclusion criteria. Meta-analysis confirmed greater hip abductor strength in the control group (standardized mean difference = SMD -0.93, 95%CI -1.70 to -0.16) and the unaffected limb (SMD -0.26, 95%CI -0.48 to -0.04). Meta-analyses showed no differences in muscle size either between groups or limbs. Few electromyography studies have been reported and meta-analysis was not possible. Hip abductor strength is reduced in OA patients when compared to healthy controls and to the unaffected limb. Data on muscle size and activity is limited.

Is Rest Really Rest? Resting State Functional Connectivity during Rest and Motor Task Paradigms.

PubMed

Jurkiewicz, Michael T; Crawley, Adrian P; Mikulis, David J

2018-04-18

Numerous studies have identified the default mode network (DMN) within the brain of healthy individuals, which has been attributed to the ongoing mental activity of the brain during the wakeful resting-state. While engaged during specific resting-state fMRI paradigms, it remains unclear as to whether traditional block-design simple movement fMRI experiments significantly influence the default mode network or other areas. Using blood-oxygen level dependent (BOLD) fMRI we characterized the pattern of functional connectivity in healthy subjects during a resting-state paradigm and compared this to the same resting-state analysis performed on motor task data residual time courses after regressing out the task paradigm. Using seed-voxel analysis to define the DMN, the executive control network (ECN), and sensorimotor, auditory and visual networks, the resting-state analysis of the residual time courses demonstrated reduced functional connectivity in the motor network and reduced connectivity between the insula and the ECN compared to the standard resting-state datasets. Overall, performance of simple self-directed motor tasks does little to change the resting-state functional connectivity across the brain, especially in non-motor areas. This would suggest that previously acquired fMRI studies incorporating simple block-design motor tasks could be mined retrospectively for assessment of the resting-state connectivity.

A realistic analysis of the phonon growth characteristics in a degenerate semiconductor using a simplified model of Fermi-Dirac distribution

NASA Astrophysics Data System (ADS)

Basu, A.; Das, B.; Middya, T. R.; Bhattacharya, D. P.

2017-01-01

The phonon growth characteristic in a degenerate semiconductor has been calculated under the condition of low temperature. If the lattice temperature is high, the energy of the intravalley acoustic phonon is negligibly small compared to the average thermal energy of the electrons. Hence one can traditionally assume the electron-phonon collisions to be elastic and approximate the Bose-Einstein (B.E.) distribution for the phonons by the simple equipartition law. However, in the present analysis at the low lattice temperatures, the interaction of the non equilibrium electrons with the acoustic phonons becomes inelastic and the simple equipartition law for the phonon distribution is not valid. Hence the analysis is made taking into account the inelastic collisions and the complete form of the B.E. distribution. The high-field distribution function of the carriers given by Fermi-Dirac (F.D.) function at the field dependent carrier temperature, has been approximated by a well tested model that apparently overcomes the intrinsic problem of correct evaluation of the integrals involving the product and powers of the Fermi function. Hence the results thus obtained are more reliable compared to the rough estimation that one may obtain from using the exact F.D. function, but taking recourse to some over simplified approximations.

Comparative expression profiling reveals gene functions in female meiosis and gametophyte development in Arabidopsis.

PubMed

Zhao, Lihua; He, Jiangman; Cai, Hanyang; Lin, Haiyan; Li, Yanqiang; Liu, Renyi; Yang, Zhenbiao; Qin, Yuan

2014-11-01

Megasporogenesis is essential for female fertility, and requires the accomplishment of meiosis and the formation of functional megaspores. The inaccessibility and low abundance of female meiocytes make it particularly difficult to elucidate the molecular basis underlying megasporogenesis. We used high-throughput tag-sequencing analysis to identify genes expressed in female meiocytes (FMs) by comparing gene expression profiles from wild-type ovules undergoing megasporogenesis with those from the spl mutant ovules, which lack megasporogenesis. A total of 862 genes were identified as FMs, with levels that are consistently reduced in spl ovules in two biological replicates. Fluorescence-assisted cell sorting followed by RNA-seq analysis of DMC1:GFP-labeled female meiocytes confirmed that 90% of the FMs are indeed detected in the female meiocyte protoplast profiling. We performed reverse genetic analysis of 120 candidate genes and identified four FM genes with a function in female meiosis progression in Arabidopsis. We further revealed that KLU, a putative cytochrome P450 monooxygenase, is involved in chromosome pairing during female meiosis, most likely by affecting the normal expression pattern of DMC1 in ovules during female meiosis. Our studies provide valuable information for functional genomic analyses of plant germline development as well as insights into meiosis. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).

PubMed

Xu, Yuantao; Wu, Guizhi; Hao, Baohai; Chen, Lingling; Deng, Xiuxin; Xu, Qiang

2015-11-23

With the availability of rapidly increasing number of genome and transcriptome sequences, lineage-specific genes (LSGs) can be identified and characterized. Like other conserved functional genes, LSGs play important roles in biological evolution and functions. Two set of citrus LSGs, 296 citrus-specific genes (CSGs) and 1039 orphan genes specific to sweet orange, were identified by comparative analysis between the sweet orange genome sequences and 41 genomes and 273 transcriptomes. With the two sets of genes, gene structure and gene expression pattern were investigated. On average, both the CSGs and orphan genes have fewer exons, shorter gene length and higher GC content when compared with those evolutionarily conserved genes (ECs). Expression profiling indicated that most of the LSGs expressed in various tissues of sweet orange and some of them exhibited distinct temporal and spatial expression patterns. Particularly, the orphan genes were preferentially expressed in callus, which is an important pluripotent tissue of citrus. Besides, part of the CSGs and orphan genes expressed responsive to abiotic stress, indicating their potential functions during interaction with environment. This study identified and characterized two sets of LSGs in citrus, dissected their sequence features and expression patterns, and provided valuable clues for future functional analysis of the LSGs in sweet orange.

Proteomic profiling of ATM kinase proficient and deficient cell lines upon blockage of proteasome activity☆

PubMed Central

Marzano, Valeria; Santini, Simonetta; Rossi, Claudia; Zucchelli, Mirco; D'Alessandro, Annamaria; Marchetti, Carlo; Mingardi, Michele; Stagni, Venturina; Barilà, Daniela; Urbani, Andrea

2012-01-01

Ataxia Telangiectasia Mutated (ATM) protein kinase is a key effector in the modulation of the functionality of some important stress responses, including DNA damage and oxidative stress response, and its deficiency is the hallmark of Ataxia Telangiectasia (A-T), a rare genetic disorder. ATM modulates the activity of hundreds of target proteins, essential for the correct balance between proliferation and cell death. The aim of this study is to evaluate the phenotypic adaptation at the protein level both in basal condition and in presence of proteasome blockage in order to identify the molecules whose level and stability are modulated through ATM expression. We pursued a comparative analysis of ATM deficient and proficient lymphoblastoid cells by label-free shotgun proteomic experiments comparing the panel of proteins differentially expressed. Through a non-supervised comparative bioinformatic analysis these data provided an insight on the functional role of ATM deficiency in cellular carbohydrate metabolism's regulation. This hypothesis has been demonstrated by targeted metabolic fingerprint analysis SRM (Selected Reaction Monitoring) on specific thermodynamic checkpoints of glycolysis. This article is part of a Special Issue entitled: Translational Proteomics. PMID:22641158

'Executive' functions and normal aging: selective impairment in conditional exclusion compared to abstraction and inhibition.

PubMed

Silver, Henry; Goodman, Craig; Gur, Ruben C; Gur, Raquel E; Bilker, Warren B

2011-01-01

Some executive functions may be selectively impaired in normal aging over and above the general cognitive decline. We examined the performance of healthy high functioning young (n = 77) and older (n = 57) individuals on three 'executive' tests: conditional exclusion, abstraction, and inhibition of prepotent responses. We compared their relationships to each other and to other cognitive functions including attention, psychomotor speed and working memory. Conditional exclusion was significantly more impaired than abstraction or inhibition in the elderly compared to the younger group and unlike them, showed a nonlinear relationship with age. These findings were independent of other cognitive functions. Analysis of PCET performance characteristics showed that older individuals were particularly impaired in attaining the last of the three achievable categories, were slower, and had fewer error monitoring resources compared to the younger group. Conditional exclusion shows an age-related pattern of impairment distinct from inhibition and abstraction. We propose that in healthy well-functioning individuals, it taps processes integrating task set establishment and shifting in context of accumulating information. It may thus be useful as a specific marker of complex cognitive functions in studies of normal cognitive aging and in early detection of cognitive dysfunction. Copyright © 2010 S. Karger AG, Basel.

Frontier production function estimates for steam electric generation: a comparative analysis

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

Kopp, R.J.; Smith, V.K.

1980-04-01

The performance of three frontier steam electric generation estimators is compared in terms of the consideration given to new production technologies and their technical efficiency. The Cobb-Douglas, constant elasticity of substitution, and translog production functions are examined, using the Aigner-Chu linear programming, the sophisticated Aigner-Lovell-Schmidt stochastic frontier, and the direct method of adjusted ordinary least squares frontier estimators. The use of Cobb-Douglas specification is judged to have narrowed the perceived difference between competing estimators. The choice of frontier estimator is concluded to have a greater effect on the plant efficiency than functional form. 19 references. (DCK)

Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development

USDA-ARS?s Scientific Manuscript database

Chromoplasts are unique plastids that accumulate massive amounts of carotenoids. To gain a general and comparative characterization of chromoplast proteins, we performed proteomic analysis of chromoplasts from six carotenoid-rich crops: watermelon, tomato, carrot, orange cauliflower, red papaya, and...

Efficient reliability analysis of structures with the rotational quasi-symmetric point- and the maximum entropy methods

NASA Astrophysics Data System (ADS)

Xu, Jun; Dang, Chao; Kong, Fan

2017-10-01

This paper presents a new method for efficient structural reliability analysis. In this method, a rotational quasi-symmetric point method (RQ-SPM) is proposed for evaluating the fractional moments of the performance function. Then, the derivation of the performance function's probability density function (PDF) is carried out based on the maximum entropy method in which constraints are specified in terms of fractional moments. In this regard, the probability of failure can be obtained by a simple integral over the performance function's PDF. Six examples, including a finite element-based reliability analysis and a dynamic system with strong nonlinearity, are used to illustrate the efficacy of the proposed method. All the computed results are compared with those by Monte Carlo simulation (MCS). It is found that the proposed method can provide very accurate results with low computational effort.

Assigning protein functions by comparative genome analysis protein phylogenetic profiles

DOEpatents

Pellegrini, Matteo; Marcotte, Edward M.; Thompson, Michael J.; Eisenberg, David; Grothe, Robert; Yeates, Todd O.

2003-05-13

A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

A time-frequency analysis method to obtain stable estimates of magnetotelluric response function based on Hilbert-Huang transform

NASA Astrophysics Data System (ADS)

Cai, Jianhua

2017-05-01

The time-frequency analysis method represents signal as a function of time and frequency, and it is considered a powerful tool for handling arbitrary non-stationary time series by using instantaneous frequency and instantaneous amplitude. It also provides a possible alternative to the analysis of the non-stationary magnetotelluric (MT) signal. Based on the Hilbert-Huang transform (HHT), a time-frequency analysis method is proposed to obtain stable estimates of the magnetotelluric response function. In contrast to conventional methods, the response function estimation is performed in the time-frequency domain using instantaneous spectra rather than in the frequency domain, which allows for imaging the response parameter content as a function of time and frequency. The theory of the method is presented and the mathematical model and calculation procedure, which are used to estimate response function based on HHT time-frequency spectrum, are discussed. To evaluate the results, response function estimates are compared with estimates from a standard MT data processing method based on the Fourier transform. All results show that apparent resistivities and phases, which are calculated from the HHT time-frequency method, are generally more stable and reliable than those determined from the simple Fourier analysis. The proposed method overcomes the drawbacks of the traditional Fourier methods, and the resulting parameter minimises the estimation bias caused by the non-stationary characteristics of the MT data.

Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data.

PubMed

Oakley, Todd H; Gu, Zhenglong; Abouheif, Ehab; Patel, Nipam H; Li, Wen-Hsiung

2005-01-01

Understanding the evolution of gene function is a primary challenge of modern evolutionary biology. Despite an expanding database from genomic and developmental studies, we are lacking quantitative methods for analyzing the evolution of some important measures of gene function, such as gene-expression patterns. Here, we introduce phylogenetic comparative methods to compare different models of gene-expression evolution in a maximum-likelihood framework. We find that expression of duplicated genes has evolved according to a nonphylogenetic model, where closely related genes are no more likely than more distantly related genes to share common expression patterns. These results are consistent with previous studies that found rapid evolution of gene expression during the history of yeast. The comparative methods presented here are general enough to test a wide range of evolutionary hypotheses using genomic-scale data from any organism.

Effectiveness of aquatic exercise for treatment of knee osteoarthritis: Systematic review and meta-analysis.

PubMed

Lu, Meili; Su, Youxin; Zhang, Yingjie; Zhang, Ziyi; Wang, Wenting; He, Zhen; Liu, Feiwen; Li, Yanan; Liu, Changyan; Wang, Yiru; Sheng, Lu; Zhan, Zhengxuan; Wang, Xu; Zheng, Naixi

2015-08-01

This paper presents a systematic review and meta-analysis of the effectiveness of aquatic exercise for treatment of knee osteoarthritis (OA). PubMed, the Cochrane Library, Embase, CAMbase, and the Web of Science were screened through to June 2014. Only randomized controlled trials (RCTs) comparing aquatic exercise with control conditions were included. Two authors independently selected trials for inclusion, assessed the included trials, and extracted data. Outcome measures included pain, physical function, joint stiffness, quality of life (QOL), and safety. Pooled outcomes were analyzed using standardized mean difference (SMD). There is a lack of high quality studies in this area. Six RCTs (398 participants) were included. There was moderate evidence for a moderate effect on physical function in favor of aquatic exercise immediately after the intervention, but no evidence for pain or QOL when comparing aquatic exercise with nonexercise. Only one trial reported 3 months of follow-up measurements, which demonstrated limited evidence for pain improvement with aquatic exercise and no evidence for QOL or physical function when comparing aquatic exercise with nonexercise. There was limited evidence for pain improvement with land-based exercise and no evidence for QOL or physical function, when comparing aquatic exercise with land-based exercise according to follow-up measurements. No evidence was found for pain, physical function, stiffness, QOL, or mental health with aquatic exercise immediately after the intervention when comparing aquatic exercise with land-based exercise. Two studies reported aquatic exercise was not associated with serious adverse events. Aquatic exercise appears to have considerable short-term benefits compared with land-based exercise and nonexercise in patients with knee OA. Based on these results, aquatic exercise is effective and safe and can be considered as an adjuvant treatment for patients with knee OA. Studies in this area are still too scarce and too short-term to provide further recommendations on how to apply this therapy.

Statistical inference of dynamic resting-state functional connectivity using hierarchical observation modeling.

PubMed

Sojoudi, Alireza; Goodyear, Bradley G

2016-12-01

Spontaneous fluctuations of blood-oxygenation level-dependent functional magnetic resonance imaging (BOLD fMRI) signals are highly synchronous between brain regions that serve similar functions. This provides a means to investigate functional networks; however, most analysis techniques assume functional connections are constant over time. This may be problematic in the case of neurological disease, where functional connections may be highly variable. Recently, several methods have been proposed to determine moment-to-moment changes in the strength of functional connections over an imaging session (so called dynamic connectivity). Here a novel analysis framework based on a hierarchical observation modeling approach was proposed, to permit statistical inference of the presence of dynamic connectivity. A two-level linear model composed of overlapping sliding windows of fMRI signals, incorporating the fact that overlapping windows are not independent was described. To test this approach, datasets were synthesized whereby functional connectivity was either constant (significant or insignificant) or modulated by an external input. The method successfully determines the statistical significance of a functional connection in phase with the modulation, and it exhibits greater sensitivity and specificity in detecting regions with variable connectivity, when compared with sliding-window correlation analysis. For real data, this technique possesses greater reproducibility and provides a more discriminative estimate of dynamic connectivity than sliding-window correlation analysis. Hum Brain Mapp 37:4566-4580, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Functional sequencing read annotation for high precision microbiome analysis

PubMed Central

Zhu, Chengsheng; Miller, Maximilian; Marpaka, Srinayani; Vaysberg, Pavel; Rühlemann, Malte C; Wu, Guojun; Heinsen, Femke-Anouska; Tempel, Marie; Zhao, Liping; Lieb, Wolfgang; Franke, Andre; Bromberg, Yana

2018-01-01

Abstract The vast majority of microorganisms on Earth reside in often-inseparable environment-specific communities—microbiomes. Meta-genomic/-transcriptomic sequencing could reveal the otherwise inaccessible functionality of microbiomes. However, existing analytical approaches focus on attributing sequencing reads to known genes/genomes, often failing to make maximal use of available data. We created faser (functional annotation of sequencing reads), an algorithm that is optimized to map reads to molecular functions encoded by the read-correspondent genes. The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates microbiome molecular functionality. mi-faser’s minutes-per-microbiome processing speed is significantly faster than that of other methods, allowing for large scale comparisons. Microbiome function vectors can be compared between different conditions to highlight environment-specific and/or time-dependent changes in functionality. Here, we identified previously unseen oil degradation-specific functions in BP oil-spill data, as well as functional signatures of individual-specific gut microbiome responses to a dietary intervention in children with Prader–Willi syndrome. Our method also revealed variability in Crohn's Disease patient microbiomes and clearly distinguished them from those of related healthy individuals. Our analysis highlighted the microbiome role in CD pathogenicity, demonstrating enrichment of patient microbiomes in functions that promote inflammation and that help bacteria survive it. PMID:29194524

Multiple-Respondent Anecdotal Assessments: An Analysis of Interrater Agreement and Correspondence with Analogue Assessment Outcomes

ERIC Educational Resources Information Center

Smith, Carla M.; Smith, Richard G.; Dracobly, Joseph D.; Pace, Amy Peterson

2012-01-01

We evaluated interrater agreement across multiple respondents on anecdotal assessments and compared cases in which agreement was obtained with outcomes of functional analyses. Experiment 1 evaluated agreement among multiple respondents on the function of problem behavior for 27 individuals across 42 target behaviors using the Motivation Assessment…

Directory of Graduate Programs in the Speech Communication Arts and Sciences 1975-1976.

ERIC Educational Resources Information Center

Hall, Robert N., Ed.

The primary function of this directory is to serve prospective graduate students, teachers, administrators and counselors who desire current information about graduate programs in speech communication. A secondary function is to provide a comparative analysis of the information presented. Many of the fundamental questions that a student might ask…

Parametric Methods for Dynamic 11C-Phenytoin PET Studies.

PubMed

Mansor, Syahir; Yaqub, Maqsood; Boellaard, Ronald; Froklage, Femke E; de Vries, Anke; Bakker, Esther D M; Voskuyl, Rob A; Eriksson, Jonas; Schwarte, Lothar A; Verbeek, Joost; Windhorst, Albert D; Lammertsma, Adriaan A

2017-03-01

In this study, the performance of various methods for generating quantitative parametric images of dynamic 11 C-phenytoin PET studies was evaluated. Methods: Double-baseline 60-min dynamic 11 C-phenytoin PET studies, including online arterial sampling, were acquired for 6 healthy subjects. Parametric images were generated using Logan plot analysis, a basis function method, and spectral analysis. Parametric distribution volume (V T ) and influx rate ( K 1 ) were compared with those obtained from nonlinear regression analysis of time-activity curves. In addition, global and regional test-retest (TRT) variability was determined for parametric K 1 and V T values. Results: Biases in V T observed with all parametric methods were less than 5%. For K 1 , spectral analysis showed a negative bias of 16%. The mean TRT variabilities of V T and K 1 were less than 10% for all methods. Shortening the scan duration to 45 min provided similar V T and K 1 with comparable TRT performance compared with 60-min data. Conclusion: Among the various parametric methods tested, the basis function method provided parametric V T and K 1 values with the least bias compared with nonlinear regression data and showed TRT variabilities lower than 5%, also for smaller volume-of-interest sizes (i.e., higher noise levels) and shorter scan duration. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Comparative studies on molecular structure, vibrational spectra and hyperpolarizabilies of NLO chromophore Ethyl 4-Dimethylaminobenzoate

NASA Astrophysics Data System (ADS)

Amalanathan, M.; Jasmine, G. Femina; Roy, S. Dawn Dharma

2017-08-01

The molecular structure, vibrational spectra and polarizabilities of Ethyl 4-Dimethylaminobenzoate (EDAB) was investigated by density functional theory employing Becke's three parameter hybrid exchange functional with Lee-Yang-Parr (B3LYP) co-relational functional involving 6-311++G(d,p) basis set and compared with some other levels. A detailed interpretation of the IR and Raman spectra of EDBA have been reported and analyzed. Complete vibrational assignments of the vibrational modes have been done on the basis of the potential energy distribution (TED) using VEDA software. The molecular electrostatic potential mapped onto total density surface has been obtained. A study on the electronic properties, such as absorption wavelength, and frontier molecular orbitals energy, was performed using DFT approach. The stability of the molecule arising from hyper conjugative interactions and accompanying charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The natural and Mulliken charge also calculated and compared with different level of calculation. The dipole moment, polarizability and first, second order hyperpolarizabilities of the title molecule were calculated and compared with the experimental values. The energy gap between frontier orbitals has been used along with electric moments and first order hyperpolarizability, to understand the non linear optical (NLO) activity of the molecule. The NLO activity of molecule was confirmed by SHG analysis.

Gait analysis in children with haemophilia: first Italian experience at the Turin Haemophilia Centre.

PubMed

Forneris, E; Andreacchio, A; Pollio, B; Mannucci, C; Franchini, M; Mengoli, C; Pagliarino, M; Messina, M

2016-05-01

To investigate the functional status in haemophilia patients referred to an Italian paediatric haemophilia centre using gait analysis, verifying any differences between mild, moderate or severe haemophilia at a functional level. Forty-two patients (age 4-18) presenting to the Turin Paediatric Haemophilia Centre who could walk independently were included. Therapy included prophylaxis (n = 21), on-demand (n = 17) or immune tolerance induction + inhibitor (n = 4). Patients performed a test of gait analysis. Temporal, spatial and kinematic parameters were calculated for patient subgroups by disease severity and background treatment, and compared with normal values. Moderate (35.7%) or severe (64.3%) haemophilia patients showed obvious variations from normal across a variety of temporal and spatial gait analysis parameters, including step speed and length, double support, swing phase, load asymmetry, stance phase, swing phase and speed. Kinematic parameters were characterized by frequent foot external rotation with deficient plantar flexion during the stance phase, retropelvic tilt, impaired power generation distally and reduced ground reaction forces. Both Gait Deviation Index and Gait Profile Score values for severe haemophilia patients indicated abnormal gait parameters, which were worst in patients with a history of past or current use of inhibitors and those receiving on-demand therapy. Functional evaluation identified changes in gait pattern in patients with severe and moderate haemophilia, compared with normal values. Gait analysis may be a useful tool to facilitate early diagnosis of joint damage, prevent haemophilic arthropathy, design a personalized rehabilitative treatment and monitor functional status over time. © 2016 John Wiley & Sons Ltd.

Does Compare-Contrast Text Structure Help Students with Autism Spectrum Disorder Comprehend Science Text?

ERIC Educational Resources Information Center

Carnahan, Christina R.; Williamson, Pamela S.

2013-01-01

Using a single-subject reversal design, this study evaluated the use of a compare-contrast strategy on the ability of students with autism spectrum disorder to comprehend science text. Three middle school students with high-functioning autism and their teacher participated in this study. A content analysis comparing the number of meaning units in…

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecul...

THE MASS MEDIA AS AN EDUCATIONAL INSTITUTION.

ERIC Educational Resources Information Center

GANS, HERBERT J.

THE TEACHING AND LEARNING PROVIDED BY BOTH THE MASS MEDIA AND THE SCHOOLS SHOULD BE ANALYZED. THIS RESEARCH WOULD CONCENTRATE ON NETWORK TELEVISION AND THE URBAN AND SUBURBAN LOWER MIDDLE CLASS SCHOOLS AND COMPARE THEIR SUCCESS AS EDUCATIONAL INSTITUTIONS. THE ANALYSIS COULD COMPARE THE STRUCTURES OF THESE INSTITUTIONS AND THEIR FUNCTIONS AND…

Learning in the Making: A Comparative Case Study of Three Makerspaces

ERIC Educational Resources Information Center

Sheridan, Kimberly M.; Halverson, Erica Rosenfeld; Litts, Breanne K.; Brahms, Lisa; Jacobs-Priebe, Lynette; Owens, Trevor

2014-01-01

Through a comparative case study, Sheridan and colleagues explore how makerspaces may function as learning environments. Drawing on field observations, interviews, and analysis of artifacts, videos, and other documents, the authors describe features of three makerspaces and how participants learn and develop through complex design and making…

Comparison of intra-articular hyaluronic acid and methylprednisolone for pain management in knee osteoarthritis: A meta-analysis of randomized controlled trials.

PubMed

Ran, Jian; Yang, Xiaohui; Ren, Zheng; Wang, Jian; Dong, Hui

2018-05-01

We performed a meta-analysis of randomized controlled trials (RCTs) to compare the efficacy and safety of intra-articular methylprednisolone and hyaluronic acid (HA) in term of pain reduction and improvements of knee function in patients with knee osteoarthritis (OA). The PubMed, EMBASE, ScienceDirect, and Cochrane Library databases were systematically searched for literature up to January 2018. RCTs involving HA and methylprednisolone in knee OA were included. Two independent reviewers performed independent data abstraction. The I 2 statistic was used to assess heterogeneity. A fixed or random effects model was adopted for meta-analysis. All meta-analyses were performed by using STATA 14.0. Five RCTs with 1004 patients were included in the meta-analysis. The present meta-analysis indicated that there were no significant differences in terms of WOMAC pain, physical function and stiffness at 4 week, 12 weeks and 26 weeks between HA and methylprednisolone groups. No increased risk of adverse events were identified in both groups. Both HA and methylprednisolone injections were effective therapies for patients with knee OA. Methylprednisolone showed comparable efficacy in reducing pain and improving functional recovery to HA. And no significant difference was found in long-term of follow-up in terms of adverse effects. Copyright © 2018 IJS Publishing Group Ltd. All rights reserved.

Effect of exercise on cognitive function in chronic disease patients: a meta-analysis and systematic review of randomized controlled trials

PubMed Central

Cai, Hong; Li, Guichen; Hua, Shanshan; Liu, Yufei; Chen, Li

2017-01-01

Background The purpose of this study was to conduct a meta-analysis and systematic review to assess the effect of exercise on cognitive function in people with chronic diseases. Methods PubMed, Web of Science, Embase, the Cochrane Library, CINAHL, PsycINFO, and three Chinese databases were electronically searched for papers that were published until September 2016. This meta-analysis and systematic review included randomized controlled trials that evaluated the effect of exercise on cognitive function compared with control group for people with chronic diseases. Results Totally, 35 studies met the inclusion criteria, with 3,113 participants. The main analysis revealed a positive overall random effect of exercise intervention on cognitive function in patients with chronic diseases. The secondary analysis revealed that aerobic exercise interventions and aerobic included exercise interventions had a positive effect on cognition in patients with chronic diseases. The intervention offering low frequency had a positive effect on cognitive function in patients with chronic diseases. Finally, we found that interventions offered at both low exercise intensity and moderate exercise intensity had a positive effect on cognitive function in patients with chronic diseases. The secondary analysis also revealed that exercise interventions were beneficial in Alzheimer’s disease patients when grouped by disease type. Conclusion This meta-analysis and systematic review suggests that exercise interventions positively influence cognitive function in patients with chronic diseases. Beneficial effect was independent of the type of disease, type of exercise, frequency, and the intensity of the exercise intervention. PMID:28546744

Adult males with haemophilia have a different macrovascular and microvascular endothelial function profile compared with healthy controls.

PubMed

Sun, H; Yang, M; Fung, M; Chan, S; Jawi, M; Anderson, T; Poon, M-C; Jackson, S

2017-09-01

Endothelial function has been identified as an independent predictor of cardiovascular risk in the general population. It is unclear if the haemophilia population has a different endothelial function profile compared to the healthy population. This prospective study aims to assess if there is a difference in endothelial function between haemophilia patients and healthy controls, and the impact of endothelial function on vascular outcomes in the haemophilia population. Baseline cardiovascular risk factors and endothelial function were presented. Adult males with haemophilia A or B recruited from the British Columbia and Southern Alberta haemophilia treatment centres were matched to healthy male controls by age and cardiovascular risk factors. Macrovascular endothelial function was assessed by brachial artery flow-mediated dilation (FMD) and nitroglycerin-mediated dilation (NMD), and microvascular endothelial function was assessed by hyperaemic velocity time integral (VTI). Multivariable linear regression was used to assess the association between haemophilia and endothelial function. A total of 81 patients with haemophilia and 243 controls were included. Patients with haemophilia had a similar FMD and NMD compared to controls, although haemophilia was associated with higher FMD on multivariable analysis. Haemophilia was associated with significantly lower VTI on univariate and multivariable analyses, regardless of haemophilia type and severity. Adult males with haemophilia appear to have lower microvascular endothelial function compared to healthy controls. Future studies to assess the impact of endothelial dysfunction on cardiovascular events in the haemophilia population are needed. © 2017 John Wiley & Sons Ltd.

Mild thyroid hormone excess is associated with a decreased physical function in elderly men.

PubMed

Ceresini, Graziano; Ceda, Gian Paolo; Lauretani, Fulvio; Maggio, Marcello; Bandinelli, Stefania; Guralnik, Jack M; Cappola, Anne R; Usberti, Elisa; Morganti, Simonetta; Valenti, Giorgio; Ferrucci, Luigi

2011-12-01

In the adult, subclinical hyperthyroidism (Shyper) may alter skeletal muscle mass and strength. However, whether these effects are present in elderly subjects is not known. We explored the relationship between mild hyperthyroidism and physical function in a population-based sample of older persons. In a cross-sectional analysis, calf muscle cross-sectional area (CMA), handgrip strength, nerve conduction velocity (NCV), and Short Physical Performance Battery (SPPB) scores were compared between 364 euthyroid (Eut) and 28 Shyper men as well as between 502 Eut and 39 Shyper women. In a longitudinal analysis, we evaluated the relationship between baseline plasma TSH, FT3 and FT4 and the 3-year change in SPPB score in 304 men and 409 women who were euthyroid at enrolment. At the cross-sectional analysis, Shyper men, but not women, had a significantly (p = 0.02) lower SPPB score than Eut controls, although with comparable CMA, grip strength and NCV, and were more likely to have poor physical performance (odds ratio = 2.97, p < 0.05). Longitudinal analysis showed that in Eut men higher baseline FT4 was significantly (p = 0.02) predictive of a lower SPPB score at the 3-year follow-up. Even a modest thyroid hormone excess is associated with a reduced physical function in elderly men.

Multimodal interventions including nutrition in the prevention and management of disease-related malnutrition in adults: a systematic review of randomised control trials.

PubMed

Thorne, Frances; Baldwin, Christine

2014-06-01

There has been a move to improve nutritional status in malnourished patients through the use of multimodal interventions (MI). There are currently no systematic reviews that have examined their effectiveness. This analysis aimed to examine the effects on nutritional, clinical, functional and patient-centred outcomes. A systematic review and meta-analysis using Cochrane methodology. 15 studies were included in the analysis, 13 comparing MI with usual care and 2 comparing MI with a nutrition intervention alone. Quality of studies varied and studies reported few relevant outcomes. Only 3 outcomes were compatible with meta-analysis; weight, mortality and length of stay (LOS). No statistically significant differences between groups were found. Narrative review was inconclusive. There was no evidence of benefit in the intervention groups in relation to body composition, functional status or quality of life (QoL). Intervention groups appeared to show a trend towards increased energy and protein intake however data was provided by only 2 studies (301 participants). No conclusive evidence of benefit for MI on any of the reviewed outcomes was found. Well designed, high quality trials addressing the impact of MI on relevant nutritional, functional and clinical outcomes are required. Copyright © 2014 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Global Landscape of a Co-Expressed Gene Network in Barley and its Application to Gene Discovery in Triticeae Crops

PubMed Central

Mochida, Keiichi; Uehara-Yamaguchi, Yukiko; Yoshida, Takuhiro; Sakurai, Tetsuya; Shinozaki, Kazuo

2011-01-01

Accumulated transcriptome data can be used to investigate regulatory networks of genes involved in various biological systems. Co-expression analysis data sets generated from comprehensively collected transcriptome data sets now represent efficient resources that are capable of facilitating the discovery of genes with closely correlated expression patterns. In order to construct a co-expression network for barley, we analyzed 45 publicly available experimental series, which are composed of 1,347 sets of GeneChip data for barley. On the basis of a gene-to-gene weighted correlation coefficient, we constructed a global barley co-expression network and classified it into clusters of subnetwork modules. The resulting clusters are candidates for functional regulatory modules in the barley transcriptome. To annotate each of the modules, we performed comparative annotation using genes in Arabidopsis and Brachypodium distachyon. On the basis of a comparative analysis between barley and two model species, we investigated functional properties from the representative distributions of the gene ontology (GO) terms. Modules putatively involved in drought stress response and cellulose biogenesis have been identified. These modules are discussed to demonstrate the effectiveness of the co-expression analysis. Furthermore, we applied the data set of co-expressed genes coupled with comparative analysis in attempts to discover potentially Triticeae-specific network modules. These results demonstrate that analysis of the co-expression network of the barley transcriptome together with comparative analysis should promote the process of gene discovery in barley. Furthermore, the insights obtained should be transferable to investigations of Triticeae plants. The associated data set generated in this analysis is publicly accessible at http://coexpression.psc.riken.jp/barley/. PMID:21441235

A comparative analysis of localized and propagating surface plasmon resonance sensors: the binding of concanavalin a to a monosaccharide functionalized self-assembled monolayer.

PubMed

Yonzon, Chanda Ranjit; Jeoung, Eunhee; Zou, Shengli; Schatz, George C; Mrksich, Milan; Van Duyne, Richard P

2004-10-06

A comparative analysis of the properties of two optical biosensor platforms: (1) the propagating surface plasmon resonance (SPR) sensor based on a planar, thin film gold surface and (2) the localized surface plasmon resonance (LSPR) sensor based on surface confined Ag nanoparticles fabricated by nanosphere lithography (NSL) are presented. The binding of Concanavalin A (ConA) to mannose-functionalized self-assembled monolayers (SAMs) was chosen to highlight the similarities and differences between the responses of the real-time angle shift SPR and wavelength shift LSPR biosensors. During the association phase in the real-time binding studies, both SPR and LSPR sensors exhibited qualitatively similar signal vs time curves. However, in the dissociation phase, the SPR sensor showed an approximately 5 times greater loss of signal than the LSPR sensor. A comprehensive set of nonspecific binding studies demonstrated that this signal difference was not the consequence of greater nonspecific binding to the LSPR sensor but rather a systematic function of the Ag nanoparticle's nanoscale structure. Ag nanoparticles with larger aspect ratios showed larger dissociation phase responses than those with smaller aspect ratios. A theoretical analysis based on finite element electrodynamics demonstrates that this results from the characteristic decay length of the electromagnetic fields surrounding Ag nanoparticles being of comparable dimensions to the ConA molecules. Finally, an elementary (2 x 1) multiplexed version of an LSPR carbohydrate sensing chip to probe the simultaneous binding of ConA to mannose and galactose-functionalized SAMs has been demonstrated.

Pituitary gland volumes in bipolar disorder.

PubMed

Clark, Ian A; Mackay, Clare E; Goodwin, Guy M

2014-12-01

Bipolar disorder has been associated with increased Hypothalamic-Pituitary-Adrenal axis function. The mechanism is not well understood, but there may be associated increases in pituitary gland volume (PGV) and these small increases may be functionally significant. However, research investigating PGV in bipolar disorder reports mixed results. The aim of the current study was twofold. First, to assess PGV in two novel samples of patients with bipolar disorder and matched healthy controls. Second, to perform a meta-analysis comparing PGV across a larger sample of patients and matched controls. Sample 1 consisted of 23 established patients and 32 matched controls. Sample 2 consisted of 39 medication-naïve patients and 42 matched controls. PGV was measured on structural MRI scans. Seven further studies were identified comparing PGV between patients and matched controls (total n; 244 patients, 308 controls). Both novel samples showed a small (approximately 20mm(3) or 4%), but non-significant, increase in PGV in patients. Combining the two novel samples showed a significant association of age and PGV. Meta-analysis showed a trend towards a larger pituitary gland in patients (effect size: .23, CI: -.14, .59). While results suggest a possible small difference in pituitary gland volume between patients and matched controls, larger mega-analyses with sample sizes greater even than those used in the current meta-analysis are still required. There is a small but potentially functionally significant increase in PGV in patients with bipolar disorder compared to controls. Results demonstrate the difficulty of finding potentially important but small effects in functional brain disorders. Copyright © 2014 Elsevier B.V. All rights reserved.

Efficacy of dipeptidyl-peptidase-4 inhibitors and impact on β-cell function in Asian and Caucasian type 2 diabetes mellitus patients: A meta-analysis.

PubMed

Cai, Xiaoling; Han, Xueyao; Luo, Yingying; Ji, Linong

2015-05-01

This work aimed to compare the efficacy of dipeptidyl peptidase-IV (DPP-4) inhibitors and their impact on β-cell function in Asian and Caucasian patients with type 2 diabetes mellitus. Databases were systematically searched and qualifying studies that compared DPP-4 inhibitors with other antidiabetic medications in type 2 diabetes were included. A total of 68 studies were included in the meta-analysis. Comparison of DPP-4 inhibitors with placebo in Asian patients showed a decrease in glycosylated hemoglobin (HbA1c ) favoring DPP-4 inhibitors (weighted mean difference [WMD], -0.81%; 95% confidence interval [CI], -0.95% to -0.68%; P < 0.001). Comparison of HbA1c changes between Asian and Caucasian patients showed a significant between-group difference of -0.18% (95% CI, -0.32% to -0.04%; P = 0.011) when compared with placebo. In Asian patients, the homeostatic model assessment for β-cell function (HOMA-β) was increased with DPP-4 inhibitors compared with placebo (WMD, 7.90; 95% CI, 4.29 to 11.51; P < 0.001), although to a lesser extent in Caucasian patients. Comparisons between Asian and Caucasian patients showed a significant between-group difference of -4.97 (95% CI, -9.86 to -0.09; P = 0.046) compared with placebo. Body weight increase with DPP-4 inhibitors compared with placebo was comparable in Asian and Caucasian studies (WMD, 0.37 kg and 0.45 kg and 95% CI, 0.04-0.69 and 0.27-0.62, respectively). The glucose-lowering efficacy of DPP-4 inhibitors was greater in Asian patients than in Caucasian patients, although the effect on β-cell function was inferior in Asian patients. The effect of DPP-4 inhibitors on insulin resistance and body weight in Asian patients was comparable with that observed in Caucasian patients. © 2014 Ruijin Hospital, Shanghai Jiaotong University School of Medicine and Wiley Publishing Asia Pty Ltd.

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis.

PubMed

Zheng, Qi; Wang, Xiu-Jie

2008-07-01

Gene Ontology (GO) analysis has become a commonly used approach for functional studies of large-scale genomic or transcriptomic data. Although there have been a lot of software with GO-related analysis functions, new tools are still needed to meet the requirements for data generated by newly developed technologies or for advanced analysis purpose. Here, we present a Gene Ontology Enrichment Analysis Software Toolkit (GOEAST), an easy-to-use web-based toolkit that identifies statistically overrepresented GO terms within given gene sets. Compared with available GO analysis tools, GOEAST has the following improved features: (i) GOEAST displays enriched GO terms in graphical format according to their relationships in the hierarchical tree of each GO category (biological process, molecular function and cellular component), therefore, provides better understanding of the correlations among enriched GO terms; (ii) GOEAST supports analysis for data from various sources (probe or probe set IDs of Affymetrix, Illumina, Agilent or customized microarrays, as well as different gene identifiers) and multiple species (about 60 prokaryote and eukaryote species); (iii) One unique feature of GOEAST is to allow cross comparison of the GO enrichment status of multiple experiments to identify functional correlations among them. GOEAST also provides rigorous statistical tests to enhance the reliability of analysis results. GOEAST is freely accessible at http://omicslab.genetics.ac.cn/GOEAST/

Emotional functioning of adolescents and adults with congenital heart disease: a meta-analysis.

PubMed

Jackson, Jamie L; Misiti, Brian; Bridge, Jeffrey A; Daniels, Curt J; Vannatta, Kathryn

2015-01-01

This study aimed to quantitatively compare findings of emotional functioning across studies of adolescents and adults with congenital heart disease (CHD) through meta-analysis. The current meta-analysis included 22 studies of adolescent and adult survivors of CHD who completed measures of emotional functioning. Effect sizes were represented by Hedge's g. Heterogeneity was calculated and possible moderators (i.e., lesion severity, age, study location, study quality) were examined. Overall, adolescent and adult survivors of CHD did not differ in emotional functioning from healthy controls or normative data. However, significant heterogeneity was found, and there was a trend for degree of lesion severity to moderate emotional functioning. Further analysis of lesion severity indicated that individuals with moderate lesions reported better emotional functioning than controls/normative data. Limitations in existing literature precluded examination of patient age as a moderator. Study location and quality did not explain a significant portion of the variance in effects. Findings suggest that differences in emotional functioning may exist across lesion severities, and individuals with moderately severe lesions are emotionally thriving. Given the diversity within CHD lesion classifications, future studies should include other indicators of disease severity, such as measures of morbidity, to determine how disease may affect emotional functioning among survivors of CHD. Furthermore, authors and journals need to ensure that research is reported in enough detail to facilitate meta-analysis, a critically important tool in answering discrepancies in the literature. © 2014 Wiley Periodicals, Inc.

Comparisons of synthesized and individual reinforcement contingencies during functional analysis.

PubMed

Fisher, Wayne W; Greer, Brian D; Romani, Patrick W; Zangrillo, Amanda N; Owen, Todd M

2016-09-01

Researchers typically modify individual functional analysis (FA) conditions after results are inconclusive (Hanley, Iwata, & McCord, 2003). Hanley, Jin, Vanselow, and Hanratty (2014) introduced a marked departure from this practice, using an interview-informed synthesized contingency analysis (IISCA). In the test condition, they delivered multiple contingencies simultaneously (e.g., attention and escape) after each occurrence of problem behavior; in the control condition, they delivered those same reinforcers noncontingently and continuously. In the current investigation, we compared the results of the IISCA with a more traditional FA in which we evaluated each putative reinforcer individually. Four of 5 participants displayed destructive behavior that was sensitive to the individual contingencies evaluated in the traditional FA. By contrast, none of the participants showed a response pattern consistent with the assumption of the IISCA. We discuss the implications of these findings on the development of accurate and efficient functional analyses. © 2016 Society for the Experimental Analysis of Behavior.

Genomic Encyclopedia of Fungi

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

Grigoriev, Igor

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supportedmore » by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.« less

Executive Functions in Children with Specific Language Impairment: A Meta-Analysis

ERIC Educational Resources Information Center

Pauls, Laura J.; Archibald, Lisa M. D.

2016-01-01

Purpose: Mounting evidence demonstrates deficits in children with specific language impairment (SLI) beyond the linguistic domain. Using meta-analysis, this study examined differences in children with and without SLI on tasks measuring inhibition and cognitive flexibility. Method: Databases were searched for articles comparing children (4-14…

Microhabitat analysis using radiotelemetry locations and polytomous logistic regression

Treesearch

Malcolm P. North; Joel H. Reynolds

1996-01-01

Microhabitat analyses often use discriminant function analysis (DFA) to compare vegetation structures or environmental conditions between sites classified by a study animal's presence or absence. These presence/absence studies make questionable assumptions about the habitat value of the comparison sites and the microhabitat data often violate the DFA's...

Functional Connectivity and Genetic Profile of a “Double-Cortex”-Like Malformation

PubMed Central

Sprugnoli, Giulia; Vatti, Giampaolo; Rossi, Simone; Cerase, Alfonso; Renieri, Alessandra; Mencarelli, Maria A.; Zara, Federico; Rossi, Alessandro; Santarnecchi, Emiliano

2018-01-01

Laminar heterotopia is a rare condition consisting in an extra layer of gray matter under properly migrated cortex; it configures an atypical presentation of periventricular nodular heterotopia (PNH) or a double cortex (DC) syndrome. We conducted an original functional MRI (fMRI) analysis in a drug-resistant epilepsy patient with “double-cortex”-like malformation to reveal her functional connectivity (FC) as well as a wide genetic analysis to identify possible genetic substrates. Heterotopias were segmented into region of interests (ROIs), whose voxel-wise FC was compared to that of (i) its normally migrated counterpart, (ii) its contralateral homologous, and (iii) those of 30 age-matched healthy controls. Extensive genetic analysis was conducted to screen cortical malformations-associated genes. Compared to healthy controls, both laminar heterotopias and the overlying cortex showed significant reduction of FC with the contralateral hemisphere. Two heterozygous variants of uncertain clinical significance were found, involving autosomal recessive disease-causing genes, FAT4 and COL18A1. This first FC analysis of a unique case of “double-cortex”-like malformation revealed a hemispheric connectivity segregation both in the laminar cortex as in the correctly migrated one, with a new pattern of genes’ mutations. Our study suggests the altered FC could have an electrophysiological and functional impact on large-scale brain networks, and the involvement of not yet identified genes in “double-cortex”-like malformation with a possible role of rare variants in recessive genes as pathogenic cofactors. PMID:29946244

FUNCTIONAL ANALYSIS AND TREATMENT OF ELOPEMENT ACROSS TWO SCHOOL SETTINGS

PubMed Central

Lang, Russell; Davis, Tonya; O'Reilly, Mark; Machalicek, Wendy; Rispoli, Mandy; Sigafoos, Jeff; Lancioni, Giulio; Regester, April

2010-01-01

The elopement of a child with Asperger syndrome was assessed using functional analyses and was treated in two school settings (classroom and resource room). Functional analyses indicated that elopement was maintained by access to attention in the resource room and obtaining a preferred activity in the classroom. Attention- and tangible-based interventions were compared in an alternating treatments design in both settings. Results validated the findings of the functional analyses. Implications for the assessment and treatment of elopement are discussed. PMID:20808501

The relationship of renal function to outcome: A post hoc analysis from the EdoxabaN versus warfarin in subjectS UndeRgoing cardiovErsion of Atrial Fibrillation (ENSURE-AF) study.

PubMed

Lip, Gregory Y H; Al-Saady, Naab; Ezekowitz, Michael D; Banach, Maciej; Goette, Andreas

2017-11-01

The ENSURE-AF study (NCT 02072434) of anticoagulation for electrical cardioversion in nonvalvular atrial fibrillation (NVAF) showed comparable low rates of bleeding and thromboembolism between the edoxaban and the enoxaparin-warfarin treatment arms. This post hoc analysis investigated the relationship between renal function and clinical outcomes. ENSURE-AF was a multicenter, PROBE evaluation trial of edoxaban 60 mg, or dose reduced to 30 mg/d for weight≤60 kg, creatinine clearance (CrCl; Cockcroft-Gault) ≤50 mL/min, or concomitant P-glycoprotein inhibitors compared with therapeutically monitored enoxaparin-warfarin in 2,199 NVAF patients undergoing electrical cardioversion. Efficacy and safety outcomes and time in therapeutic range in the warfarin arm were analyzed in relation to CrCl in prespecified ranges ≥15 and ≤30, >30 and ≤50, >50 and <80, and ≥80 mL/min, and an exploratory ≥95-mL/min analysis. A total of 1,095 subjects were randomized to edoxaban and 1,104 to enoxaparin-warfarin. Mean age was 64.3±10 and 64.2±11 years. Mean time in therapeutic range was progressively lower with reducing CrCl strata, being 66.8% in those with CrCl >30 to ≤50 compared with 71.8% in those with CrCl ≥80. The odds ratios for the primary efficacy and safety end points were comparable for the different predefined renal function strata; given the small numbers, the 95% CI included 1.0. In the subset of those with CrCl ≥95, the odds ratios showed consistency with the other CrCl strata. When CrCl was assessed as a continuous variable, there was a nonsignificant trend toward higher major or clinically relevant nonmajor bleeding with reducing CrCl levels, with no significant differences between the 2 treatment arms. When we assessed CrCl at baseline compared with end of treatment, there were no significant differences in CrCl change between the edoxaban and enoxaparin-warfarin arms. The proportions with worsening of renal function (defined as a decrease of >20% from baseline) were similar in the 2 treatment arms. Given the small number of events in ENSURE-AF, no effect of renal (dys)function was demonstrated in comparing edoxaban to enoxaparin-warfarin for cardioversion; efficacy and safety of edoxaban remained consistent even in patients with normal or supranormal renal function. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative study of DFT+U functionals for non-collinear magnetism

NASA Astrophysics Data System (ADS)

Ryee, Siheon; Han, Myung Joon

2018-07-01

We performed comparative analysis for DFT+U functionals to better understand their applicability to non-collinear magnetism. Taking LiNiPO4 and Sr2IrO4 as examples, we investigated the results out of two formalisms based on charge-only density and spin density functional plus U calculations. Our results show that the ground state spin order in terms of tilting angle is strongly dependent on Hund J. In particular, the opposite behavior of canting angles as a function of J is found for LiNiPO4. The dependence on the other physical parameters such as Hubbard U and Slater parameterization is investigated. We also discuss the formal aspects of these functional dependences as well as parameter dependences. The current study provides useful information and important intuition for the first-principles calculation of non-collinear magnetic materials.

VALUING BENEFITS FROM WATER QUALITY IMPROVEMENTS USING KUHN TUCKER MODEL - A COMPARATIVE ANALYSIS ON UTILITY FUNCTIONAL FORMS-

NASA Astrophysics Data System (ADS)

Okuyama, Tadahiro

Kuhn-Tucker model, which has studied in recent years, is a benefit valuation technique using the revealed-preference data, and the feature is to treatvarious patterns of corner solutions flexibly. It is widely known for the benefit calculation using the revealed-preference data that a value of a benefit changes depending on a functional form. However, there are little studies which examine relationship between utility functions and values of benefits in Kuhn-Tucker model. The purpose of this study is to analysis an influence of the functional form to the value of a benefit. Six types of utility functions are employed for benefit calculations. The data of the recreational activity of 26 beaches of Miyagi Prefecture were employed. Calculation results indicated that Phaneuf and Siderelis (2003) and Whitehead et al.(2010)'s functional forms are useful for benefit calculations.

Long-term effects of an intergenerational program on functional capacity in older adults: Results from a seven-year follow-up of the REPRINTS study.

PubMed

Sakurai, Ryota; Yasunaga, Masashi; Murayama, Yoh; Ohba, Hiromi; Nonaka, Kumiko; Suzuki, Hiroyuki; Sakuma, Naoko; Nishi, Mariko; Uchida, Hayato; Shinkai, Shoji; Rebok, George W; Fujiwara, Yoshinori

2016-01-01

Social engagement activities can help older adults maintain mental and physical functioning levels. This study examined the long-term effects of the intergenerational picture-book reading program "REPRINTS" (Research of Productivity by Intergenerational Sympathy) on older adults. After baseline assessment, participants were allowed to decide which condition they wanted to participate in: the REPRINTS intervention or control group involving only assessments. REPRINTS participants participated in group activities that involved playing a hand game and reading picture books to children at kindergartens, elementary schools, and public childcare centers, once every one-two weeks. A follow-up assessment, which focused on functional capacity (i.e., instrumental activities of daily living, intellectual activity, and social function), was conducted after seven years. The analysis included responses from 62 REPRINTS (mean age [SD]=66.2 [5.7]) and 100 control-group participants (mean age [SD]=68.0 [4.7]). A logistic regression analysis examining intervention effects revealed that control-group participants were more likely to reduce intellectual activity and interactions with children compared to REPRINTS participants (p=.013 and .003, respectively). Furthermore, the REPRINTS group maintained greater functional reach compared to the control group (p<.001). However, the REPRINTS group was likely to stay indoors more often, compared to the control group (p=.045). The present study indicates that the REPRINTS intergenerational program has long-term, positive effects that help maintain and promote intellectual activity, physical functioning, and intergenerational exchange, although the effect of the increasing amount of physical activity is unclear. Copyright © 2016. Published by Elsevier Ireland Ltd.

Relationship between Speech Production and Perception in People Who Stutter

PubMed Central

Lu, Chunming; Long, Yuhang; Zheng, Lifen; Shi, Guang; Liu, Li; Ding, Guosheng; Howell, Peter

2016-01-01

Speech production difficulties are apparent in people who stutter (PWS). PWS also have difficulties in speech perception compared to controls. It is unclear whether the speech perception difficulties in PWS are independent of, or related to, their speech production difficulties. To investigate this issue, functional MRI data were collected on 13 PWS and 13 controls whilst the participants performed a speech production task and a speech perception task. PWS performed poorer than controls in the perception task and the poorer performance was associated with a functional activity difference in the left anterior insula (part of the speech motor area) compared to controls. PWS also showed a functional activity difference in this and the surrounding area [left inferior frontal cortex (IFC)/anterior insula] in the production task compared to controls. Conjunction analysis showed that the functional activity differences between PWS and controls in the left IFC/anterior insula coincided across the perception and production tasks. Furthermore, Granger Causality Analysis on the resting-state fMRI data of the participants showed that the causal connection from the left IFC/anterior insula to an area in the left primary auditory cortex (Heschl’s gyrus) differed significantly between PWS and controls. The strength of this connection correlated significantly with performance in the perception task. These results suggest that speech perception difficulties in PWS are associated with anomalous functional activity in the speech motor area, and the altered functional connectivity from this area to the auditory area plays a role in the speech perception difficulties of PWS. PMID:27242487

Assessment of lung function in a large cohort of patients with acromegaly.

PubMed

Störmann, Sylvère; Gutt, Bodo; Roemmler-Zehrer, Josefine; Bidlingmaier, Martin; Huber, Rudolf M; Schopohl, Jochen; Angstwurm, Matthias W

2017-07-01

Acromegaly is associated with increased mortality due to respiratory disease. To date, lung function in patients with acromegaly has only been assessed in small studies, with contradicting results. We assessed lung function parameters in a large cohort of patients with acromegaly. Lung function of acromegaly patients was prospectively assessed using spirometry, blood gas analysis and body plethysmography. Biochemical indicators of acromegaly were assessed through measurement of growth hormone and IGF-I levels. This study was performed at the endocrinology outpatient clinic of a tertiary referral center in Germany. We prospectively tested lung function of 109 acromegaly patients (53 male, 56 female; aged 24-82 years; 80 with active acromegaly) without severe acute or chronic pulmonary disease. We compared lung volume, air flow, airway resistance and blood gases to normative data. Acromegaly patients had greater lung volumes (maximal vital capacity, intra-thoracic gas volume and residual volume: P  < 0.001, total lung capacity: P  = 0.006) and showed signs of small airway obstruction (reduced maximum expiratory flow when 75% of the forced vital capacity (FVC) has been exhaled: P  < 0.001, lesser peak expiratory flow: P  = 0.01). There was no significant difference between active and inactive acromegaly. Female patients had significantly altered lung function in terms of subclinical airway obstruction. In our cross-sectional analysis of lung function in 109 patients with acromegaly, lung volumes were increased compared to healthy controls. Additionally, female patients showed signs of subclinical airway obstruction. There was no difference between patients with active acromegaly compared with patients biochemically in remission. © 2017 European Society of Endocrinology.

The interval testing procedure: A general framework for inference in functional data analysis.

PubMed

Pini, Alessia; Vantini, Simone

2016-09-01

We introduce in this work the Interval Testing Procedure (ITP), a novel inferential technique for functional data. The procedure can be used to test different functional hypotheses, e.g., distributional equality between two or more functional populations, equality of mean function of a functional population to a reference. ITP involves three steps: (i) the representation of data on a (possibly high-dimensional) functional basis; (ii) the test of each possible set of consecutive basis coefficients; (iii) the computation of the adjusted p-values associated to each basis component, by means of a new strategy here proposed. We define a new type of error control, the interval-wise control of the family wise error rate, particularly suited for functional data. We show that ITP is provided with such a control. A simulation study comparing ITP with other testing procedures is reported. ITP is then applied to the analysis of hemodynamical features involved with cerebral aneurysm pathology. ITP is implemented in the fdatest R package. © 2016, The International Biometric Society.

Erectile dysfunction in older male stroke patients: correlation between side of hemiplegia and erectile function.

PubMed

Sikiru, Lamina; Shmaila, Hanif; Yusuf, Gagarawa Saidu

2009-06-01

This study was conducted to determine the effects of hemiplegia on erectile function in stroke patients. One hundred and five stroke patients grouped into left (61.78 +/- 7.79 years) and 55 right hemiplegic (62.11 +/- 9.32 years) and 40 age-matched controls (64.00 +/- 8.53 years). The International Index of Erectile Function questionnaire was used for data collection. One way analysis of variance and Spearman correlation tests were used in data analysis. Erectile function was significantly decreased in the both right (IIEF-5, 7.55 +/- 4.07) and left hemiplegic groups (IIEF-5, 10.40 +/- 5.70) compared with the control group (IIEF-5, 20.50 +/- 4.2 7) p < 0.05. Side of hemiplegia significantly correlated with erectile dysfunction at p < 0.01. Conclusively, stroke mostly affects erectile function of right hemiplegia.

Comparative gait analysis of ankle arthrodesis and arthroplasty: initial findings of a prospective study.

PubMed

Hahn, Michael E; Wright, Elise S; Segal, Ava D; Orendurff, Michael S; Ledoux, William R; Sangeorzan, Bruce J

2012-04-01

Little is known about functional outcomes of ankle arthroplasty compared with arthrodesis. This study compared pre-surgical and post-surgical gait measures in both patient groups. Eighteen patients with end-stage ankle arthritis participated in an ongoing longitudinal study (pre-surgery, 12 months post-surgery) involving gait analysis, assessment of pain and physical function. Outcome measures included temporal-distance, kinematic and kinetic data, the Short Form 36 (SF-36) body pain score, and average daily step count. A mixed effects linear model was used to detect effects of surgical group (arthrodesis and arthroplasty, n = 9 each) with walking speed as a covariate (α = 0.05). Both groups were similar in demographics and anthropometrics. Followup time was the same for each group. There were no complications in either group. Pain decreased (p < 0.001) and gait function improved (gait velocity, p = 0.02; stride length, p = 0.035) in both groups. Neither group increased average daily step count. Joint range of motion (ROM) differences were observed between groups after surgery (increased hip ROM in arthrodesis, p = 0.001; increased ankle ROM in arthroplasty, p = 0.036). Peak plantar flexor moment increased in arthrodesis patients and decreased in arthroplasty patients (p = 0.042). Initial findings of this ongoing clinical study indicate pain reduction and improved gait function 12 months after surgery for both treatments. Arthroplasty appears to regain more natural ankle joint function, with increased ROM. Long-term follow up should may reveal more clinically meaningful differences.

Disrupted functional brain connectivity in partial epilepsy: a resting-state fMRI study.

PubMed

Luo, Cheng; Qiu, Chuan; Guo, Zhiwei; Fang, Jiajia; Li, Qifu; Lei, Xu; Xia, Yang; Lai, Yongxiu; Gong, Qiyong; Zhou, Dong; Yao, Dezhong

2011-01-01

Examining the spontaneous activity to understand the neural mechanism of brain disorder is a focus in recent resting-state fMRI. In the current study, to investigate the alteration of brain functional connectivity in partial epilepsy in a systematical way, two levels of analyses (functional connectivity analysis within resting state networks (RSNs) and functional network connectivity (FNC) analysis) were carried out on resting-state fMRI data acquired from the 30 participants including 14 healthy controls(HC) and 16 partial epilepsy patients. According to the etiology, all patients are subdivided into temporal lobe epilepsy group (TLE, included 7 patients) and mixed partial epilepsy group (MPE, 9 patients). Using group independent component analysis, eight RSNs were identified, and selected to evaluate functional connectivity and FNC between groups. Compared with the controls, decreased functional connectivity within all RSNs was found in both TLE and MPE. However, dissociating patterns were observed within the 8 RSNs between two patient groups, i.e, compared with TLE, we found decreased functional connectivity in 5 RSNs increased functional connectivity in 1 RSN, and no difference in the other 2 RSNs in MPE. Furthermore, the hierarchical disconnections of FNC was found in two patient groups, in which the intra-system connections were preserved for all three subsystems while the lost connections were confined to intersystem connections in patients with partial epilepsy. These findings may suggest that decreased resting state functional connectivity and disconnection of FNC are two remarkable characteristics of partial epilepsy. The selective impairment of FNC implicated that it is unsuitable to understand the partial epilepsy only from global or local perspective. We presumed that studying epilepsy in the multi-perspective based on RSNs may be a valuable means to assess the functional changes corresponding to specific RSN and may contribute to the understanding of the neuro-pathophysiological mechanism of epilepsy.

Comparative analysis of Homo sapiens and Mus musculus cyclin-dependent kinase (CDK) inhibitor genes p16 (MTS1) and p15 (MTS2).

PubMed

Jiang, P; Stone, S; Wagner, R; Wang, S; Dayananth, P; Kozak, C A; Wold, B; Kamb, A

1995-12-01

Cyclin-dependent kinase inhibitors are a growing family of molecules that regulate important transitions in the cell cycle. At least one of these molecules, p16, has been implicated in human tumorigenesis while its close homolog, p15, is induced by cell contact and transforming growth factor-beta (TGF-beta). To investigate the evolutionary and functional features of p15 and p16, we have isolated mouse (Mus musculus) homologs of each gene. Comparative analysis of these sequences provides evidence that the genes have similar functions in mouse and human. In addition, the comparison suggests that a gene conversion event is part of the evolution of the human p15 and p16 genes.

Evaluation of Contact Heat Transfer Coefficient and Phase Transformation during Hot Stamping of a Hat-Type Part

PubMed Central

Kim, Heung-Kyu; Lee, Seong Hyeon; Choi, Hyunjoo

2015-01-01

Using an inverse analysis technique, the heat transfer coefficient on the die-workpiece contact surface of a hot stamping process was evaluated as a power law function of contact pressure. This evaluation was to determine whether the heat transfer coefficient on the contact surface could be used for finite element analysis of the entire hot stamping process. By comparing results of the finite element analysis and experimental measurements of the phase transformation, an evaluation was performed to determine whether the obtained heat transfer coefficient function could provide reasonable finite element prediction for workpiece properties affected by the hot stamping process. PMID:28788046

Meta-analysis of executive functioning in ecstasy/polydrug users.

PubMed

Roberts, C A; Jones, A; Montgomery, C

2016-06-01

Ecstasy/3,4-methylenedioxymethamphetamine (MDMA) use is proposed to cause damage to serotonergic (5-HT) axons in humans. Therefore, users should show deficits in cognitive processes that rely on serotonin-rich, prefrontal areas of the brain. However, there is inconsistency in findings to support this hypothesis. The aim of the current study was to examine deficits in executive functioning in ecstasy users compared with controls using meta-analysis. We identified k = 39 studies, contributing 89 effect sizes, investigating executive functioning in ecstasy users and polydrug-using controls. We compared function-specific task performance in 1221 current ecstasy users and 1242 drug-using controls, from tasks tapping the executive functions - updating, switching, inhibition and access to long-term memory. The significant main effect demonstrated overall executive dysfunction in ecstasy users [standardized mean difference (SMD) = -0.18, 95% confidence interval (CI) -0.26 to -0.11, Z = 5.05, p < 0.001, I 2 = 82%], with a significant subgroup effect (χ 2 = 22.06, degrees of freedom = 3, p < 0.001, I 2 = 86.4%) demonstrating differential effects across executive functions. Ecstasy users showed significant performance deficits in access (SMD = -0.33, 95% CI -0.46 to -0.19, Z = 4.72, p < 0.001, I 2 = 74%), switching (SMD = -0.19, 95% CI -0.36 to -0.02, Z = 2.16, p < 0.05, I 2 = 85%) and updating (SMD = -0.26, 95% CI -0.37 to -0.15, Z = 4.49, p < 0.001, I 2 = 82%). No differences were observed in inhibitory control. We conclude that this is the most comprehensive analysis of executive function in ecstasy users to date and provides a behavioural correlate of potential serotonergic neurotoxicity.

Upgrading from VVI to DDD pacing Mode during elective replacement of pulse generator: a comparative clinical-functional analysis.

PubMed

Teno, Luiz Antonio Castilho; Costa, Roberto; Martinelli Filho, Martino; Castilho, Fabian Cecchi Teno; Ruiz, Ivan

2007-02-01

Evaluate the clinical and functional behavior of the ventricular and atrioventricular stimulation modes in the elective replacement of pulse generator in patients with chagasic cardiopathy and atrioventricular block. Twenty-seven patients under ventricular and atrioventricular stimulation were comparatively evaluated at the beginning of the study, and alternately in ventricular and atrioventricular modes in two 90-day phases, with regard to: the clinical behavior evaluated according to quality of life and functional class, and the functional behavior evaluated by transthoracic echocardiography and the six-minute walk test. The statistical analysis was performed with patients at baseline, and under ventricular and atrioventricular modes, using the chi-square test and the repeated measures analysis of variance, and taking into consideration a 0.05 level of significance. The mean quality-of-life scores were: functional capacity (VVI 71.3+/-18.2 , DDD 69.3+/-20.4); overall health status (VVI 68.1+/-21.8, DDD 69.4+/-19.4) and vitality (VVI 64.8+/-24.6 , DDD 67.6+/-25.5); on echocardiography: LVEF (VVI 52.5+/-12.8 , DDD 51.8+/-14.9), LVDD (VVI 53.0+/-7.7 , DDD 42.4+/-7.8), LA (VVI 38.6+/-5.4 DDD 38.5+/-5.1), and in the six-minute walk test: distance walked (VVI 463.4+/-84.7, DDD 462.6+/-63.4). There were four cases of complications, three of them associated with the change in stimulation mode. This study showed no differences between the two stimulation modes in the clinical behavior assessed by quality of life and functional class, and in the functional behavior, evaluated according to the ecochardiographic findings and the six-minute walk test.

eShadow: A tool for comparing closely related sequences

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

Ovcharenko, Ivan; Boffelli, Dario; Loots, Gabriela G.

2004-01-15

Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human to primate or mouse to rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualizationmore » of the resulting conservation profile. eShadow also includes a versatile optimization module capable of training the underlying Hidden Markov Model to differentially predict functional sequences. This module grants the tool high flexibility in the analysis of multiple sequence alignments and in comparing sequences with different divergence rates. Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements. The eShadow tool is publicly available at http://eshadow.dcode.org/« less

Lookup Tables Versus Stacked Rasch Analysis in Comparing Pre- and Postintervention Adult Strabismus-20 Data.

PubMed

Leske, David A; Hatt, Sarah R; Liebermann, Laura; Holmes, Jonathan M

2016-02-01

We compare two methods of analysis for Rasch scoring pre- to postintervention data: Rasch lookup table versus de novo stacked Rasch analysis using the Adult Strabismus-20 (AS-20). One hundred forty-seven subjects completed the AS-20 questionnaire prior to surgery and 6 weeks postoperatively. Subjects were classified 6 weeks postoperatively as "success," "partial success," or "failure" based on angle and diplopia status. Postoperative change in AS-20 scores was compared for all four AS-20 domains (self-perception, interactions, reading function, and general function) overall and by success status using two methods: (1) applying historical Rasch threshold measures from lookup tables and (2) performing a stacked de novo Rasch analysis. Change was assessed by analyzing effect size, improvement exceeding 95% limits of agreement (LOA), and score distributions. Effect sizes were similar for all AS-20 domains whether obtained from lookup tables or stacked analysis. Similar proportions exceeded 95% LOAs using lookup tables versus stacked analysis. Improvement in median score was observed for all AS-20 domains using lookup tables and stacked analysis ( P < 0.0001 for all comparisons). The Rasch-scored AS-20 is a responsive and valid instrument designed to measure strabismus-specific health-related quality of life. When analyzing pre- to postoperative change in AS-20 scores, Rasch lookup tables and de novo stacked Rasch analysis yield essentially the same results. We describe a practical application of lookup tables, allowing the clinician or researcher to score the Rasch-calibrated AS-20 questionnaire without specialized software.

Lookup Tables Versus Stacked Rasch Analysis in Comparing Pre- and Postintervention Adult Strabismus-20 Data

PubMed Central

Leske, David A.; Hatt, Sarah R.; Liebermann, Laura; Holmes, Jonathan M.

2016-01-01

Purpose We compare two methods of analysis for Rasch scoring pre- to postintervention data: Rasch lookup table versus de novo stacked Rasch analysis using the Adult Strabismus-20 (AS-20). Methods One hundred forty-seven subjects completed the AS-20 questionnaire prior to surgery and 6 weeks postoperatively. Subjects were classified 6 weeks postoperatively as “success,” “partial success,” or “failure” based on angle and diplopia status. Postoperative change in AS-20 scores was compared for all four AS-20 domains (self-perception, interactions, reading function, and general function) overall and by success status using two methods: (1) applying historical Rasch threshold measures from lookup tables and (2) performing a stacked de novo Rasch analysis. Change was assessed by analyzing effect size, improvement exceeding 95% limits of agreement (LOA), and score distributions. Results Effect sizes were similar for all AS-20 domains whether obtained from lookup tables or stacked analysis. Similar proportions exceeded 95% LOAs using lookup tables versus stacked analysis. Improvement in median score was observed for all AS-20 domains using lookup tables and stacked analysis (P < 0.0001 for all comparisons). Conclusions The Rasch-scored AS-20 is a responsive and valid instrument designed to measure strabismus-specific health-related quality of life. When analyzing pre- to postoperative change in AS-20 scores, Rasch lookup tables and de novo stacked Rasch analysis yield essentially the same results. Translational Relevance We describe a practical application of lookup tables, allowing the clinician or researcher to score the Rasch-calibrated AS-20 questionnaire without specialized software. PMID:26933524

Effects of Aquatic Therapy and Land-Based Therapy versus Land-Based Therapy Alone on Range of Motion, Edema, and Function after Hip or Knee Replacement: A Systematic Review and Meta-analysis.

PubMed

Gibson, Alison J; Shields, Nora

2015-01-01

To determine whether aquatic therapy in combination with land-based therapy improves patient outcomes after hip or knee arthroplasty compared with land-based therapy alone. For this systematic review, six online databases (MEDLINE, CINAHL, AMED, EMBASE, Cochrane, and PEDro) were searched from the earliest date available until September 2013. Controlled trials published in English in a peer-reviewed journal that compared aquatic therapy in combination with land-based therapy with land-based therapy alone were included; trial quality was assessed using the PEDro scale. Data were presented as standardized mean differences (SMDs), their associated 95% CIs, and meta-analyses. Three small trials of moderate quality were included in the qualitative analysis. Meta-analysis of two of these studies found moderate-quality evidence that aquatic therapy in combination with land-based therapy improves functional outcomes (SMD=0.53; 95% CI, 0.03-1.03), knee range of motion (measured in knee or hip arthroplasty; SMD=0.78; 95% CI, 0.27-1.29), and edema (SMD=-0.66; 95% CI, -1.16 to -0.15) compared with land-based therapy alone. The results for improved functional outcomes were not considered clinically significant. It is not possible to draw confident conclusions from this review because of the small number of studies of limited quality and the modest differences found. Further studies of sound methodological quality are required to confirm the results. Economic analysis alongside randomized controlled trials is needed to examine the cost-effectiveness of these clinical outcomes.

Endovascular Therapy is Effective and Safe for Patients with Severe Ischemic Stroke: Pooled Analysis of IMS III and MR CLEAN Data

PubMed Central

Broderick, Joseph P.; Berkhemer, Olvert A.; Palesch, Yuko Y.; Dippel, Diederik W.J.; Foster, Lydia D.; Roos, Yvo B.W.E.M.; van der Lugt, Aad; Tomsick, Thomas A.; Majoie, Charles B.L.M.; van Zwam, Wim H.; Demchuk, Andrew M.; van Oostenbrugge, Robert J.; Khatri, Pooja; Lingsma, Hester F.; Hill, Michael D.; Roozenbeek, Bob; Jauch, Edward C.; Jovin, Tudor G.; Yan, Bernard; von Kummer, Rüdiger; Molina, Carlos A.; Goyal, Mayank; Schonewille, Wouter J.; Mazighi, Mikael; Engelter, Stefan T.; Anderson, Craig S.; Spilker, Judith; Carrozzella, Janice; Ryckborst, Karla J.; Janis, L. Scott; Simpson, Kit

2015-01-01

Background and Purpose We assessed the effect of endovascular treatment in acute ischemic stroke patients with severe neurological deficit (NIHSS ≥20) following a pre-specified analysis plan. Methods The pooled analysis of the IMS III and MR CLEAN trial included participants with an NIHSS ≥20 prior to intravenous (IV) t-PA treatment (IMS III) or randomization (MR CLEAN) who were treated with IV t-PA ≤ 3 hours of stroke onset. Our hypothesis was that participants with severe stroke randomized to endovascular therapy following IV t-PA would have improved 90-day outcome (distribution of modified Rankin scale [mRS] scores), as compared to those who received IV t-PA alone. Results Among 342 participants in the pooled analysis (194 from IMS III, 148 from MR CLEAN), an ordinal logistic regression model showed that the endovascular group had superior 90-day outcome compared to the IV t-PA group (adjusted odds ratio [aOR] 1.78; 95% confidence interval [CI] 1.20-2.66). In the logistic regression model of the dichotomous outcome (mRS 0-2, or ‘functional independence’), the endovascular group had superior outcomes (aOR 1.97; 95% CI 1.09-3.56). Functional independence (mRS ≤2) at 90 days was 25% in the endovascular group as compared to 14% in the IV t-PA group. Conclusions Endovascular therapy following IV t-PA within 3 hours of symptom onset improves functional outcome at 90 days after severe ischemic stroke. PMID:26486865

Accuracy and efficiency of computer-aided anatomical analysis using 3D visualization software based on semi-automated and automated segmentations.

PubMed

An, Gao; Hong, Li; Zhou, Xiao-Bing; Yang, Qiong; Li, Mei-Qing; Tang, Xiang-Yang

2017-03-01

We investigated and compared the functionality of two 3D visualization software provided by a CT vendor and a third-party vendor, respectively. Using surgical anatomical measurement as baseline, we evaluated the accuracy of 3D visualization and verified their utility in computer-aided anatomical analysis. The study cohort consisted of 50 adult cadavers fixed with the classical formaldehyde method. The computer-aided anatomical analysis was based on CT images (in DICOM format) acquired by helical scan with contrast enhancement, using a CT vendor provided 3D visualization workstation (Syngo) and a third-party 3D visualization software (Mimics) that was installed on a PC. Automated and semi-automated segmentations were utilized in the 3D visualization workstation and software, respectively. The functionality and efficiency of automated and semi-automated segmentation methods were compared. Using surgical anatomical measurement as a baseline, the accuracy of 3D visualization based on automated and semi-automated segmentations was quantitatively compared. In semi-automated segmentation, the Mimics 3D visualization software outperformed the Syngo 3D visualization workstation. No significant difference was observed in anatomical data measurement by the Syngo 3D visualization workstation and the Mimics 3D visualization software (P>0.05). Both the Syngo 3D visualization workstation provided by a CT vendor and the Mimics 3D visualization software by a third-party vendor possessed the needed functionality, efficiency and accuracy for computer-aided anatomical analysis. Copyright © 2016 Elsevier GmbH. All rights reserved.

Bayesian inference on risk differences: an application to multivariate meta-analysis of adverse events in clinical trials.

PubMed

Chen, Yong; Luo, Sheng; Chu, Haitao; Wei, Peng

2013-05-01

Multivariate meta-analysis is useful in combining evidence from independent studies which involve several comparisons among groups based on a single outcome. For binary outcomes, the commonly used statistical models for multivariate meta-analysis are multivariate generalized linear mixed effects models which assume risks, after some transformation, follow a multivariate normal distribution with possible correlations. In this article, we consider an alternative model for multivariate meta-analysis where the risks are modeled by the multivariate beta distribution proposed by Sarmanov (1966). This model have several attractive features compared to the conventional multivariate generalized linear mixed effects models, including simplicity of likelihood function, no need to specify a link function, and has a closed-form expression of distribution functions for study-specific risk differences. We investigate the finite sample performance of this model by simulation studies and illustrate its use with an application to multivariate meta-analysis of adverse events of tricyclic antidepressants treatment in clinical trials.

Genome-wide comparative analysis of four Indian Drosophila species.

PubMed

Mohanty, Sujata; Khanna, Radhika

2017-12-01

Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics. The comparative genomics analysis, e.g. gene predictions and annotations, functional and orthogroup analysis of coding sequences and genome wide SNP distribution were performed. The whole genome of Zaprionus indianus of Indian origin published earlier by us and the genome sequences of previously sequenced 12 Drosophila species available in the NCBI database were included in the analysis. The present work is a part of our ongoing genomics project of Indian Drosophila species.

Efficacy and safety profile of xanthines in COPD: a network meta-analysis.

PubMed

Cazzola, Mario; Calzetta, Luigino; Barnes, Peter J; Criner, Gerard J; Martinez, Fernando J; Papi, Alberto; Gabriella Matera, Maria

2018-06-30

Theophylline can still have a role in the management of stable chronic obstructive pulmonary disease (COPD), but its use remains controversial, mainly due to its narrow therapeutic window. Doxofylline, another xanthine, is an effective bronchodilator and displays a better safety profile than theophylline. Therefore, we performed a quantitative synthesis to compare the efficacy and safety profile of different xanthines in COPD.The primary end-point of this meta-analysis was the impact of xanthines on lung function. In addition, we assessed the risk of adverse events by normalising data on safety as a function of person-weeks. Data obtained from 998 COPD patients were selected from 14 studies and meta-analysed using a network approach.The combined surface under the cumulative ranking curve (SUCRA) analysis of efficacy (change from baseline in forced expiratory volume in 1 s) and safety (risk of adverse events) showed that doxofylline was superior to aminophylline (comparable efficacy and significantly better safety), bamiphylline (significantly better efficacy and comparable safety), and theophylline (comparable efficacy and significantly better safety).Considering the overall efficacy/safety profile of the investigated agents, the results of this quantitative synthesis suggest that doxofylline seems to be the best xanthine for the treatment of COPD. Copyright ©ERS 2018.

Creep analysis of silicone for podiatry applications.

PubMed

Janeiro-Arocas, Julia; Tarrío-Saavedra, Javier; López-Beceiro, Jorge; Naya, Salvador; López-Canosa, Adrián; Heredia-García, Nicolás; Artiaga, Ramón

2016-10-01

This work shows an effective methodology to characterize the creep-recovery behavior of silicones before their application in podiatry. The aim is to characterize, model and compare the creep-recovery properties of different types of silicone used in podiatry orthotics. Creep-recovery phenomena of silicones used in podiatry orthotics is characterized by dynamic mechanical analysis (DMA). Silicones provided by Herbitas are compared by observing their viscoelastic properties by Functional Data Analysis (FDA) and nonlinear regression. The relationship between strain and time is modeled by fixed and mixed effects nonlinear regression to compare easily and intuitively podiatry silicones. Functional ANOVA and Kohlrausch-Willians-Watts (KWW) model with fixed and mixed effects allows us to compare different silicones observing the values of fitting parameters and their physical meaning. The differences between silicones are related to the variations of breadth of creep-recovery time distribution and instantaneous deformation-permanent strain. Nevertheless, the mean creep-relaxation time is the same for all the studied silicones. Silicones used in palliative orthoses have higher instantaneous deformation-permanent strain and narrower creep-recovery distribution. The proposed methodology based on DMA, FDA and nonlinear regression is an useful tool to characterize and choose the proper silicone for each podiatry application according to their viscoelastic properties. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Impact of Massage Therapy on Function in Pain Populations-A Systematic Review and Meta-Analysis of Randomized Controlled Trials: Part III, Surgical Pain Populations.

PubMed

Boyd, Courtney; Crawford, Cindy; Paat, Charmagne F; Price, Ashley; Xenakis, Lea; Zhang, Weimin

2016-09-01

Pain is multi-dimensional and may be better addressed through a holistic, biopsychosocial approach. Massage therapy is commonly practiced among patients seeking pain management; however, its efficacy is unclear. This systematic review and meta-analysis is the first to rigorously assess the quality of the evidence for massage therapy's efficacy in treating pain, function-related, and health-related quality of life outcomes in surgical pain populations. Key databases were searched from inception through February 2014. Eligible randomized controlled trials were assessed for methodological quality using SIGN 50 Checklist. Meta-analysis was applied at the outcome level. A professionally diverse steering committee interpreted the results to develop recommendations. Twelve high quality and four low quality studies were included in the review. Results indicate massage therapy is effective for treating pain [standardized mean difference (SMD) = -0.79] and anxiety (SMD = -0.57) compared to active comparators. Based on the available evidence, weak recommendations are suggested for massage therapy, compared to active comparators for reducing pain intensity/severity and anxiety in patients undergoing surgical procedures. This review also discusses massage therapy safety, challenges within this research field, how to address identified research gaps, and next steps for future research. © 2016 American Academy of Pain Medicine.

Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function.

PubMed

Di, Chao; Xu, Wenying; Su, Zhen; Yuan, Joshua S

2010-10-07

PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out to dissect the PHB gene function. The conserved gene evolution indicated that the study in the model species can be translated to human and mammalian studies.

A Wavelet Support Vector Machine Combination Model for Singapore Tourist Arrival to Malaysia

NASA Astrophysics Data System (ADS)

Rafidah, A.; Shabri, Ani; Nurulhuda, A.; Suhaila, Y.

2017-08-01

In this study, wavelet support vector machine model (WSVM) is proposed and applied for monthly data Singapore tourist time series prediction. The WSVM model is combination between wavelet analysis and support vector machine (SVM). In this study, we have two parts, first part we compare between the kernel function and second part we compare between the developed models with single model, SVM. The result showed that kernel function linear better than RBF while WSVM outperform with single model SVM to forecast monthly Singapore tourist arrival to Malaysia.

Sensing the effects of mouth breathing by using 3-tesla MRI

NASA Astrophysics Data System (ADS)

Park, Chan-A.; Kang, Chang-Ki

2017-06-01

We investigated the effects of mouth breathing and typical nasal breathing on brain function by using blood-oxygenation-level-dependent (BOLD) functional magnetic resonance imaging (fMRI). The study had two parts: the first test was a simple contrast between mouth and nasal breathing, and the second test involved combined breathing modes, e.g., mouth inspiration and nasal expiration. Eleven healthy participants performed the combined breathing task while undergoing 3T fMRI. In the group-level analysis, contrast images acquired by using an individual participantlevel analysis were processed using the one-sample t test. We also conducted a region-of-interest analysis comparing signal intensity changes between the breathing modes; the region was selected using an automated anatomical labeling map. The results demonstrated that the BOLD signal in the hippocampus and brainstem was significantly decreased in mouth breathing relative to nasal breathing. On the other hand, both the precentral and postcentral gyri showed activation that was more significant in mouth breathing compared to nasal breathing. This study suggests that the BOLD activity patterns between mouth and nasal breathing may be induced differently, especially in the hippocampus, which could provide clues to explain the effects on brain cognitive function due to mouth breathing.

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison.

PubMed

Dai, Qi; Yang, Yanchun; Wang, Tianming

2008-10-15

Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use the information on the k-word distributions, Markov model or both. Motivated by adding k-word distributions to Markov model directly, we investigated two novel statistical measures for sequence comparison, called wre.k.r and S2.k.r. The proposed measures were tested by similarity search, evaluation on functionally related regulatory sequences and phylogenetic analysis. This offers the systematic and quantitative experimental assessment of our measures. Moreover, we compared our achievements with these based on alignment or alignment-free. We grouped our experiments into two sets. The first one, performed via ROC (receiver operating curve) analysis, aims at assessing the intrinsic ability of our statistical measures to search for similar sequences from a database and discriminate functionally related regulatory sequences from unrelated sequences. The second one aims at assessing how well our statistical measure is used for phylogenetic analysis. The experimental assessment demonstrates that our similarity measures intending to incorporate k-word distributions into Markov model are more efficient.

First Functional and Mutational Analysis of Group 3 N-Acetylneuraminate Lyases from Lactobacillus antri and Lactobacillus sakei 23K

PubMed Central

García-García, María Inmaculada; Gil-Ortiz, Fernando; García-Carmona, Francisco; Sánchez-Ferrer, Álvaro

2014-01-01

N-acetyl neuraminate lyases (NALs) catalyze the reversible aldol cleavage of N-acetyl neuraminic acid (Neu5Ac) to pyruvate and N-acetyl-D-mannosamine (ManNAc). Previous phylogenetic studies divided NALs into four different groups. Groups 1 and 2 have been well characterized at both kinetic and molecular levels, but no NAL from group 3 has been studied to date. In this work, a functional characterization of two group 3 members was performed using the recombinant NALs from Lactobacillus antri and Lactobacillus sakei 23K, revealing an optimal pH of between 6.0 and 7.0, low stability at basic pHs (>8.0), low optimal temperatures and, especially, low catalytic efficiency compared with their counterparts in group 1 and 2. The mutational analysis carried out showed that a plausible molecular reason for the low activity shown by Lactobacillus antri and Lactobacillus sakei 23k NALs compared with group 1 and 2 NALs could be the relatively small sugar-binding pocket they contain. A functional divergence analysis concluding that group 3 is more closely related to group 2 than to group 1. PMID:24817128

Analysis of the respirogram phase of Korean wrestling athletes compared with nonathletes for sports physiotherapy research

PubMed Central

Shin, Yong-Sub; Yang, Seung-Min; Kim, Mee-Young; Lee, Lim-Kyu; Park, Byoung-Sun; Lee, Won-Deok; Noh, Ji-Woong; Kim, Ju-Hyun; Lee, Jeong-Uk; Kwak, Taek-Yong; Lee, Tae-Hyun; Kim, Ju-Young; Park, Jaehong; Kim, Junghwan

2016-01-01

[Purpose] Respiratory function is important for patients including athletes who require physical therapy for respiratory dysfunction. The purpose of the present study was to analyze the differences in the respirograms between Korean wrestling athletes and nonathletes according to phase for the study of sports physiotherapy. [Subjects and Methods] Respiratory function was measured using spirometry in both the athletes and nonathletes while they were in a sitting position. [Results] Spirometry parameters in the athletes were significantly higher than in the nonathletes. In respirogram phasic analysis, the expiratory area and total area of forced vital capacity were significantly increased in the athletes compared with the nonathletes. The slopes of the forced vital capacity for athletes at slopes 1, 2, and 3 of the A area were significantly increased. In correlative analysis, chest circumference was significantly correlated with slope 3 of the A area of the forced vital capacity. [Conclusion] The results suggest that the differences in changes in the phases of the respirogram between the Korean wrestling athletes and nonathletes may in part contribute to our understanding of respiratory function in sports physiotherapy research. PMID:27064260

Architectural and Functional Design and Evaluation of E-Learning VUIS Based on the Proposed IEEE LTSA Reference Model.

ERIC Educational Resources Information Center

O'Droma, Mairtin S.; Ganchev, Ivan; McDonnell, Fergal

2003-01-01

Presents a comparative analysis from the Institute of Electrical and Electronics Engineers (IEEE) Learning Technology Standards Committee's (LTSC) of the architectural and functional design of e-learning delivery platforms and applications, e-learning course authoring tools, and learning management systems (LMSs), with a view of assessing how…

Web-Based OPACs in Indian Academic Libraries: A Functional Comparison

ERIC Educational Resources Information Center

Kapoor, Kanta; Goyal, O. P.

2007-01-01

Purpose: The paper seeks to provide a comparative analysis of the functionality of five web-based OPACs available in Indian academic libraries. Design/methodology/approach: Same-topic searches were carried out by three researchers on the web-based OPACs of Libsys, VTLS's iPortal, NewGenLib, Troodon, and Alice for Windows, implemented in five…

Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

PubMed

Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

2016-04-01

To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes.

Functional Heart Valve Scaffolds Obtained by Complete Decellularization of Porcine Aortic Roots in a Novel Differential Pressure Gradient Perfusion System

PubMed Central

Sierad, Leslie Neil; Shaw, Eliza Laine; Bina, Alexander; Brazile, Bryn; Rierson, Nicholas; Patnaik, Sourav S.; Kennamer, Allison; Odum, Rebekah; Cotoi, Ovidiu; Terezia, Preda; Branzaniuc, Klara; Smallwood, Harrison; Deac, Radu; Egyed, Imre; Pavai, Zoltan; Szanto, Annamaria; Harceaga, Lucian; Suciu, Horatiu; Raicea, Victor; Olah, Peter; Simionescu, Agneta; Liao, Jun; Movileanu, Ionela

2015-01-01

There is a great need for living valve replacements for patients of all ages. Such constructs could be built by tissue engineering, with perspective of the unique structure and biology of the aortic root. The aortic valve root is composed of several different tissues, and careful structural and functional consideration has to be given to each segment and component. Previous work has shown that immersion techniques are inadequate for whole-root decellularization, with the aortic wall segment being particularly resistant to decellularization. The aim of this study was to develop a differential pressure gradient perfusion system capable of being rigorous enough to decellularize the aortic root wall while gentle enough to preserve the integrity of the cusps. Fresh porcine aortic roots have been subjected to various regimens of perfusion decellularization using detergents and enzymes and results compared to immersion decellularized roots. Success criteria for evaluation of each root segment (cusp, muscle, sinus, wall) for decellularization completeness, tissue integrity, and valve functionality were defined using complementary methods of cell analysis (histology with nuclear and matrix stains and DNA analysis), biomechanics (biaxial and bending tests), and physiologic heart valve bioreactor testing (with advanced image analysis of open–close cycles and geometric orifice area measurement). Fully acellular porcine roots treated with the optimized method exhibited preserved macroscopic structures and microscopic matrix components, which translated into conserved anisotropic mechanical properties, including bending and excellent valve functionality when tested in aortic flow and pressure conditions. This study highlighted the importance of (1) adapting decellularization methods to specific target tissues, (2) combining several methods of cell analysis compared to relying solely on histology, (3) developing relevant valve-specific mechanical tests, and (4) in vitro testing of valve functionality. PMID:26467108

[Kinesiotherapy effect on quality of life, sexual function and climacteric symptoms in women with fibromyalgia].

PubMed

Lisboa, Lilian Lira; Sonehara, Elisa; Oliveira, Katia Cristina Araújo Nogueira de; Andrade, Sandra Cristina de; Azevedo, George Dantas

2015-01-01

To evaluate the effect of the kinesiotherapy in the quality of life, sexual function and menopause-related symptoms and compare in climacteric women with and without fibromyalgia (FM). the group was composed of 90 climacteric women divided in 2 groups: FM (47) and control (43). The patients were analyzed on their quality of life (Utian Quality of Life [UQoL]), sexual function (Sexual Quotient-Female Version [SQ-F] questionnaire) and intensity of the climacteric symptoms (Blatt-Kupperman menopausal index [BKMI]). Both groups performed pelvic floor kinesiotherapy, composed of 20 sessions, twice a week. Statistical analysis was performed using Student's t-test, mixed-design analysis of variance (ANOVA) and Cohen's Kappa. In the quality of life, an improvement was noticed in both groups for all domains analyzed. In the comparison between groups it was noticed a difference in the emotional (p=0.01), health (p=0.03) and sexual (p=0.001) domains with considerable gains verified in the control group. Improvement was also noticed in the sexual function. In the analysis between groups, FM group showed a lower score compared to the control group (p < 0.001). With respect to the climacteric symptoms, there was no difference in the analysis between groups after the intervention (p < 0.001). The pelvic floor kinesiotherapy promotes a positive effect in the domains of quality of life, sexual function and climacteric symptoms in women with and without fibromyalgia in the climacteric period; however, fibromyalgia seems to be a limiting factor to achieve better results in some of the aspects evaluated. Copyright © 2015 Elsevier Editora Ltda. All rights reserved.

Decline of kidney function during the pre-dialysis period in chronic kidney disease patients: a systematic review and meta-analysis.

PubMed

Janmaat, Cynthia J; van Diepen, Merel; van Hagen, Cheyenne Ce; Rotmans, Joris I; Dekker, Friedo W; Dekkers, Olaf M

2018-01-01

Substantial heterogeneity exists in reported kidney function decline in pre-dialysis chronic kidney disease (CKD). By design, kidney function decline can be studied in CKD 3-5 cohorts or dialysis-based studies. In the latter, patients are selected based on the fact that they initiated dialysis, possibly leading to an overestimation of the true underlying kidney function decline in the pre-dialysis period. We performed a systematic review and meta-analysis to compare the kidney function decline during pre-dialysis in CKD stage 3-5 patients, in these two different study types. We searched PubMed, EMBASE, Web of Science and Cochrane to identify eligible studies reporting an estimated glomerular filtration rate (eGFR) decline (mL/min/1.73 m 2 ) in adult pre-dialysis CKD patients. Random-effects meta-analysis was performed to obtain weighted mean annual eGFR decline. We included 60 studies (43 CKD 3-5 cohorts and 17 dialysis-based studies). The meta-analysis yielded a weighted annual mean (95% CI) eGFR decline during pre-dialysis of 2.4 (95% CI: 2.2, 2.6) mL/min/1.73 m 2 in CKD 3-5 cohorts compared to 8.5 (95% CI: 6.8, 10.1) in dialysis-based studies (difference 6.0 [95% CI: 4.8, 7.2]). To conclude, dialysis-based studies report faster mean annual eGFR decline during pre-dialysis than CKD 3-5 cohorts. Thus, eGFR decline data from CKD 3-5 cohorts should be used to guide clinical decision making in CKD patients and for power calculations in randomized controlled trials with CKD progression during pre-dialysis as the outcome.

Nationwide analysis of adrenocortical carcinoma reveals higher perioperative morbidity in functional tumors.

PubMed

Parikh, Punam P; Rubio, Gustavo A; Farra, Josefina C; Lew, John I

2017-08-25

Current adrenalectomy outcomes for functional adrenocortical carcinoma (ACC) remain unclear. This study examines nationwide in-hospital post-adrenalectomy outcomes for ACC. A retrospective analysis of the Nationwide Inpatient Sample database (2006-2011) to identify unilateral adrenalectomy patients for functional or nonfunctional ACC was performed. Patient demographics, comorbidities and postoperative outcomes were evaluated by t-test, Chi-square and multivariate regression. Of 2199 patients who underwent adrenalectomy, 87% had nonfunctional and 13% had functional ACC (86% hypercortisolism, 16% hyperaldosteronism, 4% hyperandrogenism). Functional ACC patients had significantly more comorbidities, and experienced certain postoperative complications more frequently including wound issues, adrenocortical insufficiency and acute kidney injury with longer hospital stay compared to nonfunctional ACC (P < 0.01). On multivariate analysis, functional ACC was an independent prognosticator for wound complications (28.1, 95%CI 4.59-176.6). Patients with functional ACC manifest significant comorbidities with certain in-hospital complications. Such high-risk patients require appropriate preoperative medical optimization prior to adrenalectomy. Patients with functional adrenocortical carcinoma (ACC) have significant preoperative comorbidities and experience higher rates of certain postoperative complications including wound complications, hematoma formation, adrenal insufficiency, pulmonary embolism and acute kidney injury. Functional ACC patients also necessitate longer hospitalizations. These patients should undergo appropriate preoperative counseling in preparation for adrenalectomy. Copyright © 2017 Elsevier Inc. All rights reserved.

Characterization of Microbiota in Children with Chronic Functional Constipation.

PubMed

de Meij, Tim G J; de Groot, Evelien F J; Eck, Anat; Budding, Andries E; Kneepkens, C M Frank; Benninga, Marc A; van Bodegraven, Adriaan A; Savelkoul, Paul H M

2016-01-01

Disruption of the intestinal microbiota is considered an etiological factor in pediatric functional constipation. Scientifically based selection of potential beneficial probiotic strains in functional constipation therapy is not feasible due to insufficient knowledge of microbiota composition in affected subjects. The aim of this study was to describe microbial composition and diversity in children with functional constipation, compared to healthy controls. Fecal samples from 76 children diagnosed with functional constipation according to the Rome III criteria (median age 8.0 years; range 4.2-17.8) were analyzed by IS-pro, a PCR-based microbiota profiling method. Outcome was compared with intestinal microbiota profiles of 61 healthy children (median 8.6 years; range 4.1-17.9). Microbiota dissimilarity was depicted by principal coordinate analysis (PCoA), diversity was calculated by Shannon diversity index. To determine the most discriminative species, cross validated logistic ridge regression was performed. Applying total microbiota profiles (all phyla together) or per phylum analysis, no disease-specific separation was observed by PCoA and by calculation of diversity indices. By ridge regression, however, functional constipation and controls could be discriminated with 82% accuracy. Most discriminative species were Bacteroides fragilis, Bacteroides ovatus, Bifidobacterium longum, Parabacteroides species (increased in functional constipation) and Alistipes finegoldii (decreased in functional constipation). None of the commonly used unsupervised statistical methods allowed for microbiota-based discrimination of children with functional constipation and controls. By ridge regression, however, both groups could be discriminated with 82% accuracy. Optimization of microbiota-based interventions in constipated children warrants further characterization of microbial signatures linked to clinical subgroups of functional constipation.

A Comparative Analysis of the Audience for Broadcast Sports and In-Person Sports.

ERIC Educational Resources Information Center

Melton, Gary Warren; Galician, Mary-Lou

A study examined the uses and functions of broadcast sports programming as compared with in-person attendance of sporting events by focusing on the motivations, behavior, and attitudes of audiences toward such activities. Subjects, 219 students from a major western university, completed a survey instrument. Findings indicated that: (1) sports…

Spectral Discrete Probability Density Function of Measured Wind Turbine Noise in the Far Field

PubMed Central

Ashtiani, Payam; Denison, Adelaide

2015-01-01

Of interest is the spectral character of wind turbine noise at typical residential set-back distances. In this paper, a spectral statistical analysis has been applied to immission measurements conducted at three locations. This method provides discrete probability density functions for the Turbine ONLY component of the measured noise. This analysis is completed for one-third octave sound levels, at integer wind speeds, and is compared to existing metrics for measuring acoustic comfort as well as previous discussions on low-frequency noise sources. PMID:25905097

Radiometric analysis of photographic data by the effective exposure method

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

Constantine, B J

1972-04-01

The effective exposure method provides for radiometric analysis of photographic data. A three-dimensional model, where density is a function of energy and wavelength, is postulated to represent the film response function. Calibration exposures serve to eliminate the other factors which affect image density. The effective exposure causing an image can be determined by comparing the image density with that of a calibration exposure. If the relative spectral distribution of the source is known, irradiance and/or radiance can be unfolded from the effective exposure expression.

The effects of videotape modeling on staff acquisition of functional analysis methodology.

PubMed

Moore, James W; Fisher, Wayne W

2007-01-01

Lectures and two types of video modeling were compared to determine their relative effectiveness in training 3 staff members to conduct functional analysis sessions. Video modeling that contained a larger number of therapist exemplars resulted in mastery-level performance eight of the nine times it was introduced, whereas neither lectures nor partial video modeling produced significant improvements in performance. Results demonstrated that video modeling provided an effective training strategy but only when a wide range of exemplars of potential therapist behaviors were depicted in the videotape.

The Effects of Videotape Modeling on Staff Acquisition of Functional Analysis Methodology

PubMed Central

Moore, James W; Fisher, Wayne W

2007-01-01

Lectures and two types of video modeling were compared to determine their relative effectiveness in training 3 staff members to conduct functional analysis sessions. Video modeling that contained a larger number of therapist exemplars resulted in mastery-level performance eight of the nine times it was introduced, whereas neither lectures nor partial video modeling produced significant improvements in performance. Results demonstrated that video modeling provided an effective training strategy but only when a wide range of exemplars of potential therapist behaviors were depicted in the videotape. PMID:17471805

A novel analysis method for near infrared spectroscopy based on Hilbert-Huang transform

NASA Astrophysics Data System (ADS)

Zhou, Zhenyu; Yang, Hongyu; Liu, Yun; Ruan, Zongcai; Luo, Qingming; Gong, Hui; Lu, Zuhong

2007-05-01

Near Infrared Imager (NIRI) has been widely used to access the brain functional activity non-invasively. We use a portable, multi-channel and continuous-wave NIR topography instrument to measure the concentration changes of each hemoglobin species and map cerebral cortex functional activation. By extracting some essential features from the BOLD signals, optical tomography is able to be a new way of neuropsychological studies. Fourier spectral analysis provides a common framework for examining the distribution of global energy in the frequency domain. However, this method assumes that the signal should be stationary, which limits its application in non-stationary system. The hemoglobin species concentration changes are of such kind. In this work we develop a new signal processing method using Hilbert-Huang transform to perform spectral analysis of the functional NIRI signals. Compared with wavelet based multi-resolution analysis (MRA), we demonstrated the extraction of task related signal for observation of activation in the prefrontal cortex (PFC) in vision stimulation experiment. This method provides a new analysis tool for functional NIRI signals. Our experimental results show that the proposed approach provides the unique method for reconstructing target signal without losing original information and enables us to understand the episode of functional NIRI more precisely.

Dissociable executive functions in behavioral variant frontotemporal and Alzheimer dementias

PubMed Central

Feigenbaum, Dana; Rankin, Katherine P.; Smith, Glenn E.; Boxer, Adam L.; Wood, Kristie; Hanna, Sherrie M.; Miller, Bruce L.; Kramer, Joel H.

2013-01-01

Objective: The objective of this study was to determine which aspects of executive functions are most affected in behavioral variant frontotemporal dementia (bvFTD) and best differentiate this syndrome from Alzheimer disease (AD). Methods: We compared executive functions in 22 patients diagnosed with bvFTD, 26 with AD, and 31 neurologically healthy controls using a conceptually driven and comprehensive battery of executive function tests, the NIH EXAMINER battery (http://examiner.ucsf.edu). Results: The bvFTD and the AD patients were similarly impaired compared with controls on tests of working memory, category fluency, and attention, but the patients with bvFTD showed significantly more severe impairments than the patients with AD on tests of letter fluency, antisaccade accuracy, social decision-making, and social behavior. Discriminant function analysis with jackknifed cross-validation classified the bvFTD and AD patient groups with 73% accuracy. Conclusions: Executive function assessment can support bvFTD diagnosis when measures are carefully selected to emphasize frontally specific functions. PMID:23658382

Methods to evaluate functional nerve recovery in adult rats: walking track analysis, video analysis and the withdrawal reflex.

PubMed

Dijkstra, J R; Meek, M F; Robinson, P H; Gramsbergen, A

2000-03-15

The aim of this study was to compare different methods for the evaluation of functional nerve recovery. Three groups of adult male Wistar rats were studied. In group A, a 12-mm gap between nerve ends was bridged by an autologous nerve graft; in rats of group B we performed a crush lesion of the sciatic nerve and group C consisted of non-operated control rats. The withdrawal reflex, elicited by an electric stimulus, was used to evaluate the recovery of sensory nerve function. To investigate motor nerve recovery we analyzed the walking pattern. Three different methods were used to obtain data for footprint analysis: photographic paper with thickened film developer on the paws, normal white paper with finger paint, and video recordings. The footprints were used to calculate the sciatic function index (SFI). From the video recordings, we also analyzed stepcycles. The withdrawal reflex is a convenient and reproducible test for the evaluation of global sensory nerve recovery. Recording walking movements on video and the analysis of footplacing is a perfect although time-consuming method for the evaluation of functional aspects of motor nerve recovery.

The Impact of Massage Therapy on Function in Pain Populations-A Systematic Review and Meta-Analysis of Randomized Controlled Trials: Part I, Patients Experiencing Pain in the General Population.

PubMed

Crawford, Cindy; Boyd, Courtney; Paat, Charmagne F; Price, Ashley; Xenakis, Lea; Yang, EunMee; Zhang, Weimin

2016-07-01

Pain is multi-dimensional and may be better addressed through a holistic, biopsychosocial approach. Massage therapy is commonly practiced among patients seeking pain management; however, its efficacy is unclear. This systematic review and meta-analysis is the first to rigorously assess the quality of massage therapy research and evidence for its efficacy in treating pain, function-related and health-related quality of life outcomes across all pain populations. Key databases were searched from inception through February 2014. Eligible randomized controlled trials were assessed for methodological quality using SIGN 50 Checklist. Meta-analysis was applied at the outcome level. A diverse steering committee interpreted the results to develop recommendations. Sixty high quality and seven low quality studies were included in the review. Results demonstrate massage therapy effectively treats pain compared to sham [standardized mean difference (SMD) = -.44], no treatment (SMD = -1.14), and active (SMD = -0.26) comparators. Compared to active comparators, massage therapy was also beneficial for treating anxiety (SMD = -0.57) and health-related quality of life (SMD = 0.14). Based on the evidence, massage therapy, compared to no treatment, should be strongly recommended as a pain management option. Massage therapy is weakly recommended for reducing pain, compared to other sham or active comparators, and improving mood and health-related quality of life, compared to other active comparators. Massage therapy safety, research challenges, how to address identified research gaps, and necessary next steps for implementing massage therapy as a viable pain management option are discussed.

The Impact of Massage Therapy on Function in Pain Populations—A Systematic Review and Meta-Analysis of Randomized Controlled Trials: Part I, Patients Experiencing Pain in the General Population

PubMed Central

Crawford, Cindy; Boyd, Courtney; Paat, Charmagne F; Price, Ashley; Xenakis, Lea; Yang, EunMee; Zhang, Weimin; Buckenmaier, Chester; Buckenmaier, Pamela; Cambron, Jerrilyn; Deery, Christopher; Schwartz, Jan; Werner, Ruth; Whitridge, Pete

2016-01-01

Abstract Purpose Pain is multi-dimensional and may be better addressed through a holistic, biopsychosocial approach. Massage therapy is commonly practiced among patients seeking pain management; however, its efficacy is unclear. This systematic review and meta-analysis is the first to rigorously assess the quality of massage therapy research and evidence for its efficacy in treating pain, function-related and health-related quality of life outcomes across all pain populations. Methods Key databases were searched from inception through February 2014. Eligible randomized controlled trials were assessed for methodological quality using SIGN 50 Checklist. Meta-analysis was applied at the outcome level. A diverse steering committee interpreted the results to develop recommendations. Results Sixty high quality and seven low quality studies were included in the review. Results demonstrate massage therapy effectively treats pain compared to sham [standardized mean difference (SMD) = −.44], no treatment (SMD = −1.14), and active (SMD = −0.26) comparators. Compared to active comparators, massage therapy was also beneficial for treating anxiety (SMD = −0.57) and health-related quality of life (SMD = 0.14). Conclusion Based on the evidence, massage therapy, compared to no treatment, should be strongly recommended as a pain management option. Massage therapy is weakly recommended for reducing pain, compared to other sham or active comparators, and improving mood and health-related quality of life, compared to other active comparators. Massage therapy safety, research challenges, how to address identified research gaps, and necessary next steps for implementing massage therapy as a viable pain management option are discussed. PMID:27165971

Heart failure analysis dashboard for patient's remote monitoring combining multiple artificial intelligence technologies.

PubMed

Guidi, G; Pettenati, M C; Miniati, R; Iadanza, E

2012-01-01

In this paper we describe an Heart Failure analysis Dashboard that, combined with a handy device for the automatic acquisition of a set of patient's clinical parameters, allows to support telemonitoring functions. The Dashboard's intelligent core is a Computer Decision Support System designed to assist the clinical decision of non-specialist caring personnel, and it is based on three functional parts: Diagnosis, Prognosis, and Follow-up management. Four Artificial Intelligence-based techniques are compared for providing diagnosis function: a Neural Network, a Support Vector Machine, a Classification Tree and a Fuzzy Expert System whose rules are produced by a Genetic Algorithm. State of the art algorithms are used to support a score-based prognosis function. The patient's Follow-up is used to refine the diagnosis.

New real-time algorithms for arbitrary, high precision function generation with applications to acoustic transducer excitation

NASA Astrophysics Data System (ADS)

Gaydecki, P.

2009-07-01

A system is described for the design, downloading and execution of arbitrary functions, intended for use with acoustic and low-frequency ultrasonic transducers in condition monitoring and materials testing applications. The instrumentation comprises a software design tool and a powerful real-time digital signal processor unit, operating at 580 million multiplication-accumulations per second (MMACs). The embedded firmware employs both an established look-up table approach and a new function interpolation technique to generate the real-time signals with very high precision and flexibility. Using total harmonic distortion (THD) analysis, the purity of the waveforms have been compared with those generated using traditional analogue function generators; this analysis has confirmed that the new instrument has a consistently superior signal-to-noise ratio.

A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction.

PubMed

Abulnaga, S Mazdak; Yang, Zhen; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M; Onyike, Chiadi U; Ying, Sarah H; Prince, Jerry L

2016-02-27

The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects' cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction

NASA Astrophysics Data System (ADS)

Abulnaga, S. Mazdak; Yang, Zhen; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M.; Onyike, Chiadi U.; Ying, Sarah H.; Prince, Jerry L.

2016-03-01

The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects' cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

How to Compare the Security Quality Requirements Engineering (SQUARE) Method with Other Methods

DTIC Science & Technology

2007-08-01

Attack Trees for Modeling and Analysis 10 2.8 Misuse and Abuse Cases 10 2.9 Formal Methods 11 2.9.1 Software Cost Reduction 12 2.9.2 Common...modern or efficient techniques. • Requirements analysis typically is either not performed at all (identified requirements are directly specified without...any analysis or modeling) or analysis is restricted to functional re- quirements and ignores quality requirements, other nonfunctional requirements

Stress analysis of advanced attack helicopter composite main rotor blade root end lug

NASA Technical Reports Server (NTRS)

Baker, D. J.

1982-01-01

Stress analysis of the Advanced Attack Helicopter (AAH) composite main rotor blade root end lug is described. The stress concentration factor determined from a finite element analysis is compared to an empirical value used in the lug design. The analysis and test data indicate that the stress concentration is primarily a function of configuration and independent of the range of material properties typical of Kevlar-49/epoxy and glass epoxy.

DIF Analysis across Genders for Reading Comprehension Part of English Language Achievement Exam as a Foreign Language

ERIC Educational Resources Information Center

Ögretmen, Tuncay

2015-01-01

The purpose of this study is to carry out differential item functioning (DIF) analysis for content areas of a reading comprehension subtest using four area indices within Item Response Theory (IRT) framework. The differences in the magnitudes of the area indices were compared based on the subject areas. The DIF analysis was carried out across…

14 CFR 417.301 - General.

Code of Federal Regulations, 2011 CFR

2011-01-01

... undergo analysis and testing that is comparable to that required by this part to demonstrate that the...) Functions, subsystems, and components. When initiated in the event of a launch vehicle failure, a flight...

14 CFR 417.301 - General.

Code of Federal Regulations, 2013 CFR

2013-01-01

... undergo analysis and testing that is comparable to that required by this part to demonstrate that the...) Functions, subsystems, and components. When initiated in the event of a launch vehicle failure, a flight...

14 CFR 417.301 - General.

Code of Federal Regulations, 2012 CFR

2012-01-01

... undergo analysis and testing that is comparable to that required by this part to demonstrate that the...) Functions, subsystems, and components. When initiated in the event of a launch vehicle failure, a flight...

14 CFR 417.301 - General.

Code of Federal Regulations, 2014 CFR

2014-01-01

... undergo analysis and testing that is comparable to that required by this part to demonstrate that the...) Functions, subsystems, and components. When initiated in the event of a launch vehicle failure, a flight...

Python package for model STructure ANalysis (pySTAN)

NASA Astrophysics Data System (ADS)

Van Hoey, Stijn; van der Kwast, Johannes; Nopens, Ingmar; Seuntjens, Piet

2013-04-01

The selection and identification of a suitable hydrological model structure is more than fitting parameters of a model structure to reproduce a measured hydrograph. The procedure is highly dependent on various criteria, i.e. the modelling objective, the characteristics and the scale of the system under investigation as well as the available data. Rigorous analysis of the candidate model structures is needed to support and objectify the selection of the most appropriate structure for a specific case (or eventually justify the use of a proposed ensemble of structures). This holds both in the situation of choosing between a limited set of different structures as well as in the framework of flexible model structures with interchangeable components. Many different methods to evaluate and analyse model structures exist. This leads to a sprawl of available methods, all characterized by different assumptions, changing conditions of application and various code implementations. Methods typically focus on optimization, sensitivity analysis or uncertainty analysis, with backgrounds from optimization, machine-learning or statistics amongst others. These methods also need an evaluation metric (objective function) to compare the model outcome with some observed data. However, for current methods described in literature, implementations are not always transparent and reproducible (if available at all). No standard procedures exist to share code and the popularity (and amount of applications) of the methods is sometimes more dependent on the availability than the merits of the method. Moreover, new implementations of existing methods are difficult to verify and the different theoretical backgrounds make it difficult for environmental scientists to decide about the usefulness of a specific method. A common and open framework with a large set of methods can support users in deciding about the most appropriate method. Hence, it enables to simultaneously apply and compare different methods on a fair basis. We developed and present pySTAN (python framework for STructure Analysis), a python package containing a set of functions for model structure evaluation to provide the analysis of (hydrological) model structures. A selected set of algorithms for optimization, uncertainty and sensitivity analysis is currently available, together with a set of evaluation (objective) functions and input distributions to sample from. The methods are implemented model-independent and the python language provides the wrapper functions to apply administer external model codes. Different objective functions can be considered simultaneously with both statistical metrics and more hydrology specific metrics. By using so-called reStructuredText (sphinx documentation generator) and Python documentation strings (docstrings), the generation of manual pages is semi-automated and a specific environment is available to enhance both the readability and transparency of the code. It thereby enables a larger group of users to apply and compare these methods and to extend the functionalities.

The Effects of Family Therapies for Adolescent Delinquency and Substance Abuse: A Meta-Analysis

ERIC Educational Resources Information Center

Baldwin, Scott A.; Christian, Sarah; Berkeljon, Arjan; Shadish, William R.

2012-01-01

This meta-analysis summarizes results from k = 24 studies comparing either Brief Strategic Family Therapy, Functional Family Therapy, Multidimensional Family Therapy, or Multisystemic Therapy to either treatment-as-usual, an alternative therapy, or a control group in the treatment of adolescent substance abuse and delinquency. Additionally, the…

Argumentation in a Multi Party Asynchronous Computer Mediated Conference: A Generic Analysis

ERIC Educational Resources Information Center

Coffin, Caroline; Painter, Clare; Hewings, Ann

2005-01-01

This paper draws on systemic functional linguistic genre analysis to illuminate the way in which post graduate applied linguistics students structure their argumentation within a multi party asynchronous computer mediated conference. Two conference discussions within the same postgraduate course are compared in order to reveal the way in which…

Agreement between Descriptive and Experimental Analyses of Behavior under Naturalistic Test Conditions

ERIC Educational Resources Information Center

Martens, Brian K.; Gertz, Lynne E.; Werder, Candace Susan de Lacy; Rymanowski, Jennifer L.

2010-01-01

We compared the results of a contingency space analysis (CSA) of behavior-consequence recordings to the results of functional analysis (FA) test conditions involving antecedent stimuli and verbal statements that both differed from and mimicked those in the natural environment. Three preschool children with autism spectrum disorder participated.…

High-resolution NMR study of light and heavy crude oils: “structure-property” analysis

NASA Astrophysics Data System (ADS)

Rakhmatullin, I.; Efimov, S.; Varfolomeev, M.; Klochkov, V.

2018-05-01

Measurements of three light and one heavy crude oil samples were carried out by high-resolution nuclear magnetic resonance (NMR) spectroscopy methods. Quantitative fractions of aromatic molecules and functional groups constituting oil hydrocarbons were determined, and comparative analysis of the oil samples of different viscosity and origin was done.

Comparing Students with and without Reading Difficulties on Reading Comprehension Assessments: A Meta-Analysis

ERIC Educational Resources Information Center

Collins, Alyson A.; Lindström, Esther R.; Compton, Donald L.

2018-01-01

Researchers have increasingly investigated sources of variance in reading comprehension test scores, particularly with students with reading difficulties (RD). The purpose of this meta-analysis was to determine if the achievement gap between students with RD and typically developing (TD) students varies as a function of different reading…

[Critic analysis of a comparative meta-analysis on the morbidity, functional and carcinologic results after radical prostatectomy according to surgical approach. Work of cancerology committee of the French urological association].

PubMed

Bastide, C; Rozet, F; Salomon, L; Mongiat-Artus, P; Beuzeboc, P; Cormier, L; Eiss, D; Gaschignard, N; Peyromaure, M; Richaud, P; Soulié, M

2010-09-01

Surgical approach for radical prostatectomy is even today a subject of debate in the urologic community. Many comparative studies between retropubic and laparoscopic approach (robotic assisted or not) were reported since 10 years without being able to decide between the supporters of retropubic or laparoscopic approach. The committee of cancer research of the French urological association took hold this question after a recent meta-analysis publication on this subject. Although imperfect, this meta-analysis exists and permits to conclude partially on the advantages and the inconveniences supposed for each surgical approach. Regarding morbidity after radical prostatectomy, the only significant difference reported concerns the hemorrhagic risk in favour of the laparoscopic approach. Regarding oncologic results, the only exploitable data concern positive surgical margins rate, which is identical whatever surgical approach. Concerning the functional results, no difference was reported in the literature between different surgical approaches. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Task-evoked brain functional magnetic susceptibility mapping by independent component analysis (χICA).

PubMed

Chen, Zikuan; Calhoun, Vince D

2016-03-01

Conventionally, independent component analysis (ICA) is performed on an fMRI magnitude dataset to analyze brain functional mapping (AICA). By solving the inverse problem of fMRI, we can reconstruct the brain magnetic susceptibility (χ) functional states. Upon the reconstructed χ dataspace, we propose an ICA-based brain functional χ mapping method (χICA) to extract task-evoked brain functional map. A complex division algorithm is applied to a timeseries of fMRI phase images to extract temporal phase changes (relative to an OFF-state snapshot). A computed inverse MRI (CIMRI) model is used to reconstruct a 4D brain χ response dataset. χICA is implemented by applying a spatial InfoMax ICA algorithm to the reconstructed 4D χ dataspace. With finger-tapping experiments on a 7T system, the χICA-extracted χ-depicted functional map is similar to the SPM-inferred functional χ map by a spatial correlation of 0.67 ± 0.05. In comparison, the AICA-extracted magnitude-depicted map is correlated with the SPM magnitude map by 0.81 ± 0.05. The understanding of the inferiority of χICA to AICA for task-evoked functional map is an ongoing research topic. For task-evoked brain functional mapping, we compare the data-driven ICA method with the task-correlated SPM method. In particular, we compare χICA with AICA for extracting task-correlated timecourses and functional maps. χICA can extract a χ-depicted task-evoked brain functional map from a reconstructed χ dataspace without the knowledge about brain hemodynamic responses. The χICA-extracted brain functional χ map reveals a bidirectional BOLD response pattern that is unavailable (or different) from AICA. Copyright © 2016 Elsevier B.V. All rights reserved.

Female Sexual Function Following Surgical Treatment of Stress Urinary Incontinence: Systematic Review and Meta-Analysis.

PubMed

Bicudo-Fürst, Maria Cláudia; Borba Leite, Pedro Henrique; Araújo Glina, Felipe Placco; Baccaglini, Willy; de Carvalho Fürst, Rafael Vilhena; Bezerra, Carlos Alberto; Glina, Sidney

2018-04-01

The impact of surgery for stress urinary incontinence (SUI) on female sexual function has received attention in the medical literature, but not in a structured manner. To assess the most recent evidence on the impact of surgical management for female SUI on female sexual function. The review and meta-analysis of available articles published in Medline, Cochrane, LILACS, SCOPUS, Web of Science, CINHAL, and EMBASE included prospective randomized and non-randomized studies that assessed patients who underwent surgical treatment for UI through 2 validated questionnaires: the Pelvic Organ Prolapse Urinary Incontinence Sexual Questionnaire (PISQ-12) and the Female Sexual Function Index (FSFI). The following terms were searched: (urinary incontinence OR female OR woman OR women) AND (suburethral slings OR transobturator tape* OR transobturator suburethral tape OR trans-obturator tape* OR urethral sling* OR midurethral sling* OR mid-urethral sling* OR "standard midurethral slings" OR tensionless vaginal tape* OR mini sling* OR Burch* OR "Burch colposuspension" OR "urologic surgical procedures" OR "tension-free vaginal tape" OR pubovaginal sling) AND (sexual behavior OR "Female Sexual Function Index" OR FSFI OR sexual function OR "Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire" OR PISQ-12). 1,043 articles were retrieved; 9 studies were included for qualitative analysis and 4 were included for meta-analysis. 25 articles were excluded because they used questionnaires other than the FSFI and PISQ-12. Meta-analysis of 2 studies composed of 411 women who underwent to retropubic and transobturator sling intervention and completed the PISQ-12 questionnaire showed an increase in sexual function of 2.40 points after transobturator compared with retropubic sling intervention (95% CI = -2.48 to -2.32; I 2  = 35%, P < .00001). However, 2 other studies composed of 183 women comparing the same techniques, but using the FSFI, did not show a statistically significant difference (95% CI = -1.77 to 3.78; I 2  = 0%, P = .48). The impact of UI surgery on sexual function is uncertain because of the imprecision of the effect and inconsistency among studies. Only limited evidence on the impact of the transobturator vs the retropubic sling was found. Bicudo-Fürst MC, Borba Leite PH, Araújo Glina FP, et al. Female Sexual Function Following Surgical Treatment of Stress Urinary Incontinence: Systematic Review and Meta-Analysis. Sex Med Rev 2018;6:224-233. Copyright © 2017. Published by Elsevier Inc.

Meta-analysis of safety and efficacy for direct oral anticoagulation treatment of non-valvular atrial fibrillation in relation to renal function.

PubMed

Zou, Rongjun; Tao, Jun; Shi, Wanting; Yang, Minglei; Li, Hongmu; Lin, Xifeng; Yang, Songran; Hua, Ping

2017-12-01

We performed a meta-analysis of the safety and efficacy of anticoagulation treatment for atrial fibrillation (AF) in relation to renal function. We also examined the change in estimated glomerular filtration rate (eGFR) from baseline and compared the outcomes for patients with stable and worsening renal function. We selected studies that used randomized controlled trials in which outcomes for direct oral anticoagulants (DOACs) (dabigatran, rivaroxaban, apixaban, or edoxaban) were compared with those for warfarin in AF patients with normal, mild or moderate renal function, except the severe one (creatinine clearance<30). We assessed five clinical trials, involving 72,608 patients. Pooled analysis indicated that the risk of stroke was lower for DOACs than for warfarin among patients with mild renal impairment (Risk ratio, 0.79; 95% confidence interval, 0.68-0.91) and moderate renal impairment (0.80, 0.69-0.92). No major differences were found in patients with normal renal function. Additionally, DOACs were associated with fewer major bleeds among patients with normal (0.77, 0.70-0.84), mild (0.86, 0.77-0.95), and moderate renal impairment (0.73, 0.65-0.82). Among those treated with DOACs, a lower dosage was associated with lower risk of major bleeding (0.75, 0.68-0.83) and higher risk of stroke or systemic embolism (1.28, 1.12-1.47). Further, DOACs tended to be associated with a lower estimated glomerular filtration rate (eGFR) than warfarin even after 30months. Finally, we found significant differences in the risk of stroke (2.09, 1.64-2.68) and major bleeding (2.01, 1.66-2.42) between patients with stable and worsening renal function. DOACs have a greater clinical benefit than warfarin with respect to renal function. They are associated with a comparatively lower risk of stroke and major bleeding, as well lower eGFR. This suggests these agents are a better choice in patients with renal disease. Copyright © 2017. Published by Elsevier Ltd.

Real-Life Impact of Executive Function Impairments in Adults Who Were Born Very Preterm.

PubMed

Kroll, Jasmin; Karolis, Vyacheslav; Brittain, Philip J; Tseng, Chieh-En Jane; Froudist-Walsh, Sean; Murray, Robin M; Nosarti, Chiara

2017-05-01

Children and adolescents who were born very preterm (≤32 weeks' gestation) are vulnerable to experiencing cognitive problems, including in executive function. However, it remains to be established whether cognitive deficits are evident in adulthood and whether these exert a significant effect on an individual's real-lifeachievement. Using a cross-sectional design, we tested a range of neurocognitive abilities, with a focus on executive function, in a sample of 122 very preterm individuals and 89 term-born controls born between 1979 and 1984. Associations between executive function and a range of achievement measures, indicative of a successful transition to adulthood, were examined. Very preterm adults performed worse compared to controls on measures of intellectual ability and executive function with moderate to large effect sizes. They also demonstrated significantly lower achievement levels in terms of years spent in education, employment status, and on a measure of functioning in work and social domains. Results of regression analysis indicated a stronger positive association between executive function and real-life achievement in the very preterm group compared to controls. Very preterm born adults demonstrate executive function impairments compared to full-term controls, and these are associated with lower achievement in several real-life domains. (JINS, 2017, 23, 381-389).

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

TAM 2.0: tool for MicroRNA set analysis.

PubMed

Li, Jianwei; Han, Xiaofen; Wan, Yanping; Zhang, Shan; Zhao, Yingshu; Fan, Rui; Cui, Qinghua; Zhou, Yuan

2018-06-06

With the rapid accumulation of high-throughput microRNA (miRNA) expression profile, the up-to-date resource for analyzing the functional and disease associations of miRNAs is increasingly demanded. We here describe the updated server TAM 2.0 for miRNA set enrichment analysis. Through manual curation of over 9000 papers, a more than two-fold growth of reference miRNA sets has been achieved in comparison with previous TAM, which covers 9945 and 1584 newly collected miRNA-disease and miRNA-function associations, respectively. Moreover, TAM 2.0 allows users not only to test the functional and disease annotations of miRNAs by overrepresentation analysis, but also to compare the input de-regulated miRNAs with those de-regulated in other disease conditions via correlation analysis. Finally, the functions for miRNA set query and result visualization are also enabled in the TAM 2.0 server to facilitate the community. The TAM 2.0 web server is freely accessible at http://www.scse.hebut.edu.cn/tam/ or http://www.lirmed.com/tam2/.

Ole e 13 is the unique food allergen in olive: Structure-functional, substrates docking, and molecular allergenicity comparative analysis.

PubMed

Jimenez-Lopez, J C; Robles-Bolivar, P; Lopez-Valverde, F J; Lima-Cabello, E; Kotchoni, S O; Alché, J D

2016-05-01

Thaumatin-like proteins (TLPs) are enzymes with important functions in pathogens defense and in the response to biotic and abiotic stresses. Last identified olive allergen (Ole e 13) is a TLP, which may also importantly contribute to food allergy and cross-allergenicity to pollen allergen proteins. The goals of this study are the characterization of the structural-functionality of Ole e 13 with a focus in its catalytic mechanism, and its molecular allergenicity by extensive analysis using different molecular computer-aided approaches covering a) functional-regulatory motifs, b) comparative study of linear sequence, 2-D and 3D structural homology modeling, c) molecular docking with two different β-D-glucans, d) conservational and evolutionary analysis, e) catalytic mechanism modeling, and f) IgE-binding, B- and T-cell epitopes identification and comparison to other allergenic TLPs. Sequence comparison, structure-based features, and phylogenetic analysis identified Ole e 13 as a thaumatin-like protein. 3D structural characterization revealed a conserved overall folding among plants TLPs, with mayor differences in the acidic (catalytic) cleft. Molecular docking analysis using two β-(1,3)-glucans allowed to identify fundamental residues involved in the endo-1,3-β-glucanase activity, and defining E84 as one of the conserved residues of the TLPs responsible of the nucleophilic attack to initiate the enzymatic reaction and D107 as proton donor, thus proposing a catalytic mechanism for Ole e 13. Identification of IgE-binding, B- and T-cell epitopes may help designing strategies to improve diagnosis and immunotherapy to food allergy and cross-allergenic pollen TLPs. Copyright © 2016 Elsevier Inc. All rights reserved.

How a submarine returns to periscope depth: analysing complex socio-technical systems using Cognitive Work Analysis.

PubMed

Stanton, Neville A; Bessell, Kevin

2014-01-01

This paper presents the application of Cognitive Work Analysis to the description of the functions, situations, activities, decisions, strategies, and competencies of a Trafalgar class submarine when performing the function of returning to periscope depth. All five phases of Cognitive Work Analysis are presented, namely: Work Domain Analysis, Control Task Analysis, Strategies Analysis, Social Organisation and Cooperation Analysis, and Worker Competencies Analysis. Complex socio-technical systems are difficult to analyse but Cognitive Work Analysis offers an integrated way of analysing complex systems with the core of functional means-ends analysis underlying all of the other representations. The joined-up analysis offers a coherent framework for understanding how socio-technical systems work. Data were collected through observation and interviews at different sites across the UK. The resultant representations present a statement of how the work domain and current activities are configured in this complex socio-technical system. This is intended to provide a baseline, from which all future conceptions of the domain may be compared. The strength of the analysis is in the multiple representations from which the constraints acting on the work may be analysed. Future research needs to challenge the assumptions behind these constraints in order to develop new ways of working. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Site-Selective Modification of Cellulose Nanocrystals with Isophorone Diisocyanate and Formation of Polyurethane-CNC Composites.

PubMed

Girouard, Natalie M; Xu, Shanhong; Schueneman, Gregory T; Shofner, Meisha L; Meredith, J Carson

2016-01-20

The unequal reactivity of the two isocyanate groups in an isophorone diisocyante (IPDI) monomer was exploited to yield modified cellulose nanocrystals (CNCs) with both urethane and isocyanate functionality. The chemical functionality of the modified CNCs was verified with ATR-FTIR analysis and elemental analysis. The selectivity for the secondary isocyanate group using dibutyl tin dilaurate (DBTDL) as the reaction catalyst was confirmed with (13)C NMR. The modified CNCs showed improvements in the onset of thermal degradation by 35 °C compared to the unmodified CNCs. Polyurethane composites based on IPDI and a trifunctional polyether alcohol were synthesized using unmodified (um-CNC) and modified CNCs (m-CNC). The degree of nanoparticle dispersion was qualitatively assessed with polarized optical microscopy. It was found that the modification step facilitated superior nanoparticle dispersion compared to the um-CNCs, which resulted in increases in the tensile strength and work of fracture of over 200% compared to the neat matrix without degradation of elongation at break.

DCODE.ORG Anthology of Comparative Genomic Tools

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

Loots, G G; Ovcharenko, I

2005-01-11

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the noncoding encryption of gene regulation across genomes. To facilitate the use of comparative genomics to practical applications in genetics and genomics we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools: zPicture and Mulan; a phylogenetic shadowing tool: eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools: rVista and multiTF; a toolmore » for extracting cis-regulatory modules governing the expression of co-regulated genes, CREME; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ web site.« less

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

PubMed Central

Stark, Alexander; Lin, Michael F.; Kheradpour, Pouya; Pedersen, Jakob S.; Parts, Leopold; Carlson, Joseph W.; Crosby, Madeline A.; Rasmussen, Matthew D.; Roy, Sushmita; Deoras, Ameya N.; Ruby, J. Graham; Brennecke, Julius; Hodges, Emily; Hinrichs, Angie S.; Caspi, Anat; Paten, Benedict; Park, Seung-Won; Han, Mira V.; Maeder, Morgan L.; Polansky, Benjamin J.; Robson, Bryanne E.; Aerts, Stein; van Helden, Jacques; Hassan, Bassem; Gilbert, Donald G.; Eastman, Deborah A.; Rice, Michael; Weir, Michael; Hahn, Matthew W.; Park, Yongkyu; Dewey, Colin N.; Pachter, Lior; Kent, W. James; Haussler, David; Lai, Eric C.; Bartel, David P.; Hannon, Gregory J.; Kaufman, Thomas C.; Eisen, Michael B.; Clark, Andrew G.; Smith, Douglas; Celniker, Susan E.; Gelbart, William M.; Kellis, Manolis

2008-01-01

Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or ‘evolutionary signatures’, dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies. PMID:17994088

Research of GIS-services applicability for solution of spatial analysis tasks.

NASA Astrophysics Data System (ADS)

Terekhin, D. A.; Botygin, I. A.; Sherstneva, A. I.; Sherstnev, V. S.

2017-01-01

Experiments for working out the areas of applying various gis-services in the tasks of spatial analysis are discussed in this paper. Google Maps, Yandex Maps, Microsoft SQL Server are used as services of spatial analysis. All services have shown a comparable speed of analyzing the spatial data when carrying out elemental spatial requests (building up the buffer zone of a point object) as well as the preferences of Microsoft SQL Server in operating with more complicated spatial requests. When building up elemental spatial requests, internet-services show higher efficiency due to cliental data handling with JavaScript-subprograms. A weak point of public internet-services is an impossibility to handle data on a server side and a barren variety of spatial analysis functions. Microsoft SQL Server offers a large variety of functions needed for spatial analysis on the server side. The authors conclude that when solving practical problems, the capabilities of internet-services used in building up routes and completing other functions with spatial analysis with Microsoft SQL Server should be involved.

Assignment of functional activations to probabilistic cytoarchitectonic areas revisited.

PubMed

Eickhoff, Simon B; Paus, Tomas; Caspers, Svenja; Grosbras, Marie-Helene; Evans, Alan C; Zilles, Karl; Amunts, Katrin

2007-07-01

Probabilistic cytoarchitectonic maps in standard reference space provide a powerful tool for the analysis of structure-function relationships in the human brain. While these microstructurally defined maps have already been successfully used in the analysis of somatosensory, motor or language functions, several conceptual issues in the analysis of structure-function relationships still demand further clarification. In this paper, we demonstrate the principle approaches for anatomical localisation of functional activations based on probabilistic cytoarchitectonic maps by exemplary analysis of an anterior parietal activation evoked by visual presentation of hand gestures. After consideration of the conceptual basis and implementation of volume or local maxima labelling, we comment on some potential interpretational difficulties, limitations and caveats that could be encountered. Extending and supplementing these methods, we then propose a supplementary approach for quantification of structure-function correspondences based on distribution analysis. This approach relates the cytoarchitectonic probabilities observed at a particular functionally defined location to the areal specific null distribution of probabilities across the whole brain (i.e., the full probability map). Importantly, this method avoids the need for a unique classification of voxels to a single cortical area and may increase the comparability between results obtained for different areas. Moreover, as distribution-based labelling quantifies the "central tendency" of an activation with respect to anatomical areas, it will, in combination with the established methods, allow an advanced characterisation of the anatomical substrates of functional activations. Finally, the advantages and disadvantages of the various methods are discussed, focussing on the question of which approach is most appropriate for a particular situation.

Isogeometric analysis of free-form Timoshenko curved beams including the nonlinear effects of large deformations

NASA Astrophysics Data System (ADS)

Hosseini, Seyed Farhad; Hashemian, Ali; Moetakef-Imani, Behnam; Hadidimoud, Saied

2018-03-01

In the present paper, the isogeometric analysis (IGA) of free-form planar curved beams is formulated based on the nonlinear Timoshenko beam theory to investigate the large deformation of beams with variable curvature. Based on the isoparametric concept, the shape functions of the field variables (displacement and rotation) in a finite element analysis are considered to be the same as the non-uniform rational basis spline (NURBS) basis functions defining the geometry. The validity of the presented formulation is tested in five case studies covering a wide range of engineering curved structures including from straight and constant curvature to variable curvature beams. The nonlinear deformation results obtained by the presented method are compared to well-established benchmark examples and also compared to the results of linear and nonlinear finite element analyses. As the nonlinear load-deflection behavior of Timoshenko beams is the main topic of this article, the results strongly show the applicability of the IGA method to the large deformation analysis of free-form curved beams. Finally, it is interesting to notice that, until very recently, the large deformations analysis of free-form Timoshenko curved beams has not been considered in IGA by researchers.

Identifying biologically relevant differences between metagenomic communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2010-03-15

Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis. We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of 'Candidatus Accumulibacter phosphatis' in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport. Python source code and binaries are freely available from our website at http://kiwi.cs.dal.ca/Software/STAMP CONTACT: beiko@cs.dal.ca Supplementary data are available at Bioinformatics online.

Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample.

PubMed

Illeghems, Koen; Weckx, Stefan; De Vuyst, Luc

2015-09-01

A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cluster analysis differentiates high and low community functioning in schizophrenia: Subgroups differ on working memory but not other neurocognitive domains.

PubMed

Alden, Eva C; Cobia, Derin J; Reilly, James L; Smith, Matthew J

2015-10-01

Schizophrenia is characterized by impairment in multiple aspects of community functioning. Available literature suggests that community functioning may be enhanced through cognitive remediation, however, evidence is limited regarding whether specific neurocognitive domains may be treatment targets. We characterized schizophrenia subjects based on their level of community functioning through cluster analysis in an effort to identify whether specific neurocognitive domains were associated with variation in functioning. Schizophrenia (SCZ, n=60) and control (CON, n=45) subjects completed a functional capacity task, social competence role-play, functional attainment interview, and a neuropsychological battery. Multiple cluster analytic techniques were used on the measures of functioning in the schizophrenia subjects to generate functionally-defined subgroups. MANOVA evaluated between-group differences in neurocognition. The cluster analysis revealed two distinct groups, consisting of 36 SCZ characterized by high levels of community functioning (HF-SCZ) and 24 SCZ with low levels of community functioning (LF-SCZ). There was a main group effect for neurocognitive performance (p<0.001) with CON outperforming both SCZ groups in all neurocognitive domains. Post-hoc tests revealed that HF-SCZ had higher verbal working memory compared to LF-SCZ (p≤0.05, Cohen's d=0.78) but the two groups did not differ in remaining domains. The cluster analysis classified schizophrenia subjects in HF-SCZ and LF-SCZ using a multidimensional assessment of community functioning. Moreover, HF-SCZ demonstrated rather preserved verbal working memory relative to LF-SCZ. The results suggest that verbal working memory may play a critical role in community functioning, and is a potential cognitive treatment target for schizophrenia subjects. Copyright © 2015 Elsevier B.V. All rights reserved.

A randomized controlled trial of qigong for fibromyalgia

PubMed Central

2012-01-01

Introduction Fibromyalgia is difficult to treat and requires the use of multiple approaches. This study is a randomized controlled trial of qigong compared with a wait-list control group in fibromyalgia. Methods One hundred participants were randomly assigned to immediate or delayed practice groups, with the delayed group receiving training at the end of the control period. Qigong training (level 1 Chaoyi Fanhuan Qigong, CFQ), given over three half-days, was followed by weekly review/practice sessions for eight weeks; participants were also asked to practice at home for 45 to 60 minutes per day for this interval. Outcomes were pain, impact, sleep, physical function and mental function, and these were recorded at baseline, eight weeks, four months and six months. Immediate and delayed practice groups were analyzed individually compared to the control group, and as a combination group. Results In both the immediate and delayed treatment groups, CFQ demonstrated significant improvements in pain, impact, sleep, physical function and mental function when compared to the wait-list/usual care control group at eight weeks, with benefits extending beyond this time. Analysis of combined data indicated significant changes for all measures at all times for six months, with only one exception. Post-hoc analysis based on self-reported practice times indicated greater benefit with the per protocol group compared to minimal practice. Conclusions This study demonstrates that CFQ, a particular form of qigong, provides long-term benefits in several core domains in fibromyalgia. CFQ may be a useful adjuvant self-care treatment for fibromyalgia. Trial registration clinicaltrials.gov NCT00938834. PMID:22863206

Comparative Transcriptome Analysis of the Accessory Sex Gland and Testis from the Chinese Mitten Crab (Eriocheir sinensis)

PubMed Central

He, Lin; Jiang, Hui; Cao, Dandan; Liu, Lihua; Hu, Songnian; Wang, Qun

2013-01-01

The accessory sex gland (ASG) is an important component of the male reproductive system, which functions to enhance the fertility of spermatozoa during male reproduction. Certain proteins secreted by the ASG are known to bind to the spermatozoa membrane and affect its function. The ASG gene expression profile in Chinese mitten crab (Eriocheir sinensis) has not been extensively studied, and limited genetic research has been conducted on this species. The advent of high-throughput sequencing technologies enables the generation of genomic resources within a short period of time and at minimal cost. In the present study, we performed de novo transcriptome sequencing to produce a comprehensive transcript dataset for the ASG of E. sinensis using Illumina sequencing technology. This analysis yielded a total of 33,221,284 sequencing reads, including 2.6 Gb of total nucleotides. Reads were assembled into 85,913 contigs (average 218 bp), or 58,567 scaffold sequences (average 292 bp), that identified 37,955 unigenes (average 385 bp). We assembled all unigenes and compared them with the published testis transcriptome from E. sinensis. In order to identify which genes may be involved in ASG function, as it pertains to modification of spermatozoa, we compared the ASG and testis transcriptome of E. sinensis. Our analysis identified specific genes with both higher and lower tissue expression levels in the two tissues, and the functions of these genes were analyzed to elucidate their potential roles during maturation of spermatozoa. Availability of detailed transcriptome data from ASG and testis in E. sinensis can assist our understanding of the molecular mechanisms involved with spermatozoa conservation, transport, maturation and capacitation and potentially acrosome activation. PMID:23342039

Differential Effect of Active Smoking on Gene Expression in Male and Female Smokers

PubMed Central

Paul, Sunirmal; Amundson, Sally A

2015-01-01

Smoking is the second leading cause of preventable death in the United States. Cohort epidemiological studies have demonstrated that women are more vulnerable to cigarette-smoking induced diseases than their male counterparts, however, the molecular basis of these differences has remained unknown. In this study, we explored if there were differences in the gene expression patterns between male and female smokers, and how these patterns might reflect different sex-specific responses to the stress of smoking. Using whole genome microarray gene expression profiling, we found that a substantial number of oxidant related genes were expressed in both male and female smokers, however, smoking-responsive genes did indeed differ greatly between male and female smokers. Gene set enrichment analysis (GSEA) against reference oncogenic signature gene sets identified a large number of oncogenic pathway gene-sets that were significantly altered in female smokers compared to male smokers. In addition, functional annotation with Ingenuity Pathway Analysis (IPA) identified smoking-correlated genes associated with biological functions in male and female smokers that are directly relevant to well-known smoking related pathologies. However, these relevant biological functions were strikingly overrepresented in female smokers compared to male smokers. IPA network analysis with the functional categories of immune and inflammatory response gene products suggested potential interactions between smoking response and female hormones. Our results demonstrate a striking dichotomy between male and female gene expression responses to smoking. This is the first genome-wide expression study to compare the sex-specific impacts of smoking at a molecular level and suggests a novel potential connection between sex hormone signaling and smoking-induced diseases in female smokers. PMID:25621181

Cardiomyocyte-specific deletion of the G protein-coupled estrogen receptor (GPER) leads to left ventricular dysfunction and adverse remodeling: A sex-specific gene profiling analysis.

PubMed

Wang, Hao; Sun, Xuming; Chou, Jeff; Lin, Marina; Ferrario, Carlos M; Zapata-Sudo, Gisele; Groban, Leanne

2017-08-01

Activation of G protein-coupled estrogen receptor (GPER) by its agonist, G1, protects the heart from stressors such as pressure-overload, ischemia, a high-salt diet, estrogen loss, and aging, in various male and female animal models. Due to nonspecific effects of G1, the exact functions of cardiac GPER cannot be concluded from studies using systemic G1 administration. Moreover, global knockdown of GPER affects glucose homeostasis, blood pressure, and many other cardiovascular-related systems, thereby confounding interpretation of its direct cardiac actions. We generated a cardiomyocyte-specific GPER knockout (KO) mouse model to specifically investigate the functions of GPER in cardiomyocytes. Compared to wild type mice, cardiomyocyte-specific GPER KO mice exhibited adverse alterations in cardiac structure and impaired systolic and diastolic function, as measured by echocardiography. Gene deletion effects on left ventricular dimensions were more profound in male KO mice compared to female KO mice. Analysis of DNA microarray data from isolated cardiomyocytes of wild type and KO mice revealed sex-based differences in gene expression profiles affecting multiple transcriptional networks. Gene Set Enrichment Analysis (GSEA) revealed that mitochondrial genes are enriched in GPER KO females, whereas inflammatory response genes are enriched in GPER KO males, compared to their wild type counterparts of the same sex. The cardiomyocyte-specific GPER KO mouse model provides us with a powerful tool to study the functions of GPER in cardiomyocytes. The gene expression profiles of the GPER KO mice provide foundational information for further study of the mechanisms underlying sex-specific cardioprotection by GPER. Copyright © 2016 Elsevier B.V. All rights reserved.

Treatment effectiveness and fidelity of manual therapy to the knee: A systematic review and meta-analysis.

PubMed

Salamh, Paul; Cook, Chad; Reiman, Michael P; Sheets, Charles

2017-09-01

Manual therapy (MT) is a commonly used treatment for knee osteoarthritis (OA) but to date only one systematic review has explored its effectiveness. The purpos e of the present study was to perform a systematic review and meta-analysis of the literature, to determine the effectiveness and fidelity of studies using MT techniques in individuals with knee OA. Relevant studies were assessed for inclusion. Effectiveness was measured using effect sizes, and methodological bias and treatment fidelity were both explored. Effect sizes were calculated using standardized mean differences (SMD) based on pooled data depending on statistical and clinical heterogeneity, as well as risk of bias. The search captured 2,969 studies; after screening, 12 were included. Four had a low risk of bias and high treatment fidelity. For self-reported function, comparing MT with no treatment resulted in a large effect size (standardized mean difference [SMD] 0.84), as did adding MT to a comparator treatment (SMD 0.78). A significant difference was found for pain when adding MT to a comparator treatment (SMD 0.73). The findings in the present meta-analytical review support the use of MT versus a number of different comparators for improvement in self-reported knee function. Lesser support is present for pain reduction, and no endorsement of functional performance can be made at this time. Copyright © 2016 John Wiley & Sons, Ltd.

The Evolution of Self-Reported Urinary and Sexual Dysfunction over the Last Two Decades: Implications for Comparative Effectiveness Research.

PubMed

Resnick, Matthew J; Barocas, Daniel A; Morgans, Alicia K; Phillips, Sharon E; Koyama, Tatsuki; Albertsen, Peter C; Cooperberg, Matthew R; Goodman, Michael; Greenfield, Sheldon; Hamilton, Ann S; Hoffman, Karen E; Hoffman, Richard M; Kaplan, Sherrie H; McCollum, Dan; Paddock, Lisa E; Stanford, Janet L; Stroup, Antoinette M; Wu, Xiao-Cheng; Penson, David F

2015-06-01

Despite the paramount importance of patient-reported outcomes, little is known about the evolution of patient-reported urinary and sexual function over time. To evaluate differences in pretreatment urinary and sexual function in two population-based cohorts of men with prostate cancer enrolled nearly 20 yr apart. Patients were enrolled in the Prostate Cancer Outcomes Study (PCOS) or the Comparative Effectiveness Analysis of Surgery and Radiation (CEASAR) study, two population-based cohorts that enrolled patients with incident prostate cancer from 1994 to 1995 and from 2011 to 2012, respectively. Participants completed surveys at baseline and various time points thereafter. We performed multivariable logistic and linear regression analysis to investigate differences in pretreatment function between studies. The study comprised 5469 men of whom 2334 (43%) were enrolled in PCOS and 3135 (57%) were enrolled in CEASAR. Self-reported urinary incontinence was higher in CEASAR compared with PCOS (7.7% vs 4.7%; adjusted odds ratio [OR]: 1.83; 95% confidence interval [CI], 1.39-2.43). Similarly, self-reported erectile dysfunction was more common among CEASAR participants (44.7% vs 24.0%) with an adjusted OR of 3.12 (95% CI, 2.68-3.64). Multivariable linear regression models revealed less favorable self-reported baseline function among CEASAR participants in the urinary incontinence and sexual function domains. The study is limited by its observational design and possibility of unmeasured confounding. Reporting of pretreatment urinary incontinence and erectile dysfunction has increased over the past two decades. These findings may reflect sociological changes including heightened media attention and direct-to-consumer marketing, among other potential explanations. Patient reporting of urinary and sexual function has evolved and is likely contingent on continually changing societal norms. Recognizing the evolving nature of patient reporting is essential in efforts to conduct high-quality, impactful comparative effectiveness research. Copyright © 2014 European Association of Urology. All rights reserved.

Functionalization of Graphene Nanoplatelets Using Sugar Azide for Graphene/Epoxy Nanocomposites

DTIC Science & Technology

2014-06-20

temperature to 200°C in the single cantilever mode at a heating rate and frequency of 3°C/min and 1 Hz, respectively. Thermogravimetric analysis (TGA) of...14. ABSTRACT We report a covalent functionalization of graphene nanoparticles (GnPs) employing 2,3,4-Tri-O-acetyl-β-D-xylopyranosyl azide...and glass transition temperature (~10C) compared to an un-functionalized GnP based epoxy composite. 15. SUBJECT TERMS Graphene nanoparticles

Multi-scale comparison of source parameter estimation using empirical Green's function approach

NASA Astrophysics Data System (ADS)

Chen, X.; Cheng, Y.

2015-12-01

Analysis of earthquake source parameters requires correction of path effect, site response, and instrument responses. Empirical Green's function (EGF) method is one of the most effective methods in removing path effects and station responses by taking the spectral ratio between a larger and smaller event. Traditional EGF method requires identifying suitable event pairs, and analyze each event individually. This allows high quality estimations for strictly selected events, however, the quantity of resolvable source parameters is limited, which challenges the interpretation of spatial-temporal coherency. On the other hand, methods that exploit the redundancy of event-station pairs are proposed, which utilize the stacking technique to obtain systematic source parameter estimations for a large quantity of events at the same time. This allows us to examine large quantity of events systematically, facilitating analysis of spatial-temporal patterns, and scaling relationship. However, it is unclear how much resolution is scarified during this process. In addition to the empirical Green's function calculation, choice of model parameters and fitting methods also lead to biases. Here, using two regional focused arrays, the OBS array in the Mendocino region, and the borehole array in the Salton Sea geothermal field, I compare the results from the large scale stacking analysis, small-scale cluster analysis, and single event-pair analysis with different fitting methods to systematically compare the results within completely different tectonic environment, in order to quantify the consistency and inconsistency in source parameter estimations, and the associated problems.

Comparison of dose response functions for EBT3 model GafChromic™ film dosimetry system.

PubMed

Aldelaijan, Saad; Devic, Slobodan

2018-05-01

Different dose response functions of EBT3 model GafChromic™ film dosimetry system have been compared in terms of sensitivity as well as uncertainty vs. error analysis. We also made an assessment of the necessity of scanning film pieces before and after irradiation. Pieces of EBT3 film model were irradiated to different dose values in Solid Water (SW) phantom. Based on images scanned in both reflection and transmission mode before and after irradiation, twelve different response functions were calculated. For every response function, a reference radiochromic film dosimetry system was established by generating calibration curve and by performing the error vs. uncertainty analysis. Response functions using pixel values from the green channel demonstrated the highest sensitivity in both transmission and reflection mode. All functions were successfully fitted with rational functional form, and provided an overall one-sigma uncertainty of better than 2% for doses above 2 Gy. Use of pre-scanned images to calculate response functions resulted in negligible improvement in dose measurement accuracy. Although reflection scanning mode provides higher sensitivity and could lead to a more widespread use of radiochromic film dosimetry, it has fairly limited dose range and slightly increased uncertainty when compared to transmission scan based response functions. Double-scanning technique, either in transmission or reflection mode, shows negligible improvement in dose accuracy as well as a negligible increase in dose uncertainty. Normalized pixel value of the images scanned in transmission mode shows linear response in a dose range of up to 11 Gy. Copyright © 2018 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Altered resting-state functional connectivity in post-traumatic stress disorder: a perfusion MRI study

NASA Astrophysics Data System (ADS)

Li, Baojuan; Liu, Jian; Liu, Yang; Lu, Hong-Bing; Yin, Hong

2013-03-01

The majority of studies on posttraumatic stress disorder (PTSD) so far have focused on delineating patterns of activations during cognitive processes. Recently, more and more researches have started to investigate functional connectivity in PTSD subjects using BOLD-fMRI. Functional connectivity analysis has been demonstrated as a powerful approach to identify biomarkers of different brain diseases. This study aimed to detect resting-state functional connectivity abnormities in patients with PTSD using arterial spin labeling (ASL) fMRI. As a completely non-invasive technique, ASL allows quantitative estimates of cerebral blood flow (CBF). Compared with BOLD-fMRI, ASL fMRI has many advantages, including less low-frequency signal drifts, superior functional localization, etc. In the current study, ASL images were collected from 10 survivors in mining disaster with recent onset PTSD and 10 survivors without PTSD. Decreased regional CBF in the right middle temporal gyrus, lingual gyrus, and postcentral gyrus was detected in the PTSD patients. Seed-based resting-state functional connectivity analysis was performed using an area in the right middle temporal gyrus as region of interest. Compared with the non-PTSD group, the PTSD subjects demonstrated increased functional connectivity between the right middle temporal gyrus and the right superior temporal gyrus, the left middle temporal gyrus. Meanwhile, decreased functional connectivity between the right middle temporal gyrus and the right postcentral gyrus, the right superior parietal lobule was also found in the PTSD patients. This is the first study which investigated resting-state functional connectivity in PTSD using ASL images. The results may provide new insight into the neural substrates of PTSD.

Effects of Elastic Resistance Exercise on Muscle Strength and Functional Performance in Healthy Adults: A Systematic Review and Meta-Analysis.

PubMed

de Oliveira, Poliana Alves; Blasczyk, Juscelino Castro; Souza Junior, Gerson; Lagoa, Karina Ferreira; Soares, Milene; de Oliveira, Ricardo Jacó; Filho, Paulo José Barbosa Gutierres; Carregaro, Rodrigo Luiz; Martins, Wagner Rodrigues

2017-04-01

Elastic Resistance Exercise (ERE) has already demonstrated its effectiveness in older adults and, when combined with the resistance generated by fixed loads, in adults. This review summarizes the effectiveness of ERE performed as isolated method on muscle strength and functional performance in healthy adults. A database search was performed (MEDLine, Cochrane Library, PEDro and Web of Knowledge) to identify controlled clinical trials in English language. The mean difference (MD) with 95% confidence intervals (CIs) and overall effect size were calculated for all comparisons. The PEDro scale was used assess the methodological quality. From the 93 articles identified by the search strategy, 5 met the inclusion criteria, in which 3 presented high quality (PEDro > 6). Meta-analyses demonstrated that the effects of ERE were superior when compared with passive control on functional performance and muscle strength. When compared with active controls, the effect of ERE was inferior on function performance and with similar effect on muscle strength. ERE are effective to improve functional performance and muscle strength when compared with no intervention, in healthy adults. ERE are not superior to other methods of resistance training to improve functional performance and muscle strength in health adults.

Functional magnetic resonance imaging activation detection: fuzzy cluster analysis in wavelet and multiwavelet domains.

PubMed

Jahanian, Hesamoddin; Soltanian-Zadeh, Hamid; Hossein-Zadeh, Gholam-Ali

2005-09-01

To present novel feature spaces, based on multiscale decompositions obtained by scalar wavelet and multiwavelet transforms, to remedy problems associated with high dimension of functional magnetic resonance imaging (fMRI) time series (when they are used directly in clustering algorithms) and their poor signal-to-noise ratio (SNR) that limits accurate classification of fMRI time series according to their activation contents. Using randomization, the proposed method finds wavelet/multiwavelet coefficients that represent the activation content of fMRI time series and combines them to define new feature spaces. Using simulated and experimental fMRI data sets, the proposed feature spaces are compared to the cross-correlation (CC) feature space and their performances are evaluated. In these studies, the false positive detection rate is controlled using randomization. To compare different methods, several points of the receiver operating characteristics (ROC) curves, using simulated data, are estimated and compared. The proposed features suppress the effects of confounding signals and improve activation detection sensitivity. Experimental results show improved sensitivity and robustness of the proposed method compared to the conventional CC analysis. More accurate and sensitive activation detection can be achieved using the proposed feature spaces compared to CC feature space. Multiwavelet features show superior detection sensitivity compared to the scalar wavelet features. (c) 2005 Wiley-Liss, Inc.

Effects of Hurricane Katrina on nursing facility resident mortality, hospitalization, and functional decline.

PubMed

Dosa, David; Feng, Zhanlian; Hyer, Kathy; Brown, Lisa M; Thomas, Kali; Mor, Vincent

2010-09-01

The study was designed to examine the 30- and 90-day mortality and hospitalization rates among nursing facility (NF) residents in the affected areas of Louisiana and Mississippi following Hurricane Katrina and to assess the rate of significant posthurricane functional decline. A secondary data analysis was conducted using Medicare claims merged with NF resident data from the Minimum Data Set. Thirty- and 90-day mortality and hospitalization rates for long-stay (>90 days) residents residing in 141 at-risk NFs during Hurricane Katrina were compared to rates for residents residing at the same facilities during the same time period in prior nonhurricane years (2003 and 2004). Functional decline was assessed as a 4+ drop in function using a 28-point Minimum Data Set Activities of Daily Living Scale. There were statistically significant differences (all P < .0001) in mortality, hospitalization, and functional decline among residents exposed to Hurricane Katrina. At 30 days, the mortality rate was 3.88% among the exposed cohort compared with 2.10% and 2.28% for residents in 2003 and 2004, respectively. The 90-day mortality rate was 9.27% compared with 6.71% and 6.31%, respectively. These mortality differences translated into an additional 148 deaths at 30 days and 230 deaths at 90 days. The 30-day hospitalization rate was 9.87% compared with 7.21% and 7.53%, respectively. The 90-day hospitalization rate was 20.39% compared with 18.61% and 17.82%, respectively. Finally, the rate of significant functional decline among survivors was 6.77% compared with 5.81% in 2003 and 5.10% in 2004. NF residents experienced a significant increase in mortality, hospitalization, and functional decline during Hurricane Katrina.

An exploratory data analysis of electroencephalograms using the functional boxplots approach

PubMed Central

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

2015-01-01

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

Using a Mixture IRT Model to Understand English Learner Performance on Large-Scale Assessments

ERIC Educational Resources Information Center

Shea, Christine A.

2013-01-01

The purpose of this study was to determine whether an eighth grade state-level math assessment contained items that function differentially (DIF) for English Learner students (EL) as compared to English Only students (EO) and if so, what factors might have caused DIF. To determine this, Differential Item Functioning (DIF) analysis was employed.…

Manage Work Better to Better Manage Human Resources: A Comparative Study of Two Approaches to Job Analysis.

ERIC Educational Resources Information Center

Clifford, James P.

1996-01-01

The Position Classification Questionnaire (PCQ) and task inventory method (TI) were used to study the same work functions. PCQ divided functions into 16 classes for wage/salary determination. TI divided them into 28 classifications for training purposes. The two approaches were considerably different in their approach to how work should be…

Nonperturbative evaluation for anomalous dimension in 2-dimensional O (3 ) sigma model

NASA Astrophysics Data System (ADS)

Calle Jimenez, Sergio; Oka, Makoto; Sasaki, Kiyoshi

2018-06-01

We nonperturbatively calculate the wave-function renormalization in the two-dimensional O (3 ) sigma model. It is evaluated in a box with a finite spatial extent. We determine the anomalous dimension in the finite-volume scheme through an analysis of the step-scaling function. Results are compared with a perturbative evaluation, and reasonable behavior is observed.

Comparing production function models for wildfire risk analysis in the wildland-urban interface

Treesearch

D. Evan Mercer; Jeffrey P. Prestemon

2005-01-01

Wildfires create damages in the wildland-urban interface (WUI) that total hundreds of millions of dollars annually in the United States. Understanding how fires are produced in built-up areas near and within fire prone landscapes requires evaluating and quantifling the roles that humans play in fire regimes. We outline a typology of wildfire production functions (WPFs...

Comparative Network-Based Recovery Analysis and Proteomic Profiling of Neurological Changes in Valproic Acid-Treated Mice

PubMed Central

2013-01-01

Despite its prominence for characterization of complex mixtures, LC–MS/MS frequently fails to identify many proteins. Network-based analysis methods, based on protein–protein interaction networks (PPINs), biological pathways, and protein complexes, are useful for recovering non-detected proteins, thereby enhancing analytical resolution. However, network-based analysis methods do come in varied flavors for which the respective efficacies are largely unknown. We compare the recovery performance and functional insights from three distinct instances of PPIN-based approaches, viz., Proteomics Expansion Pipeline (PEP), Functional Class Scoring (FCS), and Maxlink, in a test scenario of valproic acid (VPA)-treated mice. We find that the most comprehensive functional insights, as well as best non-detected protein recovery performance, are derived from FCS utilizing real biological complexes. This outstrips other network-based methods such as Maxlink or Proteomics Expansion Pipeline (PEP). From FCS, we identified known biological complexes involved in epigenetic modifications, neuronal system development, and cytoskeletal rearrangements. This is congruent with the observed phenotype where adult mice showed an increase in dendritic branching to allow the rewiring of visual cortical circuitry and an improvement in their visual acuity when tested behaviorally. In addition, PEP also identified a novel complex, comprising YWHAB, NR1, NR2B, ACTB, and TJP1, which is functionally related to the observed phenotype. Although our results suggest different network analysis methods can produce different results, on the whole, the findings are mutually supportive. More critically, the non-overlapping information each provides can provide greater holistic understanding of complex phenotypes. PMID:23557376

Multiparametric MRI characterization and prediction in autism spectrum disorder using graph theory and machine learning.

PubMed

Zhou, Yongxia; Yu, Fang; Duong, Timothy

2014-01-01

This study employed graph theory and machine learning analysis of multiparametric MRI data to improve characterization and prediction in autism spectrum disorders (ASD). Data from 127 children with ASD (13.5±6.0 years) and 153 age- and gender-matched typically developing children (14.5±5.7 years) were selected from the multi-center Functional Connectome Project. Regional gray matter volume and cortical thickness increased, whereas white matter volume decreased in ASD compared to controls. Small-world network analysis of quantitative MRI data demonstrated decreased global efficiency based on gray matter cortical thickness but not with functional connectivity MRI (fcMRI) or volumetry. An integrative model of 22 quantitative imaging features was used for classification and prediction of phenotypic features that included the autism diagnostic observation schedule, the revised autism diagnostic interview, and intelligence quotient scores. Among the 22 imaging features, four (caudate volume, caudate-cortical functional connectivity and inferior frontal gyrus functional connectivity) were found to be highly informative, markedly improving classification and prediction accuracy when compared with the single imaging features. This approach could potentially serve as a biomarker in prognosis, diagnosis, and monitoring disease progression.

Persian version of frontal assessment battery: Correlations with formal measures of executive functioning and providing normative data for Persian population.

PubMed

Asaadi, Sina; Ashrafi, Farzad; Omidbeigi, Mahmoud; Nasiri, Zahra; Pakdaman, Hossein; Amini-Harandi, Ali

2016-01-05

Cognitive impairment in patients with Parkinson's disease (PD) mainly involves executive function (EF). The frontal assessment battery (FAB) is an efficient tool for the assessment of EFs. The aims of this study were to determine the validity and reliability of the psychometric properties of the Persian version of FAB and assess its correlation with formal measures of EFs to provide normative data for the Persian version of FAB in patients with PD. The study recruited 149 healthy participants and 49 patients with idiopathic PD. In PD patients, FAB results were compared to their performance on EF tests. Reliability analysis involved test-retest reliability and internal consistency, whereas validity analysis involved convergent validity approach. FAB scores compared in normal controls and in PD patients matched for age, education, and Mini-Mental State Examination (MMSE) score. In PD patients, FAB scores were significantly decreased compared to normal controls, and correlated with Stroop test and Wisconsin Card Sorting Test (WCST). In healthy subjects, FAB scores varied according to the age, education, and MMSE. In the FAB subtest analysis, the performances of PD patients were worse than the healthy participants on similarities, fluency tasks, and Luria's motor series. Persian version of FAB could be used as a reliable scale for the assessment of frontal lobe functions in Iranian patients with PD. Furthermore, normative data provided for the Persian version of this test improve the accuracy and confidence in the clinical application of the FAB.

Multifractal analysis of information processing in hippocampal neural ensembles during working memory under Δ9-tetrahydrocannabinol administration

PubMed Central

Fetterhoff, Dustin; Opris, Ioan; Simpson, Sean L.; Deadwyler, Sam A.; Hampson, Robert E.; Kraft, Robert A.

2014-01-01

Background Multifractal analysis quantifies the time-scale-invariant properties in data by describing the structure of variability over time. By applying this analysis to hippocampal interspike interval sequences recorded during performance of a working memory task, a measure of long-range temporal correlations and multifractal dynamics can reveal single neuron correlates of information processing. New method Wavelet leaders-based multifractal analysis (WLMA) was applied to hippocampal interspike intervals recorded during a working memory task. WLMA can be used to identify neurons likely to exhibit information processing relevant to operation of brain–computer interfaces and nonlinear neuronal models. Results Neurons involved in memory processing (“Functional Cell Types” or FCTs) showed a greater degree of multifractal firing properties than neurons without task-relevant firing characteristics. In addition, previously unidentified FCTs were revealed because multifractal analysis suggested further functional classification. The cannabinoid-type 1 receptor partial agonist, tetrahydrocannabinol (THC), selectively reduced multifractal dynamics in FCT neurons compared to non-FCT neurons. Comparison with existing methods WLMA is an objective tool for quantifying the memory-correlated complexity represented by FCTs that reveals additional information compared to classification of FCTs using traditional z-scores to identify neuronal correlates of behavioral events. Conclusion z-Score-based FCT classification provides limited information about the dynamical range of neuronal activity characterized by WLMA. Increased complexity, as measured with multifractal analysis, may be a marker of functional involvement in memory processing. The level of multifractal attributes can be used to differentially emphasize neural signals to improve computational models and algorithms underlying brain–computer interfaces. PMID:25086297

Efficacy of pirfenidone and disease severity of idiopathic pulmonary fibrosis: Extended analysis of phase III trial in Japan.

PubMed

Taguchi, Yoshio; Ebina, Masahito; Hashimoto, Seishu; Ogura, Takashi; Azuma, Arata; Taniguchi, Hiroyuki; Kondoh, Yasuhiro; Suga, Moritaka; Takahashi, Hiroki; Nakata, Koichiro; Sugiyama, Yukihiko; Kudoh, Shoji; Nukiwa, Toshihiro

2015-11-01

A phase III clinical trial of pirfenidone in patients with idiopathic pulmonary fibrosis (IPF) in Japan has revealed that pirfenidone attenuated the decline in vital capacity (VC) and improved progression-free survival (PFS). We conducted an extended analysis of the pirfenidone trial to investigate its efficacy with respect to IPF severity in the trial population. Patients in the phase III trial were stratified by baseline pulmonary functions including %VC predicted, %diffusion capacity for carbon monoxide predicted, and oxygen saturation by pulse oximetry on exertion and were categorized into mild, moderate, and severe groups of functional impairment. The efficacy of pirfenidone for VC and PFS over 52 weeks was compared among the three sub-populations. Of 264 patients, 102 (39%), 90 (34%), and 72 patients (27%) were classified as having mild, moderate, and severe grades of functional impairment, respectively. This classification was associated with arterial oxygen partial pressure at rest and degree of dyspnea at baseline. While pirfenidone attenuated VC decline at all grades of severity, covariance analysis revealed pirfenidone to have better efficacy in the sub-population with mild-grade IPF. Mixed model repeated measures analysis confirmed that pirfenidone markedly attenuated VC decline in patients with mild-grade IPF compared to its effects in patients with moderate or severe IPF. Pirfenidone also improved PFS markedly in patients with mild-grade IPF. This extended analysis suggested that pirfenidone exerted better therapeutic effects in patients with milder IPF. Further analysis with a larger population is needed to confirm these results. Copyright © 2015. Published by Elsevier B.V.

Mild thyroid hormone excess is associated with a decreased physical function in elderly men

PubMed Central

Ceresini, Graziano; Ceda, Gian Paolo; Lauretani, Fulvio; Maggio, Marcello; Bandinelli, Stefania; Guralnik, Jack M.; Cappola, Anne R.; Usberti, Elisa; Morganti, Simonetta; Valenti, Giorgio; Ferrucci, Luigi

2015-01-01

Introduction In the adult, subclinical hyperthyroidism (Shyper) may alter skeletal muscle mass and strength. However, whether these effects are present in elderly subjects is not known. We explored the relationship between mild hyperthyroidism and physical function in a population-based sample of older persons. Methods In a cross-sectional analysis, calf muscle cross-sectional area (CMA), handgrip strength, nerve conduction velocity (NCV), and Short Physical Performance Battery (SPPB) scores were compared between 364 euthyroid (Eut) and 28 Shyper men as well as between 502 Eut and 39 Shyper women. In a longitudinal analysis, we evaluated the relationship between baseline plasma TSH, FT3 and FT4 and the 3-year change in SPPB score in 304 men and 409 women who were euthyroid at enrolment. Results At the cross-sectional analysis, Shyper men, but not women, had a significantly (p = 0.02) lower SPPB score than Eut controls, although with comparable CMA, grip strength and NCV, and were more likely to have poor physical performance (odds ratio = 2.97, p< 0.05). Longitudinal analysis showed that in Eut men higher baseline FT4 was significantly (p=0.02) predictive of a lower SPPB score at the 3-year follow-up. Conclusion Even a modest thyroid hormone excess is associated with a reduced physical function in elderly men. PMID:21875391

Horizontal gene transfer in silkworm, Bombyx mori.

PubMed

Zhu, Bo; Lou, Miao-Miao; Xie, Guan-Lin; Zhang, Guo-Qing; Zhou, Xue-Ping; Li, Bin; Jin, Gu-Lei

2011-05-19

The domesticated silkworm, Bombyx mori, is the model insect for the order Lepidoptera, has economically important values, and has gained some representative behavioral characteristics compared to its wild ancestor. The genome of B. mori has been fully sequenced while function analysis of BmChi-h and BmSuc1 genes revealed that horizontal gene transfer (HGT) maybe bestow a clear selective advantage to B. mori. However, the role of HGT in the evolutionary history of B. mori is largely unexplored. In this study, we compare the whole genome of B. mori with those of 382 prokaryotic and eukaryotic species to investigate the potential HGTs. Ten candidate HGT events were defined in B. mori by comprehensive sequence analysis using Maximum Likelihood and Bayesian method combining with EST checking. Phylogenetic analysis of the candidate HGT genes suggested that one HGT was plant-to- B. mori transfer while nine were bacteria-to- B. mori transfer. Furthermore, functional analysis based on expression, coexpression and related literature searching revealed that several HGT candidate genes have added important characters, such as resistance to pathogen, to B. mori. Results from this study clearly demonstrated that HGTs play an important role in the evolution of B. mori although the number of HGT events in B. mori is in general smaller than those of microbes and other insects. In particular, interdomain HGTs in B. mori may give rise to functional, persistent, and possibly evolutionarily significant new genes.

Development of Evaluation Methods for Lower Limb Function between Aged and Young Using Principal Component Analysis

NASA Astrophysics Data System (ADS)

Nomoto, Yohei; Yamashita, Kazuhiko; Ohya, Tetsuya; Koyama, Hironori; Kawasumi, Masashi

There is the increasing concern of the society to prevent the fall of the aged. The improvement in aged people's the muscular strength of the lower-limb, postural control and walking ability are important for quality of life and fall prevention. The aim of this study was to develop multiple evaluation methods in order to advise for improvement and maintenance of lower limb function between aged and young. The subjects were 16 healthy young volunteers (mean ± S.D: 19.9 ± 0.6 years) and 10 healthy aged volunteers (mean ± S.D: 80.6 ± 6.1 years). Measurement items related to lower limb function were selected from the items which we have ever used. Selected measurement items of function of lower are distance of extroversion of the toe, angle of flexion of the toe, maximum width of step, knee elevation, moving distance of greater trochanter, walking balance, toe-gap force and rotation range of ankle joint. Measurement items summarized by the principal component analysis into lower ability evaluation methods including walking ability and muscle strength of lower limb and flexibility of ankle. The young group demonstrated the factor of 1.6 greater the assessment score of walking ability compared with the aged group. The young group demonstrated the factor of 1.4 greater the assessment score of muscle strength of lower limb compared with the aged group. The young group demonstrated the factor of 1.2 greater the assessment score of flexibility of ankle compared with the aged group. The results suggested that it was possible to assess the lower limb function of aged and young numerically and to advise on their foot function.

Meta-analysis of neuropsychological measures of executive functioning in children and adolescents with high-functioning autism spectrum disorder.

PubMed

Lai, Chun Lun Eric; Lau, Zoe; Lui, Simon S Y; Lok, Eugenia; Tam, Venus; Chan, Quinney; Cheng, Koi Man; Lam, Siu Man; Cheung, Eric F C

2017-05-01

Existing literature on the profile of executive dysfunction in autism spectrum disorder showed inconsistent results. Age, comorbid attention-deficit/hyperactivity disorder (ADHD) and cognitive abilities appeared to play a role in confounding the picture. Previous meta-analyses have focused on a few components of executive functions. This meta-analysis attempted to delineate the profile of deficit in several components of executive functioning in children and adolescents with high-functioning autism spectrum disorder (HFASD). Ninety-eight English published case-control studies comparing children and adolescents with HFASD with typically developing controls using well-known neuropsychological measures to assess executive functions were included. Results showed that children and adolescents with HFASD were moderately impaired in verbal working memory (g = 0.67), spatial working memory (g = 0.58), flexibility (g = 0.59), planning (g = 0.62), and generativity (g = 0.60) except for inhibition (g = 0.41). Subgroup analysis showed that impairments were still significant for flexibility (g = 0.57-0.61), generativity (g = 0.52-0.68), and working memory (g = 0.49-0.56) in a sample of autism spectrum disorder (ASD) subjects without comorbid ADHD or when the cognitive abilities of the ASD group and the control group were comparable. This meta-analysis confirmed the presence of executive dysfunction in children and adolescents with HFASD. These deficits are not solely accounted for by the effect of comorbid ADHD and the general cognitive abilities. Our results support the executive dysfunction hypothesis and contribute to the clinical understanding and possible development of interventions to alleviate these deficits in children and adolescents with HFASD. Autism Res 2017, 10: 911-939. © 2016 International Society for Autism Research, Wiley Periodicals, Inc. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.

Particle acceleration in step function shear flows - A microscopic analysis

NASA Technical Reports Server (NTRS)

Jokipii, J. R.; Morfill, G. E.

1990-01-01

The transport of energetic particles in a moving, scattering fluid, which has a large shear in its velocity over a distance small compared with the scattering mean free path is discussed. The analysis is complementary to an earlier paper by Earl, Jokipii, and Morfill (1988), which considered effects of more-gradual shear in the diffusion approximation. The case in which the scattering fluid undergoes a step function change in velocity, in the direction normal to the flow is considered. An analytical, approximate calculation and a Monte Carlo analysis of particle motion are presented. It is found that particles gain energy at a rate proportional to the square of the magnitude of the velocity change.

Evaluation of autonomic functions of patients with multiple system atrophy and Parkinson's disease by head-up tilt test.

PubMed

Watano, Chikako; Shiota, Yuri; Onoda, Keiichi; Sheikh, Abdullah Md; Mishima, Seiji; Nitta, Eri; Yano, Shozo; Yamaguchi, Shuhei; Nagai, Atsushi

2018-02-01

The aim of this study was to evaluate the autonomic neural function in Parkinson's disease (PD) and multiple system atrophy (MSA) with head-up tilt test and spectral analysis of cardiovascular parameters. This study included 15 patients with MSA, 15 patients with PD, and 29 healthy control (HC) subjects. High frequency power of the RR interval (RR-HF), the ratio of low frequency power of RR interval to RR-HF (RR-LF/HF) and LF power of systolic BP were used to evaluate parasympathetic, cardiac sympathetic and vasomotor sympathetic functions, respectively. Both patients with PD and MSA showed orthostatic hypotension and lower parasympathetic function (RR-HF) at tilt position as compared to HC subjects. Cardiac sympathetic function (RR-LF/HF) was significantly high in patients with PD than MSA at supine position. RR-LF/HF tended to increase in MSA and HC, but decreased in PD by tilting. Consequently, the change of the ratio due to tilting (ΔRR-LF/HF) was significantly lower in patients with PD than in HC subjects. Further analysis showed that compared to mild stage of PD, RR-LF/HF at the supine position was significantly higher in advanced stage. By tilting, it was increased in mild stage and decreased in the advanced stage of PD, causing ΔRR-LF/HF to decrease significantly in the advanced stage. Thus, we demonstrated that spectral analysis of cardiovascular parameters is useful to identify sympathetic and parasympathetic disorders in MSA and PD. High cardiac sympathetic function at the supine position, and its reduction by tilting might be a characteristic feature of PD, especially in the advanced stage.

Nutrition Status Parameters and Hydration Status by Bioelectrical Impedance Vector Analysis Were Associated With Lung Function Impairment in Children and Adolescents With Cystic Fibrosis.

PubMed

Hauschild, Daniela Barbieri; Barbosa, Eliana; Moreira, Emilia Addison Machado; Ludwig Neto, Norberto; Platt, Vanessa Borges; Piacentini Filho, Eduardo; Wazlawik, Elisabeth; Moreno, Yara Maria Franco

2016-06-01

(1) To compare nutrition and hydration status between a group of children/adolescents with cystic fibrosis (CFG; n = 46; median age, 8.5 years) and a control group without cystic fibrosis (CG). (2) To examine the association of nutrition and hydration status with lung function in the CFG. A cross-sectional study. Nutrition screening, anthropometric parameters, and bioelectrical impedance analysis (BIA) were assessed. The z scores for body mass index for age, height for age, mid upper arm circumference, triceps and subscapular skinfold thickness, mid upper arm muscle area, resistance/height, and reactance/height were calculated. Bioelectrical impedance vector analysis was conducted. Forced expiratory volume in 1 second <80% was considered lung function impairment. An adjusted logistic regression was applied (P < .05). In the CFG, lung function impairment was observed in 51.1%. All anthropometric parameters were lower, and the mean z-resistance/height and z-reactance/height were higher in the CFG (P < .05) compared with the CG. In the CFG, 43% were severely/mildly dehydrated, while none were in the CG (P = .007). In the CFG, there was an association between high nutrition risk-via nutrition screening (odds ratio [OR], 22.28; P < .05), lower values of anthropometric parameters, higher z-resistance/height (OR, 2.23; P < .05) and z-reactance/height (OR, 1.81; P < .05), and dehydration (OR, 4.94; P < .05)-and lung function impairment. The CFG exhibited a compromised nutrition status assessed by anthropometric and BIA parameters. Nutrition screening, anthropometric and BIA parameters, and hydration status were associated with lung function. © 2016 American Society for Parenteral and Enteral Nutrition.

Measuring hepatic functional reserve using low temporal resolution Gd-EOB-DTPA dynamic contrast-enhanced MRI: a preliminary study comparing galactosyl human serum albumin scintigraphy with indocyanine green retention.

PubMed

Saito, Kazuhiro; Ledsam, Joseph; Sourbron, Steven; Hashimoto, Tsuyoshi; Araki, Yoichi; Akata, Soichi; Tokuuye, Koichi

2014-01-01

To investigate if tracer kinetic modelling of low temporal resolution dynamic contrast-enhanced (DCE) MRI with Gd-EOB-DTPA could replace technetium-99 m galactosyl human serum albumin (GSA) single positron emission computed tomography (SPECT) and indocyanine green (ICG) retention for the measurement of liver functional reserve. Twenty eight patients awaiting liver resection for various cancers were included in this retrospective study that was approved by the institutional review board. The Gd-EOB-DTPA MRI sequence acquired five images: unenhanced, double arterial phase, portal phase, and 4 min after injection. Intracellular contrast uptake rate (UR) and extracellular volume (Ve) were calculated from DCE-MRI, along with the ratio of GSA radioactivity of liver to heart-plus-liver and per cent of cumulative uptake from 15-16 min (LHL15 and LU15, respectively) from GSA-scintigraphy. ICG retention at 15 min, Child-Pugh cirrhosis score (CPS) and postoperative Inuyama fibrosis criteria were also recorded. Statistical analysis was with Spearman rank correlation analysis. Comparing MRI parameters with the reference methods, significant correlations were obtained for UR and LHL15, LU15, ICG15 (all 0.4-0.6, P < 0.05); UR and CPS (-0.64, P < 0.001); Ve and Inuyama (0.44, P < 0.05). Measures of liver function obtained by routine Gd-EOB-DTPA DCE-MRI with tracer kinetic modelling may provide a suitable method for the evaluation of liver functional reserve. • Magnetic resonance imaging (MRI) provides new methods of measuring hepatic functional reserve. • DCE-MRI with Gd-EOB-DTPA offers the possibility of replacing scintigraphy. • The analysis method can be used for preoperative liver function evaluation.

Conspicuous by Their Absence: Studies Comparing and Combining Risperidone and Applied Behavior Analysis to Reduce Challenging Behavior in Children with Autism

ERIC Educational Resources Information Center

Weeden, Marc; Ehrhardt, Kristal; Poling, Alan

2009-01-01

Both risperidone, an atypical antipsychotic drug, and function-based behavior-analytic interventions are popular and empirically validated treatments for reducing challenging behavior in children with autism. The kind of research that supports their effectiveness differs, however, and no published study has directly compared their effects or…

Formula Budgeting for Higher Education: State Practices in 1979-80. Working Paper Series.

ERIC Educational Resources Information Center

Gross, Francis M.

Budget formulas used by states for state-supported colleges and universities are described, along with budgeting guidelines. A comparative analysis of the budget formulas in use in 1979-1980 reveals the similarities and differences in design among 19 states. Functional areas of expenditure used in the formula calculation are also compared for each…

The Development of a Monitoring System of Higher Education Quality in Ukraine and Germany: Comparative Component

ERIC Educational Resources Information Center

Chorna, Olga

2015-01-01

The article reveals specific features of functioning systems of higher education quality monitoring at the present stage, taking into account national traditions, historical experience and mentality of the population. The article introduces a comparative analysis of monitoring actors at national, regional and local levels in two countries. The…

Comparing Linear Discriminant Function with Logistic Regression for the Two-Group Classification Problem.

ERIC Educational Resources Information Center

Fan, Xitao; Wang, Lin

The Monte Carlo study compared the performance of predictive discriminant analysis (PDA) and that of logistic regression (LR) for the two-group classification problem. Prior probabilities were used for classification, but the cost of misclassification was assumed to be equal. The study used a fully crossed three-factor experimental design (with…

Advantages of Thesaurus Representation Using the Simple Knowledge Organization System (SKOS) Compared with Proposed Alternatives

ERIC Educational Resources Information Center

Pastor-Sanchez, Juan-Antonio; Martinez Mendez, Francisco Javier; Rodriguez-Munoz, Jose Vicente

2009-01-01

Introduction: This paper presents an analysis of the Simple Knowledge Organization System (SKOS) compared with other alternatives for thesaurus representation in the Semantic Web. Method: Based on functional and structural changes of thesauri, provides an overview of the current context in which lexical paradigm is abandoned in favour of the…

Health related quality of life in patients with neuroendocrine tumors compared with the general Norwegian population.

PubMed

Haugland, Trude; Vatn, Morten H; Veenstra, Marijke; Wahl, Astrid Klopstad; Natvig, Gerd Karin

2009-08-01

Health related quality of life (HRQoL) was characterized among patients with neuroendocrine tumor (NET) and compared with the general Norwegian population. A cross sectional, comparative design was chosen, and the samples comprised 196 NET patients and 5,258 individuals from the general Norwegian population. We used Chi-square cross tab calculations to evaluate sociodemographic characteristics, T-tests for independent samples and Analysis of Variance (ANOVA) in order to compare HRQoL (SF-36) scores across a range of background variables. Furthermore, T-tests were used to analyze differences in HRQoL scores between the samples. NET patients demonstrated significantly lower on all HRQoL subscales when compared with the general population with the lowest values on general health, physical limitation and vitality. Individuals above 70 years reported lower scores on physical functioning and physical limitations compared with those who were younger. Individuals with higher levels of education reported increased physical functioning compared with those with less education and full-time or part-time workers described higher physical functioning and less physical limitations compared with those who were retired. All SF-36 HRQoL scores were significantly lower among the NET patients when compared with the general population. Assistance from health personnel to NET patients should focus on those domains.

Effects of Timing and Intensity of Neurorehabilitation on Functional Outcome After Traumatic Brain Injury: A Systematic Review and Meta-Analysis.

PubMed

Königs, Marsh; Beurskens, Eva A; Snoep, Lian; Scherder, Erik J; Oosterlaan, Jaap

2018-06-01

To systematically review evidence on the effects of timing and intensity of neurorehabilitation on the functional recovery of patients with moderate to severe traumatic brain injury (TBI) and aggregate the available evidence using meta-analytic methods. PubMed, Embase, PsycINFO, and Cochrane Database. Electronic databases were searched for prospective controlled clinical trials assessing the effect of timing or intensity of multidisciplinary neurorehabilitation programs on functional outcome of patients with moderate or severe TBI. A total of 5961 unique records were screened for relevance, of which 58 full-text articles were assessed for eligibility by 2 independent authors. Eleven articles were included for systematic review and meta-analysis. Two independent authors performed data extraction and risk of bias analysis using the Cochrane Collaboration tool. Discrepancies between authors were resolved by consensus. Systematic review of a total of 6 randomized controlled trials, 1 quasi-randomized trial, and 4 controlled trials revealed consistent evidence for a beneficial effect of early onset neurorehabilitation in the trauma center and intensive neurorehabilitation in the rehabilitation facility on functional outcome compared with usual care. Meta-analytic quantification revealed a large-sized positive effect for early onset rehabilitation programs (d=1.02; P<.001; 95% confidence interval [CI], 0.56-1.47) and a medium-sized positive effect for intensive neurorehabilitation programs (d=.67; P<.001; 95% CI, .38-.97) compared with usual care. These effects were replicated based solely on studies with a low overall risk of bias. The available evidence indicates that early onset neurorehabilitation in the trauma center and more intensive neurorehabilitation in the rehabilitation facility promote functional recovery of patients with moderate to severe TBI compared with usual care. These findings support the integration of early onset and more intensive neurorehabilitation in the chain of care for patients with TBI. Copyright © 2018 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Expression and functional analysis of genes encoding cytokinin receptor-like histidine kinase in maize (Zea mays L.).

PubMed

Wang, Bo; Chen, Yanhong; Guo, Baojian; Kabir, Muhammad Rezaul; Yao, Yingyin; Peng, Huiru; Xie, Chaojie; Zhang, Yirong; Sun, Qixin; Ni, Zhongfu

2014-08-01

Cytokinin signaling is vital for plant growth and development which function via the two-component system (TCS). As one of the key component of TCS, transmembrane histidine kinases (HK) are encoded by a small gene family in plants. In this study, we focused on expression and functional analysis of cytokinin receptor-like HK genes (ZmHK) in maize. Firstly, bioinformatics analysis revealed that seven cloned ZmHK genes have different expression patterns during maize development. Secondly, ectopic expression by CaMV35S promoter in Arabidopsis further revealed that functional differentiation exists among these seven members. Among them, the ZmHK1a2-OX transgenic line has the lowest germination rate in the dark, ZmHK1-OX and ZmHK2a2-OX can delay leaf senescence, and seed size of ZmHK1-OX, ZmHK1a2-OX, ZmHK2-OX, ZmHK3b-OX and ZmHK2a2-OX was obviously reduced as compared to wild type. Additionally, ZmHK genes play opposite roles in shoot and root development; all ZmHK-OX transgenic lines display obvious shorter root length and reduced number of lateral roots, but enhanced shoot development compared with the wild type. Most notably, Arabidopsis response regulator ARR5 gene was up-regulated in ZmHK1-OX, ZmHK1a2-OX, ZmHK2-OX, ZmHK3b-OX and ZmHK2a2-OX as compared to wild type. Although the causal link between ZmHK genes and cytokinin signaling pathway is still an area to be further elucidated, these findings reflected that the diversification of ZmHK genes expression patterns and functions occurred in the course of maize evolution, indicating that some ZmHK genes might play different roles during maize development.

Neurocognitive function in clinically stable individuals with long-term bipolar I disorder: Comparisons with schizophrenia patients and controls.

PubMed

Lin, Pei-Yun; Wang, Peng-Wei; Chen, Cheng-Sheng; Yen, Cheng-Fang

2017-05-01

This study compared the levels of the five domains of neurocognitive function-executive function, attention, memory, verbal comprehension, and perceptual organization-among clinically stable individuals with long-term bipolar I disorder, individuals with long-term schizophrenia, and a group of controls. We recruited a total of 93 clinically stable individuals with bipolar I disorder, 94 individuals with schizophrenia, and 106 controls in this study. Their neurocognitive function was measured using a series of neurocognitive function tests: the Wechsler Adult Intelligence Scale-Third Edition (WAIS-III), Line Cancellation Test, Visual Form Discrimination, Controlled Oral Word Association Test, Wisconsin Card Sorting Test, Continuous Performance Task, and Wechsler Memory Scale-Third Edition. Neurocognitive function was compared among the three groups through a multivariate analysis of variance. The results indicated that when the effect of age was controlled, clinically stable individuals with bipolar I disorder and those with schizophrenia demonstrated poor neurocognitive function on all tests except for the WAIS-III Similarity and Information and the Line Cancellation Test. The individuals with bipolar I disorder had similar levels of neurocognitive function compared with the schizophrenia group, but higher levels of neurocognitive function on the WAIS-III Comprehension, Controlled Oral Word Association Test, and Wechsler Memory Scale-Third Edition Auditory Immediate and Delayed Index and Visual Immediate and Delayed Index. The conclusions of this study suggest that compared with controls, individuals with long-term bipolar I disorder and those with long-term schizophrenia have poorer neurocognitive function, even when clinically stable. Individuals with long-term bipolar I disorder and those with long-term schizophrenia have similar levels of deficits in several domains of neurocognitive function. Copyright © 2017. Published by Elsevier Taiwan.

A Two-Dimensional Variational Analysis Method for NSCAT Ambiguity Removal: Methodology, Sensitivity, and Tuning

NASA Technical Reports Server (NTRS)

Hoffman, R. N.; Leidner, S. M.; Henderson, J. M.; Atlas, R.; Ardizzone, J. V.; Bloom, S. C.; Atlas, Robert (Technical Monitor)

2001-01-01

In this study, we apply a two-dimensional variational analysis method (2d-VAR) to select a wind solution from NASA Scatterometer (NSCAT) ambiguous winds. 2d-VAR determines a "best" gridded surface wind analysis by minimizing a cost function. The cost function measures the misfit to the observations, the background, and the filtering and dynamical constraints. The ambiguity closest in direction to the minimizing analysis is selected. 2d-VAR method, sensitivity and numerical behavior are described. 2d-VAR is compared to statistical interpolation (OI) by examining the response of both systems to a single ship observation and to a swath of unique scatterometer winds. 2d-VAR is used with both NSCAT ambiguities and NSCAT backscatter values. Results are roughly comparable. When the background field is poor, 2d-VAR ambiguity removal often selects low probability ambiguities. To avoid this behavior, an initial 2d-VAR analysis, using only the two most likely ambiguities, provides the first guess for an analysis using all the ambiguities or the backscatter data. 2d-VAR and median filter selected ambiguities usually agree. Both methods require horizontal consistency, so disagreements occur in clumps, or as linear features. In these cases, 2d-VAR ambiguities are often more meteorologically reasonable and more consistent with satellite imagery.

Comparing the effects of the second-and third-generation oral contraceptives on sexual functioning

PubMed Central

Shahnazi, Mahnaz; Bayatipayan, Somaye; Khalili, Azizeh Farshbaf; Kochaksaraei, Fatemeh Ranjbar; Jafarabadi, Mohammad Asghari; Banoi, Kamala Gaza; Nahaee, Jila

2015-01-01

Background: The aim of this study was to compare the effects of the second- and third-generation oral contraceptives on women's reproductive sexual function. Materials and Methods: This randomized, double-blind, placebo-controlled clinical trial was conducted on 82 married women of reproductive age in Tehran. Samples were randomized into the groups receiving second- and third-generation oral contraceptive pills. Female Sexual Function Index (FSFI) tool was used before the intervention and 2 and 4 months after the intervention. Data analysis was carried out using analysis of variance (ANOVA) within repeated measures and P < 0.05 were considered significant. Results: There was a statistically significant difference in the positive and negative moods between the experimental and control groups before the intervention in the second and fourth months. The second-generation pills caused a decrease in sexual function in the second month and an increase in sexual function in the fourth month, but the third-generation pills led to an increase in sexual function in the second and fourth months. The increase in sexual function that resulted from using the third-generation pills was significantly higher than that resulted on using the second-generation pills. Conclusions: According to the results of this study, sexual functioning decreased in the second month of using the second-generation pills and sexual performance was significantly more on using the third-generation pills compared to second-generation pills. The most common type of oral contraceptive used in Iran is the second-generation oral contraceptive LD™ (low-dose estrogen), which is freely distributed in health centers. Therefore, it is necessary for women who wish to use these contraceptive methods to be educated and consulted before they start using them. The third-generation contraceptive pills can be recommended to women who wish to use oral contraceptives. PMID:25709690

Comparing Visual and Statistical Analysis of Multiple Baseline Design Graphs.

PubMed

Wolfe, Katie; Dickenson, Tammiee S; Miller, Bridget; McGrath, Kathleen V

2018-04-01

A growing number of statistical analyses are being developed for single-case research. One important factor in evaluating these methods is the extent to which each corresponds to visual analysis. Few studies have compared statistical and visual analysis, and information about more recently developed statistics is scarce. Therefore, our purpose was to evaluate the agreement between visual analysis and four statistical analyses: improvement rate difference (IRD); Tau-U; Hedges, Pustejovsky, Shadish (HPS) effect size; and between-case standardized mean difference (BC-SMD). Results indicate that IRD and BC-SMD had the strongest overall agreement with visual analysis. Although Tau-U had strong agreement with visual analysis on raw values, it had poorer agreement when those values were dichotomized to represent the presence or absence of a functional relation. Overall, visual analysis appeared to be more conservative than statistical analysis, but further research is needed to evaluate the nature of these disagreements.

Reproducibility of Cognitive Profiles in Psychosis Using Cluster Analysis.

PubMed

Lewandowski, Kathryn E; Baker, Justin T; McCarthy, Julie M; Norris, Lesley A; Öngür, Dost

2018-04-01

Cognitive dysfunction is a core symptom dimension that cuts across the psychoses. Recent findings support classification of patients along the cognitive dimension using cluster analysis; however, data-derived groupings may be highly determined by sampling characteristics and the measures used to derive the clusters, and so their interpretability must be established. We examined cognitive clusters in a cross-diagnostic sample of patients with psychosis and associations with clinical and functional outcomes. We then compared our findings to a previous report of cognitive clusters in a separate sample using a different cognitive battery. Participants with affective or non-affective psychosis (n=120) and healthy controls (n=31) were administered the MATRICS Consensus Cognitive Battery, and clinical and community functioning assessments. Cluster analyses were performed on cognitive variables, and clusters were compared on demographic, cognitive, and clinical measures. Results were compared to findings from our previous report. A four-cluster solution provided a good fit to the data; profiles included a neuropsychologically normal cluster, a globally impaired cluster, and two clusters of mixed profiles. Cognitive burden was associated with symptom severity and poorer community functioning. The patterns of cognitive performance by cluster were highly consistent with our previous findings. We found evidence of four cognitive subgroups of patients with psychosis, with cognitive profiles that map closely to those produced in our previous work. Clusters were associated with clinical and community variables and a measure of premorbid functioning, suggesting that they reflect meaningful groupings: replicable, and related to clinical presentation and functional outcomes. (JINS, 2018, 24, 382-390).

Meta-analysis of Results of Testosterone Therapy on Sexual Function Based on International Index of Erectile Function Scores.

PubMed

Corona, Giovanni; Rastrelli, Giulia; Morgentaler, Abraham; Sforza, Alessandra; Mannucci, Edoardo; Maggi, Mario

2017-12-01

The interpretation of available clinical evidence related to the effect of testosterone (T) treatment (TTh) on sexual function has been inconsistent, in part due to the use of different and self-reported measures to assess outcomes. The International Index of Erectile Function (IIEF) is the most frequently used validated tool to assess male sexual function. To perform a meta-analysis of available data evaluating the effect of TTh on male sexual function using IIEF as the primary outcome. An extensive Medline, Embase, and Cochrane search was performed including all placebo-controlled randomized clinical trials enrolling men comparing the effect of TTh on sexual function. Out of 137 retrieved articles, 14 were included in the study enrolling 2298 participants, with a mean follow-up of 40.1 wk and mean age of 60.2±6.5 yr. Using IIEF-erectile function domain (IIEF-EFD) as the outcome, we found that TTh significantly improved erectile function compared with placebo (mean difference=2.31 [1.41;3.22] IIEF-EFD score, p<0.0001). Patients with more severe hypogonadism (total T<8 nmol/l) reported greater changes in final IIEF-EFD score when compared with those with a milder T deficiency (total T<12 nmol/l; 1.47 [0.90;2.03] and 2.95 [1.86;4.03] for total T<12 nmol/l and <8 nmol/l, respectively, Q=5.61, p=0.02). The magnitude of the effect was lower in the presence of metabolic derangements, such as diabetes and obesity. Other aspects of sexual function, as evaluated by IIEF subdomains, were also improved with TTh including libido, intercourse satisfaction, orgasm, and overall sexual satisfaction. TTh significantly improves erectile function and other sexual parameters as measured by IIEF in hypogonadal men. These results argue that sexual dysfunction should be considered a hallmark manifestation of T deficiency, since those symptoms can be significantly improved with normalization of serum T. In addition, these results suggest that TTh alone may be considered a reasonable treatment for hypogonadal men with milder degrees of erectile dysfunction, whereas the addition of other treatments, such as phosphodiesterase type 5 inhibitors, may be more appropriate for men with more severe erectile dysfunction. We investigated the effect of testosterone treatment on sexual function by performing a meta-analysis of all available studies that used the most frequently used assessment tool, the International Index of Erectile Function. We found that testosterone treatment significantly improves erectile dysfunction, as well as other aspects of sexual function, in men with testosterone deficiency. This treatment may be all that is required for hypogonadal men with milder erectile dysfunction; however, additional treatments may be necessary in more severe cases. Copyright © 2017. Published by Elsevier B.V.

Insight and Treatment Outcomes in Schizophrenia: Post-hoc Analysis of a Long-term, Double-blind Study Comparing Lurasidone and Quetiapine XR.

PubMed

Harvey, Philip D; Siu, Cynthia O; Loebel, Antony D

2017-12-01

Objective: The objective of this post-hoc analysis was to evaluate the effect of lurasidone and quetiapine extended-release (XR) on insight and judgment and assess the longitudinal relationships between improvement in insight and cognitive performance, functional capacity, quality of well-being, and depressive symptoms in patients with schizophrenia. Design: Clinically unstable patients with schizophrenia (N=488) were randomized to once-daily, fixed-dose treatment with lurasidone 80mg, lurasidone 160mg, quetiapine XR 600mg, or placebo, followed by a long-term, double-blind, flexible-dose continuation study involving these agents. Results: Significantly greater improvement in insight and judgment (assessed by the Positive and Negative Syndrome Scale G12 item) for the lurasidone and quetiapine XR groups, compared to the placebo group, was observed at Week 6. Over a subsequent six-month continuation period, the flexible dose lurasidone group showed significantly greater improvement in insight from acute phase baseline compared to the flexible-dose quetiapine XR group (QXR-QXR) (p=0.032). Improvement in insight was significantly correlated with improvement in cognition ( p =0.014), functional capacity (p=0.006, UPSA-B), quality of well-being ( p =0.033, QWB), and depressive symptoms ( p =0.05, Montgomery-Åsberg Depression Rating Scale [MADRS] score) across treatment groups and study periods. Conclusion: In this post-hoc analysis, flexibly dosed lurasidone 40 to 160mg/d was found to be associated with significantly greater improvement in insight compared to flexibly dosed quetiapine XR 200 to 800mg/d over long-term treatment in patients with schizophrenia. Across treatment groups, improvement in insight and judgment was significantly associated with improvement in cognition, functional capacity, quality of well-being, and depressive symptoms over time.

Self-Reported Functional Status among the Old-Old: A Comparison of Two Israeli Cohorts

PubMed Central

Litwin, Howard; Shrira, Amit; Shmotkin, Dov

2012-01-01

OBJECTIVES To examine differences in functional status among two successive cohorts. METHODS The study was a comparative analysis of Jewish respondents aged 75–94 from two nationwide random samples: the Cross-Sectional and Longitudinal Aging Study (1989–1992; N =1200) and the Survey of Health, Ageing, and Retirement in Europe (2005–2006; N =379). Self-reported functional limitation and disability were compared by means of logistic regressions and MANCOVA, controlling for age, gender, origin, education, marital status, income, self-rated health, and home care receipt. RESULTS Reported functional limitation decreased in the later cohort (SHARE-Israel), but ADL- and IADL-disability increased. Receipt of home care moderated these effects. ADL- and IADL-disability increased among home-care-receiving respondents in the later cohort whereas functional limitation decreased among respondents not in receipt of home care. DISCUSSION The findings suggest that different measures used to assess the disablement process capture different aspects, and that contextual factors influence how older people rate their own functional capacity. PMID:22422761

Recursive feature elimination for biomarker discovery in resting-state functional connectivity.

PubMed

Ravishankar, Hariharan; Madhavan, Radhika; Mullick, Rakesh; Shetty, Teena; Marinelli, Luca; Joel, Suresh E

2016-08-01

Biomarker discovery involves finding correlations between features and clinical symptoms to aid clinical decision. This task is especially difficult in resting state functional magnetic resonance imaging (rs-fMRI) data due to low SNR, high-dimensionality of images, inter-subject and intra-subject variability and small numbers of subjects compared to the number of derived features. Traditional univariate analysis suffers from the problem of multiple comparisons. Here, we adopt an alternative data-driven method for identifying population differences in functional connectivity. We propose a machine-learning approach to down-select functional connectivity features associated with symptom severity in mild traumatic brain injury (mTBI). Using this approach, we identified functional regions with altered connectivity in mTBI. including the executive control, visual and precuneus networks. We compared functional connections at multiple resolutions to determine which scale would be more sensitive to changes related to patient recovery. These modular network-level features can be used as diagnostic tools for predicting disease severity and recovery profiles.

Proprioception in patients with posterior cruciate ligament tears: A meta-analysis comparison of reconstructed and contralateral normal knees

PubMed Central

Ko, Seung-Nam

2017-01-01

Posterior cruciate ligament (PCL) reconstruction for patients with PCL insufficiency has been associated with postoperative improvements in proprioceptive function due to mechanoreceptor regeneration. However, it is unclear whether reconstructed PCL or contralateral normal knees have better proprioceptive function outcomes. This meta-analysis was designed to compare the proprioceptive function of reconstructed PCL or contralateral normal knees in patients with PCL insufficiency. All studies that compared proprioceptive function, as assessed with threshold to detect passive movement (TTDPM) or joint position sense (JPS) in PCL reconstructed or contralateral normal knees were included. JPS was calculated by reproducing passive positioning (RPP). Five studies met the inclusion/exclusion criteria for the meta-analysis. The proprioceptive function, defined as TTDPM (95% CI: 0.25 to 0.51°; P<0.00001) and RPP (95% CI: 0.19 to 0.45°; P<0.00001), was significantly different between the reconstructed PCL and contralateral normal knees. The mean difference in angle of error between the reconstructed PCL and contralateral normal knees was 0.06° greater in TTDPM than by RPP. In addition, results from subgroup analyses, based on the starting angles and the moving directions of the knee, that evaluated TTDPM at 15° flexion to 45° extension, TTDPM at 45° flexion to 110° flexion, RPP in flexion, and RPP in extension demonstrated that mean angles of error were significantly greater, by 0.38° (P = 0.0001), 0.36° (P = 0.02), 0.36° (P<0.00001), and 0.23° (P = 0.04), respectively, in reconstructed PCL than in contralateral normal knees. The proprioceptive function of PCL reconstructed knees was decreased, compared with contralateral normal knees, as determined by both TTDPM and RPP. In addition, the amount of loss of proprioception was greater in TTDPM than in RPP, even with minute differences. Results from subgroup analysis, that evaluated the mean angles of error in moving directions through RPP, suggested that the moving direction of flexion has a significantly greater mean for angles of error than the moving direction of extension. Although the level of differences between various parameters were statistically significant, further studies are needed to determine whether the small differences (>1°) of the loss of proprioception are clinically relevant. PMID:28922423

Comparative analysis of respiratory chain and oxidative phosphorylation in Leishmania tarentolae, Crithidia fasciculata, Phytomonas serpens and procyclic stage of Trypanosoma brucei.

PubMed

Verner, Zdeněk; Cermáková, Petra; Skodová, Ingrid; Kováčová, Bianka; Lukeš, Julius; Horváth, Anton

2014-01-01

Trypanosomatids are unicellular parasites living in a wide range of host environments, which to large extent shaped their mitochondrial energy metabolism, resulting in quite large differences even among closely related flagellates. In a comparative manner, we analyzed the activities and composition of mitochondrial respiratory complexes in four species (Leishmania tarentolae, Crithidia fasciculata, Phytomonas serpens and Trypanosoma brucei), which represent the main model trypanosomatids. Moreover, we measured the activity of mitochondrial glycerol-3-phosphate dehydrogenase, the overall oxygen consumption and the mitochondrial membrane potential in each species. The comparative analysis suggests an inverse relationship between the activities of respiratory complexes I and II, as well as the overall activity of the canonical complexes and glycerol-3-phosphate dehydrogenase. Our comparative analysis shows that mitochondrial functions are highly variable in these versatile parasites. Copyright © 2014 Elsevier B.V. All rights reserved.

MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.

PubMed

Zhai, Peng; Yang, Longshu; Guo, Xiao; Wang, Zhe; Guo, Jiangtao; Wang, Xiaoqi; Zhu, Huaiqiu

2017-10-02

During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community. We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples. MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis. Moreover, since the automatically chosen two-group sample test is verified to be outperformed, MetaComp is friendly to users without adequate statistical training. These improvements are aiming to overcome the new challenges under big data era for all meta-omics data. MetaComp is available at: http://cqb.pku.edu.cn/ZhuLab/MetaComp/ and https://github.com/pzhaipku/MetaComp/ .

Effects of Aquatic Therapy and Land-Based Therapy versus Land-Based Therapy Alone on Range of Motion, Edema, and Function after Hip or Knee Replacement: A Systematic Review and Meta-analysis

PubMed Central

Shields, Nora

2015-01-01

ABSTRACT Purpose: To determine whether aquatic therapy in combination with land-based therapy improves patient outcomes after hip or knee arthroplasty compared with land-based therapy alone. Methods: For this systematic review, six online databases (MEDLINE, CINAHL, AMED, EMBASE, Cochrane, and PEDro) were searched from the earliest date available until September 2013. Controlled trials published in English in a peer-reviewed journal that compared aquatic therapy in combination with land-based therapy with land-based therapy alone were included; trial quality was assessed using the PEDro scale. Data were presented as standardized mean differences (SMDs), their associated 95% CIs, and meta-analyses. Results: Three small trials of moderate quality were included in the qualitative analysis. Meta-analysis of two of these studies found moderate-quality evidence that aquatic therapy in combination with land-based therapy improves functional outcomes (SMD=0.53; 95% CI, 0.03–1.03), knee range of motion (measured in knee or hip arthroplasty; SMD=0.78; 95% CI, 0.27–1.29), and edema (SMD=−0.66; 95% CI, −1.16 to −0.15) compared with land-based therapy alone. The results for improved functional outcomes were not considered clinically significant. Conclusions: It is not possible to draw confident conclusions from this review because of the small number of studies of limited quality and the modest differences found. Further studies of sound methodological quality are required to confirm the results. Economic analysis alongside randomized controlled trials is needed to examine the cost-effectiveness of these clinical outcomes. PMID:25931664

Korean Red Ginseng Up-regulates C21-Steroid Hormone Metabolism via Cyp11a1 Gene in Senescent Rat Testes

PubMed Central

Kim, In-Hye; Kim, Si-Kwan; Kim, Eun-Hye; Kim, Sung-Won; Sohn, Sang-Hyun; Lee, Soo Cheol; Choi, Sangdun; Pyo, Suhkneung; Rhee, Dong-Kwon

2011-01-01

Ginseng (Panax ginseng Meyer) has been shown to have anti-aging effects in animal and clinical studies. However, the molecular mechanisms by which ginseng exerts these effects remain unknown. Here, the anti-aging effect of Korean red ginseng (KRG) in rat testes was examined by system biology analysis. KRG water extract prepared in feed pellets was administered orally into 12 month old rats for 4 months, and gene expression in testes was determined by microarray analysis. Microarray analysis identified 33 genes that significantly changed. Compared to the 2 month old young rats, 13 genes (Rps9, Cyp11a1, RT1-A2, LOC365778, Sv2b, RGD1565959, RGD1304748, etc.) were up-regulated and 20 genes (RT1-Db1, Cldn5, Svs5, Degs1, Vdac3, Hbb, LOC684355, Svs5, Tmem97, Orai1, Insl3, LOC497959, etc.) were down-regulated by KRG in the older rats. Ingenuity Pathway Analysis of untreated aged rats versus aged rats treated with KRG showed that the affected most was Cyp11a1, responsible for C21-steroid hormone metabolism, and the top molecular and cellular functions are organ morphology and reproductive system development and function. When genes in young rat were compared with those in the aged rat, sperm capacitation related genes were down-regulated in the old rat. However, when genes in the old rat were compared with those in the old rat treated with KRG, KRG treatment up-regulated C21-steroid hormone metabolism. Taken together, Cyp11a1 expression is decreased in the aged rat, however, it is up-regulated by KRG suggesting that KRG seems enhance testes function via Cyp11a1. PMID:23717070

Comparison of Behavioral Intervention and Sensory-Integration Therapy in the Treatment of Self-Injurious Behavior

ERIC Educational Resources Information Center

Devlin, Sarah; Leader, Geraldine; Healy, Olive

2009-01-01

The current study investigates the comparative effects of sensory-integration therapy and behavioral interventions on rates of self-injurious behavior (SIB) in a 9-year-old boy with diagnosis of autism. A functional analysis was conducted to identify the variables maintaining the self-injurious behavior. This analysis demonstrated that SIB was…

Brain natriuretic peptide predicts functional outcome in ischemic stroke

PubMed Central

Rost, Natalia S; Biffi, Alessandro; Cloonan, Lisa; Chorba, John; Kelly, Peter; Greer, David; Ellinor, Patrick; Furie, Karen L

2011-01-01

Background Elevated serum levels of brain natriuretic peptide (BNP) have been associated with cardioembolic (CE) stroke and increased post-stroke mortality. We sought to determine whether BNP levels were associated with functional outcome after ischemic stroke. Methods We measured BNP in consecutive patients aged ≥18 years admitted to our Stroke Unit between 2002–2005. BNP quintiles were used for analysis. Stroke subtypes were assigned using TOAST criteria. Outcomes were measured as 6-month modified Rankin Scale score (“good outcome” = 0–2 vs. “poor”) as well as mortality. Multivariate logistic regression was used to assess association between the quintiles of BNP and outcomes. Predictive performance of BNP as compared to clinical model alone was assessed by comparing ROC curves. Results Of 569 ischemic stroke patients, 46% were female; mean age was 67.9 ± 15 years. In age- and gender-adjusted analysis, elevated BNP was associated with lower ejection fraction (p<0.0001) and left atrial dilatation (p<0.001). In multivariate analysis, elevated BNP decreased the odds of good functional outcome (OR 0.64, 95%CI 0.41–0.98) and increased the odds of death (OR 1.75, 95%CI 1.36–2.24) in these patients. Addition of BNP to multivariate models increased their predictive performance for functional outcome (p=0.013) and mortality (p<0.03) after CE stroke. Conclusions Serum BNP levels are strongly associated with CE stroke and functional outcome at 6 months after ischemic stroke. Inclusion of BNP improved prediction of mortality in patients with CE stroke. PMID:22116811

Methylation of FOXP3 TSDR Underlies the Impaired Suppressive Function of Tregs from Long-term Belatacept-Treated Kidney Transplant Patients

PubMed Central

Alvarez Salazar, Evelyn Katy; Cortés-Hernández, Arimelek; Alemán-Muench, Germán Rodrigo; Alberú, Josefina; Rodríguez-Aguilera, Jesús R.; Recillas-Targa, Félix; Chagoya de Sánchez, Victoria; Cuevas, Eric; Mancilla-Urrea, Eduardo; Pérez García, María; Mondragón-Ramírez, Guillermo; Vilatobá, Mario; Bostock, Ian; Hernández-Méndez, Erick; De Rungs, David; García-Zepeda, Eduardo A.; Soldevila, Gloria

2017-01-01

Regulatory T cells (Tregs) are considered key players in the prevention of allograft rejection in transplanted patients. Belatacept (BLT) is an effective alternative to calcineurin inhibitors that appears to preserve graft survival and function; however, the impact of this drug in the homeostasis of Tregs in transplanted patients remains controversial. Here, we analyzed the phenotype, function, and the epigenetic status of the Treg-specific demethylated region (TSDR) in FOXP3 of circulating Tregs from long-term kidney transplant patients under BLT or Cyclosporine A treatment. We found a significant reduction in the proportion of CD4+CD25hiCD127lo/−FOXP3+ T cells in all patients compared to healthy individual (controls). Interestingly, only BLT-treated patients displayed an enrichment of the CD45RA+ “naïve” Tregs, while the expression of Helios, a marker used to identify stable FOXP3+ thymic Tregs remained unaffected. Functional analysis demonstrated that Tregs from transplanted patients displayed a significant reduction in their suppressive capacity compared to Tregs from controls, which is associated with decreased levels of FOXP3 and CD25. Analysis of the methylation status of the FOXP3 gene showed that BLT treatment results in methylation of CpG islands within the TSDR, which could be associated with the impaired Treg suppression function. Our data indicate that analysis of circulating Tregs cannot be used as a marker for assessing tolerance toward the allograft in long-term kidney transplant patients. Trial registration number IM103008. PMID:28316600

Sexual Function in Males After Radiotherapy for Rectal Cancer

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

Bruheim, Kjersti, E-mail: Kjersti.bruheim@medisin.uio.n; Guren, Marianne G.; Dahl, Alv A.

Purpose: Knowledge of sexual problems after pre- or postoperative radiotherapy (RT) with 50 Gy for rectal cancer is limited. In this study, we aimed to compare self-rated sexual functioning in irradiated (RT+) and nonirradiated (RT-) male patients at least 2 years after surgery for rectal cancer. Methods and Materials: Patients diagnosed with rectal cancer from 1993 to 2003 were identified from the Norwegian Rectal Cancer Registry. Male patients without recurrence at the time of the study. The International Index of Erectile Function, a self-rated instrument, was used to assess sexual functioning, and serum levels of serum testosterone were measured. Results:more » Questionnaires were returned from 241 patients a median of 4.5 years after surgery. The median age was 67 years at survey. RT+ patients (n = 108) had significantly poorer scores for erectile function, orgasmic function, intercourse satisfaction, and overall satisfaction with sex life compared with RT- patients (n = 133). In multiple age-adjusted analysis, the odds ratio for moderate-severe erectile dysfunction in RT+ patients was 7.3 compared with RT- patients (p <0.001). Furthermore, erectile dysfunction of this degree was associated with low serum testosterone (p = 0.01). Conclusion: RT for rectal cancer is associated with significant long-term effects on sexual function in males.« less

Convergent close coupling versus the generalized Sturmian function approach: Wave-function analysis

NASA Astrophysics Data System (ADS)

Ambrosio, M.; Mitnik, D. M.; Gasaneo, G.; Randazzo, J. M.; Kadyrov, A. S.; Fursa, D. V.; Bray, I.

2015-11-01

We compare the physical information contained in the Temkin-Poet (TP) scattering wave function representing electron-impact ionization of hydrogen, calculated by the convergent close-coupling (CCC) and generalized Sturmian function (GSF) methodologies. The idea is to show that the ionization cross section can be extracted from the wave functions themselves. Using two different procedures based on hyperspherical Sturmian functions we show that the transition amplitudes contained in both GSF and CCC scattering functions lead to similar single-differential cross sections. The single-continuum channels were also a subject of the present studies, and we show that the elastic and excitation amplitudes are essentially the same as well.

Facile synthesis of amine-functional reduced graphene oxides as modified quick, easy, cheap, effective, rugged and safe adsorbent for multi-pesticide residues analysis of tea.

PubMed

Ma, Guicen; Zhang, Minglu; Zhu, Li; Chen, Hongping; Liu, Xin; Lu, Chengyin

2018-01-05

Amine-functional reduced graphene oxide (amine-rGO) with different carbon chain length amino groups were successfully synthesized. The graphene oxides (GO) reduction as well as amino grafting were achieved simultaneously in one step via a facile solvothermal synthetic strategy. The obtained materials were characterized by X-ray diffraction, Raman spectroscopy, Fourier-transform infrared spectrometry and X-ray photoelectron spectroscopy to confirm the modification of GO with different amino groups. The adsorption performance of catechins and caffeine from tea acetonitrile extracts on different amine functional rGO samples were evaluated. It was found that tributylamine-functional rGO (tri-BuA-rGO) exhibited the highest adsorption ability for catechins and caffeine compared to GO and other amino group functional rGO samples. It was worth to note that the adsorption capacity of catechins on tri-BuA-rGO was 11 times higher than that of GO (203.7mgg -1 vs 18.7mgg -1 ). Electrostatic interaction, π-π interaction and surface hydrophilic-hydrophobic properties of tri-BuA-rGO played important roles in the adsorption of catechins as well as caffeine. The gravimetric analysis confirmed that the tri-BuA-rGO achieved the highest efficient cleanup preformance compared with traditional dispersive solid phase extraction (dSPE) adsorbents like primary-secondary amine (PSA), graphitized carbon black (GCB) or C18. A multi-pesticides analysis method based on tri-BuA-rGO is validated on 33 representative pesticides in tea using gas chromatography coupled to tandem mass spectrometry or high-performance liquid chromatography coupled with tandem mass spectrometry. The analysis method gave a high coefficient of determination (r 2 >0.99) for each pesticide and satisfactory recoveries in a range of 72.1-120.5%. Our study demonstrated that amine functional rGO as a new type of QuEChERS adsorbent is expected to be widely applied for analysis of pesticides at trace levels. Copyright © 2017 Elsevier B.V. All rights reserved.

Impact of pretransplant renal function on survival after liver transplantation.

PubMed

Gonwa, T A; Klintmalm, G B; Levy, M; Jennings, L S; Goldstein, R M; Husberg, B S

1995-02-15

To determine the effect of pretransplant liver function on survival following orthotopic liver transplantation and to quantify the effects of cyclosporine administration on long-term renal function in patients undergoing liver transplant, we performed an analysis of a prospectively maintained database. Data from 569 consecutive patients undergoing liver transplantation alone who were treated with CsA for immunosuppression were used for this study. Actuarial graft and patient survival rates were calculated using Kaplan-Meier statistics. Glomerular filtration rates, serum creatinine, and the use of various immunosuppressives were analyzed for this study. The initial analysis demonstrated that patients presenting for liver transplant with hepatorenal syndrome have a significantly decreased acturial patient survival after liver transplant at 5 years compared with patients without hepatorenal syndrome (60% vs. 68%, P < 0.03). Patients with hepatorenal syndrome recovered their renal function after liver transplant. Patients who had hepatorenal syndrome were sicker and required longer stays in the intensive care unit, longer hospitalizations, and more dialysis treatments after transplantation compared with patients who did not have hepatorenal syndrome. The incidence of end-stage renal disease after liver transplantation in patients who had hepatorenal syndrome was 7%, compared with 2% in patients who did not have hepatorenal syndrome. To more fully examine the effect of pretransplant renal function on posttransplant survival, the non-hepatorenal syndrome patients were divided into quartiles depending upon their pretransplant renal function. The patients with the lowest pretransplant renal function had the same survival as the patients with the highest pretransplant renal function. In addition, there was no increased incidence of acute or chronic rejection in any of the groups. The patients with the lower pretransplant renal function were treated with more azathioprine to maintain renal function and had a negligible decrease in glomerular filtration rate following transplant. Conversely, patients with the highest level of renal function pretransplant had a 40% decline in renal function in the first year, but maintained stable renal function up to 4 years after transplant. We conclude that pretransplant renal function other than hepato-renal syndrome has no effect on patient survival after orthotopic liver transplant. Renal function after liver transplant is stable after an initial decline, despite continued administration of CsA.(ABSTRACT TRUNCATED AT 400 WORDS)

Comparative Analysis of the Effects of Severe Plastic Deformation and Thermomechanical Training on the Functional Stability of Ti50.5Ni24.5Pd25 High-Temperature Shape Memory Alloy

NASA Technical Reports Server (NTRS)

Atli, K. C.; Karaman, I.; Noebe, R. D.; Maier, H. J.

2010-01-01

We compare the effectiveness of a conventional thermomechanical training procedure and severe plastic deformation via equal channel angular extrusion to achieve improved functional stability in a Ti50.5Ni24.5Pd25 high-temperature shape memory alloy. Thermomechanical testing indicates that both methods result in enhanced shape memory characteristics, such as reduced irrecoverable strain and thermal hysteresis. The mechanisms responsible for the improvements are discussed in light of microstructural findings from transmission electron microscopy.

Average symbol error rate for M-ary quadrature amplitude modulation in generalized atmospheric turbulence and misalignment errors

NASA Astrophysics Data System (ADS)

Sharma, Prabhat Kumar

2016-11-01

A framework is presented for the analysis of average symbol error rate (SER) for M-ary quadrature amplitude modulation in a free-space optical communication system. The standard probability density function (PDF)-based approach is extended to evaluate the average SER by representing the Q-function through its Meijer's G-function equivalent. Specifically, a converging power series expression for the average SER is derived considering the zero-boresight misalignment errors in the receiver side. The analysis presented here assumes a unified expression for the PDF of channel coefficient which incorporates the M-distributed atmospheric turbulence and Rayleigh-distributed radial displacement for the misalignment errors. The analytical results are compared with the results obtained using Q-function approximation. Further, the presented results are supported by the Monte Carlo simulations.

Finding Success in Failure: Using Latent Profile Analysis to Examine Heterogeneity in Psychosocial Functioning among Heavy Drinkers Following Treatment

PubMed Central

Wilson, Adam D.; Bravo, Adrian J.; Witkiewitz, Katie

2016-01-01

Aims To estimate differences in post-treatment psychosocial functioning among treatment “failures” (i.e., heavy drinkers, defined as 4+/5+ drinks for women/men) from two large multi-site clinical trials, and to compare these levels of functioning to those of the purported treatment “successes” (i.e., non-heavy drinkers). Design Separate latent profile analyses of data from COMBINE and Project MATCH, comparing psychosocial outcomes across derived classes of heterogeneous treatment responders. Setting Eleven U.S. academic sites in COMBINE, 27 U.S. treatment sites local to nine research sites in Project MATCH. Participants 962 individuals in COMBINE (69% male, 77% white, mean age: 44 years) treated January 2001 to January 2004 and 1,528 individuals in Project MATCH (75% male, 80% white, mean age: 40 years) treated April 1991 to September 1994. Measurements In COMBINE, we analyzed health, quality of life, mental health symptoms, and alcohol consequences 12-months post-baseline. In Project MATCH, we examined social functioning, mental health symptoms, and alcohol consequences 15-months post-baseline. Findings Latent profile analysis of measures of functioning in both samples supported a three-profile solution for the group of treatment “failures,” characterized by high-functioning, average-functioning, and low-functioning individuals. The high-functioning treatment “failures” were generally performing better across measures of psychosocial functioning at follow-up than participants designated treatment “successes” by virtue of being abstainers or light drinkers. Conclusions Current Food and Drug Administration guidance to use heavy drinking as indicative of treatment “failure” fails to take into account substantial psychosocial improvements made by individuals who continue to occasionally drink heavily post-treatment. PMID:27367263

Characterization of Microbiota in Children with Chronic Functional Constipation

PubMed Central

de Meij, Tim G. J.; de Groot, Evelien F. J.; Eck, Anat; Budding, Andries E.; Kneepkens, C. M. Frank; Benninga, Marc A.; van Bodegraven, Adriaan A.; Savelkoul, Paul H. M.

2016-01-01

Objectives Disruption of the intestinal microbiota is considered an etiological factor in pediatric functional constipation. Scientifically based selection of potential beneficial probiotic strains in functional constipation therapy is not feasible due to insufficient knowledge of microbiota composition in affected subjects. The aim of this study was to describe microbial composition and diversity in children with functional constipation, compared to healthy controls. Study Design Fecal samples from 76 children diagnosed with functional constipation according to the Rome III criteria (median age 8.0 years; range 4.2–17.8) were analyzed by IS-pro, a PCR-based microbiota profiling method. Outcome was compared with intestinal microbiota profiles of 61 healthy children (median 8.6 years; range 4.1–17.9). Microbiota dissimilarity was depicted by principal coordinate analysis (PCoA), diversity was calculated by Shannon diversity index. To determine the most discriminative species, cross validated logistic ridge regression was performed. Results Applying total microbiota profiles (all phyla together) or per phylum analysis, no disease-specific separation was observed by PCoA and by calculation of diversity indices. By ridge regression, however, functional constipation and controls could be discriminated with 82% accuracy. Most discriminative species were Bacteroides fragilis, Bacteroides ovatus, Bifidobacterium longum, Parabacteroides species (increased in functional constipation) and Alistipes finegoldii (decreased in functional constipation). Conclusions None of the commonly used unsupervised statistical methods allowed for microbiota-based discrimination of children with functional constipation and controls. By ridge regression, however, both groups could be discriminated with 82% accuracy. Optimization of microbiota-based interventions in constipated children warrants further characterization of microbial signatures linked to clinical subgroups of functional constipation. PMID:27760208

A comparative analysis of the avirulence and translational transactivator functions of gene VI of Cauliflower mosaic virus.

PubMed

Palanichelvam, Karuppaiah; Schoelz, James E

2002-02-15

The primary function associated at present with the gene VI product of Cauliflower mosaic virus (CaMV) is that of a translational transactivator (TAV). In this capacity, it alters the host translational machinery to allow reinitiation of translation of other CaMV genes on the polycistronic 35S RNA of CaMV. In addition, the gene VI protein can elicit a specific type of plant defense response called the hypersensitive response (HR) in Nicotiana edwardsonii. In this study, we have adapted the agroinfiltration technique to compare the sequences of CaMV gene VI required for TAV function and elicitation of HR. To measure the activity of the TAV, we coagroinfiltrated gene VI of CaMV strain W260 with a bicistronic GUS reporter plasmid. TAV function could be assayed 4 days postinfiltration, before the onset of HR in N. edwardsonii. Through the use of the TAV and HR assays, we could show that the TAV functions of gene VI of CaMV strains W260 and D4 were equivalent, but only W260 gene VI elicited HR. A mutational analysis of W260 gene VI showed that the structural requirements for elicitation of HR were much more stringent than those for TAV function. Small deletions from either the 5' or 3' end of W260 gene VI abolished its ability to elicit HR, although the TAV function was retained in the mutant. The TAV function could also tolerate a small insertion within gene VI; this insertion abolished the elicitor function. This study provides direct evidence that the TAV function of gene VI is separate from its role as an elicitor of HR.

Functional connectivity decreases in autism in emotion, self, and face circuits identified by Knowledge-based Enrichment Analysis.

PubMed

Cheng, Wei; Rolls, Edmund T; Zhang, Jie; Sheng, Wenbo; Ma, Liang; Wan, Lin; Luo, Qiang; Feng, Jianfeng

2017-03-01

A powerful new method is described called Knowledge based functional connectivity Enrichment Analysis (KEA) for interpreting resting state functional connectivity, using circuits that are functionally identified using search terms with the Neurosynth database. The method derives its power by focusing on neural circuits, sets of brain regions that share a common biological function, instead of trying to interpret single functional connectivity links. This provides a novel way of investigating how task- or function-related networks have resting state functional connectivity differences in different psychiatric states, provides a new way to bridge the gap between task and resting-state functional networks, and potentially helps to identify brain networks that might be treated. The method was applied to interpreting functional connectivity differences in autism. Functional connectivity decreases at the network circuit level in 394 patients with autism compared with 473 controls were found in networks involving the orbitofrontal cortex, anterior cingulate cortex, middle temporal gyrus cortex, and the precuneus, in networks that are implicated in the sense of self, face processing, and theory of mind. The decreases were correlated with symptom severity. Copyright © 2017. Published by Elsevier Inc.

Probing the pH sensitivity of R-phycoerythrin: investigations of active conformational and functional variation.

PubMed

Liu, Lu-Ning; Su, Hai-Nan; Yan, Shi-Gan; Shao, Si-Mi; Xie, Bin-Bin; Chen, Xiu-Lan; Zhang, Xi-Ying; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2009-07-01

Crystal structures of phycobiliproteins have provided valuable information regarding the conformations and amino acid organizations of peptides and chromophores, and enable us to investigate their structural and functional relationships with respect to environmental variations. In this work, we explored the pH-induced conformational and functional dynamics of R-phycoerythrin (R-PE) by means of absorption, fluorescence and circular dichroism spectra, together with analysis of its crystal structure. R-PE presents stronger functional stability in the pH range of 3.5-10 compared to the structural stability. Beyond this range, pronounced functional and structural changes occur. Crystal structure analysis shows that the tertiary structure of R-PE is fixed by several key anchoring points of the protein. With this specific association, the fundamental structure of R-PE is stabilized to present physiological spectroscopic properties, while local variations in protein peptides are also allowed in response to environmental disturbances. The functional stability and relative structural sensitivity of R-PE allow environmental adaptation.

The effect of preoperative training on functional recovery in patients undergoing total knee arthroplasty: A systematic review and meta-analysis.

PubMed

Ma, Jian-Xiong; Zhang, Lu-Kai; Kuang, Ming-Jie; Zhao, Jie; Wang, Ying; Lu, Bin; Sun, Lei; Ma, Xin-Long

2018-03-01

A meta-analysis to evaluate the efficacy of preoperative training on functional recovery in patients undergoing total knee arthroplasty. Randomized controlled trials (RCTs) about relevant studies were searched from PubMed (1996-2017.4), Embase (1980-2017.4), and the Cochrane Library (CENTRAL 2017.4). Nine studies which evaluated the effect of preoperative training on functional recovery in patients undergoing TKA were included in our meta-analysis. Meta-analysis results were collected and analyzed by Review Manager 5.3 (Copenhagen: The Nordic Cochrane Center the Collaboration 2014). Nine studies containing 777 patients meet the inclusion criteria. Our pooled data analysis indicated that preoperative training was as effective as the control group in terms of visual analogue scale(VAS) score at ascend stairs (P = 0.41) and descend stars (P = 0.80), rang of motion (ROM) of flexion (P = 0.86) and extension (P = 0.60), short form 36 (SF-36) of physical function score (P = 0.07) and bodily pain score (P = 0.39), western Ontario and Macmaster universities osteoarthritis index (WOMAC) function score (P = 0.10), and time up and go (P = 0.28). While differences were found in length of stay (P < 0.05). Our meta-analysis demonstrated that preoperative training have the similar efficacy on functional recovery in patients following total knee arthroplasty compared with control group. However, high quality studies with more patients were needed in future. Copyright © 2018 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

Assessing prescription drug abuse using functional principal component analysis (FPCA) of wastewater data.

PubMed

Salvatore, Stefania; Røislien, Jo; Baz-Lomba, Jose A; Bramness, Jørgen G

2017-03-01

Wastewater-based epidemiology is an alternative method for estimating the collective drug use in a community. We applied functional data analysis, a statistical framework developed for analysing curve data, to investigate weekly temporal patterns in wastewater measurements of three prescription drugs with known abuse potential: methadone, oxazepam and methylphenidate, comparing them to positive and negative control drugs. Sewage samples were collected in February 2014 from a wastewater treatment plant in Oslo, Norway. The weekly pattern of each drug was extracted by fitting of generalized additive models, using trigonometric functions to model the cyclic behaviour. From the weekly component, the main temporal features were then extracted using functional principal component analysis. Results are presented through the functional principal components (FPCs) and corresponding FPC scores. Clinically, the most important weekly feature of the wastewater-based epidemiology data was the second FPC, representing the difference between average midweek level and a peak during the weekend, representing possible recreational use of a drug in the weekend. Estimated scores on this FPC indicated recreational use of methylphenidate, with a high weekend peak, but not for methadone and oxazepam. The functional principal component analysis uncovered clinically important temporal features of the weekly patterns of the use of prescription drugs detected from wastewater analysis. This may be used as a post-marketing surveillance method to monitor prescription drugs with abuse potential. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data

PubMed Central

Bryan, Kenneth; Cunningham, Pádraig

2008-01-01

Background Microarrays have the capacity to measure the expressions of thousands of genes in parallel over many experimental samples. The unsupervised classification technique of bicluster analysis has been employed previously to uncover gene expression correlations over subsets of samples with the aim of providing a more accurate model of the natural gene functional classes. This approach also has the potential to aid functional annotation of unclassified open reading frames (ORFs). Until now this aspect of biclustering has been under-explored. In this work we illustrate how bicluster analysis may be extended into a 'semi-supervised' ORF annotation approach referred to as BALBOA. Results The efficacy of the BALBOA ORF classification technique is first assessed via cross validation and compared to a multi-class k-Nearest Neighbour (kNN) benchmark across three independent gene expression datasets. BALBOA is then used to assign putative functional annotations to unclassified yeast ORFs. These predictions are evaluated using existing experimental and protein sequence information. Lastly, we employ a related semi-supervised method to predict the presence of novel functional modules within yeast. Conclusion In this paper we demonstrate how unsupervised classification methods, such as bicluster analysis, may be extended using of available annotations to form semi-supervised approaches within the gene expression analysis domain. We show that such methods have the potential to improve upon supervised approaches and shed new light on the functions of unclassified ORFs and their co-regulation. PMID:18831786

Higher Order Analysis of Turbulent Changes Found in the ELF Range Electric Field Plasma Before Major Earthquakes

NASA Astrophysics Data System (ADS)

Kosciesza, M.; Blecki, J. S.; Parrot, M.

2014-12-01

We report the structure function analysis of changes found in electric field in the ELF range plasma turbulence registered in the ionosphere over epicenter region of major earthquakes with depth less than 40 km that took place during 6.5 years of the scientific mission of the DEMETER satellite. We compare the data for the earthquakes for which we found turbulence with events without any turbulent changes. The structure functions were calculated also for the Polar CUSP region and equatorial spread F region. Basic studies of the turbulent processes were conducted with use of higher order spectra and higher order statistics. The structure function analysis was performed to locate and check if there are intermittent behaviors in the ionospheres plasma over epicenter region of the earthquakes. These registrations are correlated with the plasma parameters measured onboard DEMETER satellite and with geomagnetic indices.

Vibrational, spectroscopic, molecular docking and density functional theory studies on N-(5-aminopyridin-2-yl)acetamide

NASA Astrophysics Data System (ADS)

Asath, R. Mohamed; Rekha, T. N.; Premkumar, S.; Mathavan, T.; Benial, A. Milton Franklin

2016-12-01

Conformational analysis was carried out for N-(5-aminopyridin-2-yl)acetamide (APA) molecule. The most stable, optimized structure was predicted by the density functional theory calculations using the B3LYP functional with cc-pVQZ basis set. The optimized structural parameters and vibrational frequencies were calculated. The experimental and theoretical vibrational frequencies were assigned and compared. Ultraviolet-visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated. Frontier molecular orbitals and related molecular properties were computed, which reveals that the higher molecular reactivity and stability of the APA molecule and further density of states spectrum was simulated. The natural bond orbital analysis was also performed to confirm the bioactivity of the APA molecule. Antidiabetic activity was studied based on the molecular docking analysis and the APA molecule was identified that it can act as a good inhibitor against diabetic nephropathy.

Tract-based Spatial Statistics and fMRI Analysis in Patients with Small Cell Lung Cancer before Prophylactic Cranial Irradiation

NASA Astrophysics Data System (ADS)

Benezi, S.; Bromis, K.; Karavasilis, E.; Karanasiou, I. S.; Koutsoupidou, M.; Matsopoulos, G.; Ventouras, E.; Uzunoglu, N.; Kouloulias, V.; Papathanasiou, M.; Foteineas, A.; Efstathopoulos, E.; Kelekis, N.; Kelekis, D.

2015-09-01

Prophylactic cranial irradiation (PCI) is known to increase life expectancy to a significant degree in Small Cell Lung Cancer (SCLC) patients. The overall scope of this research is to investigate changes in structural and functional connectivity between SCLC patients and controls before and after PCI treatment. In the current study specifically we use diffusion tensor imaging (DTI) and functional Magnetic Resonance (fMRI) to identify potential alterations in white matter structure and brain function respectively, in SCLC patients before PCI compared to healthy participants. The results in DTI analysis have showed lower fractional anisotropy (FA) and higher eigenvalues in white matter regions in the patient group. Similarly, in fMRI analysis a lower level of activation in the primary somatosensory cortex was reported. The results presented herein are subject to further investigation with larger patient and control groups.

Mutual connectivity analysis (MCA) using generalized radial basis function neural networks for nonlinear functional connectivity network recovery in resting-state functional MRI

NASA Astrophysics Data System (ADS)

D'Souza, Adora M.; Abidin, Anas Zainul; Nagarajan, Mahesh B.; Wismüller, Axel

2016-03-01

We investigate the applicability of a computational framework, called mutual connectivity analysis (MCA), for directed functional connectivity analysis in both synthetic and resting-state functional MRI data. This framework comprises of first evaluating non-linear cross-predictability between every pair of time series prior to recovering the underlying network structure using community detection algorithms. We obtain the non-linear cross-prediction score between time series using Generalized Radial Basis Functions (GRBF) neural networks. These cross-prediction scores characterize the underlying functionally connected networks within the resting brain, which can be extracted using non-metric clustering approaches, such as the Louvain method. We first test our approach on synthetic models with known directional influence and network structure. Our method is able to capture the directional relationships between time series (with an area under the ROC curve = 0.92 +/- 0.037) as well as the underlying network structure (Rand index = 0.87 +/- 0.063) with high accuracy. Furthermore, we test this method for network recovery on resting-state fMRI data, where results are compared to the motor cortex network recovered from a motor stimulation sequence, resulting in a strong agreement between the two (Dice coefficient = 0.45). We conclude that our MCA approach is effective in analyzing non-linear directed functional connectivity and in revealing underlying functional network structure in complex systems.

Mutual Connectivity Analysis (MCA) Using Generalized Radial Basis Function Neural Networks for Nonlinear Functional Connectivity Network Recovery in Resting-State Functional MRI.

PubMed

DSouza, Adora M; Abidin, Anas Zainul; Nagarajan, Mahesh B; Wismüller, Axel

2016-03-29

We investigate the applicability of a computational framework, called mutual connectivity analysis (MCA), for directed functional connectivity analysis in both synthetic and resting-state functional MRI data. This framework comprises of first evaluating non-linear cross-predictability between every pair of time series prior to recovering the underlying network structure using community detection algorithms. We obtain the non-linear cross-prediction score between time series using Generalized Radial Basis Functions (GRBF) neural networks. These cross-prediction scores characterize the underlying functionally connected networks within the resting brain, which can be extracted using non-metric clustering approaches, such as the Louvain method. We first test our approach on synthetic models with known directional influence and network structure. Our method is able to capture the directional relationships between time series (with an area under the ROC curve = 0.92 ± 0.037) as well as the underlying network structure (Rand index = 0.87 ± 0.063) with high accuracy. Furthermore, we test this method for network recovery on resting-state fMRI data, where results are compared to the motor cortex network recovered from a motor stimulation sequence, resulting in a strong agreement between the two (Dice coefficient = 0.45). We conclude that our MCA approach is effective in analyzing non-linear directed functional connectivity and in revealing underlying functional network structure in complex systems.

Closed-loop spontaneous baroreflex transfer function is inappropriate for system identification of neural arc but partly accurate for peripheral arc: predictability analysis

PubMed Central

Kamiya, Atsunori; Kawada, Toru; Shimizu, Shuji; Sugimachi, Masaru

2011-01-01

Abstract Although the dynamic characteristics of the baroreflex system have been described by baroreflex transfer functions obtained from open-loop analysis, the predictability of time-series output dynamics from input signals, which should confirm the accuracy of system identification, remains to be elucidated. Moreover, despite theoretical concerns over closed-loop system identification, the accuracy and the predictability of the closed-loop spontaneous baroreflex transfer function have not been evaluated compared with the open-loop transfer function. Using urethane and α-chloralose anaesthetized, vagotomized and aortic-denervated rabbits (n = 10), we identified open-loop baroreflex transfer functions by recording renal sympathetic nerve activity (SNA) while varying the vascularly isolated intracarotid sinus pressure (CSP) according to a binary random (white-noise) sequence (operating pressure ± 20 mmHg), and using a simplified equation to calculate closed-loop-spontaneous baroreflex transfer function while matching CSP with systemic arterial pressure (AP). Our results showed that the open-loop baroreflex transfer functions for the neural and peripheral arcs predicted the time-series SNA and AP outputs from measured CSP and SNA inputs, with r2 of 0.8 ± 0.1 and 0.8 ± 0.1, respectively. In contrast, the closed-loop-spontaneous baroreflex transfer function for the neural arc was markedly different from the open-loop transfer function (enhanced gain increase and a phase lead), and did not predict the time-series SNA dynamics (r2; 0.1 ± 0.1). However, the closed-loop-spontaneous baroreflex transfer function of the peripheral arc partially matched the open-loop transfer function in gain and phase functions, and had limited but reasonable predictability of the time-series AP dynamics (r2, 0.7 ± 0.1). A numerical simulation suggested that a noise predominantly in the neural arc under resting conditions might be a possible mechanism responsible for our findings. Furthermore, the predictabilities of the neural arc transfer functions obtained in open-loop and closed-loop conditions were validated by closed-loop pharmacological (phenylephrine and nitroprusside infusions) pressure interventions. Time-series SNA responses to drug-induced AP changes predicted by the open-loop transfer function matched closely the measured responses (r2, 0.9 ± 0.1), whereas SNA responses predicted by closed-loop-spontaneous transfer function deviated greatly and were the inverse of measured responses (r, −0.8 ± 0.2). These results indicate that although the spontaneous baroreflex transfer function obtained by closed-loop analysis has been believed to represent the neural arc function, it is inappropriate for system identification of the neural arc but is essentially appropriate for the peripheral arc under resting conditions, when compared with open-loop analysis. PMID:21486839

The Impact of Massage Therapy on Function in Pain Populations—A Systematic Review and Meta-Analysis of Randomized Controlled Trials: Part III, Surgical Pain Populations

PubMed Central

Boyd, Courtney; Crawford, Cindy; Paat, Charmagne F; Price, Ashley; Xenakis, Lea; Zhang, Weimin; Buckenmaier, Chester; Buckenmaier, Pamela; Cambron, Jerrilyn; Deery, Christopher; Schwartz, Jan; Werner, Ruth; Whitridge, Pete

2016-01-01

Abstract Objective Pain is multi-dimensional and may be better addressed through a holistic, biopsychosocial approach. Massage therapy is commonly practiced among patients seeking pain management; however, its efficacy is unclear. This systematic review and meta-analysis is the first to rigorously assess the quality of the evidence for massage therapy’s efficacy in treating pain, function-related, and health-related quality of life outcomes in surgical pain populations. Methods Key databases were searched from inception through February 2014. Eligible randomized controlled trials were assessed for methodological quality using SIGN 50 Checklist. Meta-analysis was applied at the outcome level. A professionally diverse steering committee interpreted the results to develop recommendations. Results Twelve high quality and four low quality studies were included in the review. Results indicate massage therapy is effective for treating pain [standardized mean difference (SMD) = −0.79] and anxiety (SMD = −0.57) compared to active comparators. Conclusion Based on the available evidence, weak recommendations are suggested for massage therapy, compared to active comparators for reducing pain intensity/severity and anxiety in patients undergoing surgical procedures. This review also discusses massage therapy safety, challenges within this research field, how to address identified research gaps, and next steps for future research. PMID:27165970

Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins.

PubMed

Macaulay, Iain C; Tijssen, Marloes R; Thijssen-Timmer, Daphne C; Gusnanto, Arief; Steward, Michael; Burns, Philippa; Langford, Cordelia F; Ellis, Peter D; Dudbridge, Frank; Zwaginga, Jaap-Jan; Watkins, Nicholas A; van der Schoot, C Ellen; Ouwehand, Willem H

2007-04-15

To identify previously unknown platelet receptors we compared the transcriptomes of in vitro differentiated megakaryocytes (MKs) and erythroblasts (EBs). RNA was obtained from purified, biologically paired MK and EB cultures and compared using cDNA microarrays. Bioinformatical analysis of MK-up-regulated genes identified 151 transcripts encoding transmembrane domain-containing proteins. Although many of these were known platelet genes, a number of previously unidentified or poorly characterized transcripts were also detected. Many of these transcripts, including G6b, G6f, LRRC32, LAT2, and the G protein-coupled receptor SUCNR1, encode proteins with structural features or functions that suggest they may be involved in the modulation of platelet function. Immunoblotting on platelets confirmed the presence of the encoded proteins, and flow cytometric analysis confirmed the expression of G6b, G6f, and LRRC32 on the surface of platelets. Through comparative analysis of expression in platelets and other blood cells we demonstrated that G6b, G6f, and LRRC32 are restricted to the platelet lineage, whereas LAT2 and SUCNR1 were also detected in other blood cells. The identification of the succinate receptor SUCNR1 in platelets is of particular interest, because physiologically relevant concentrations of succinate were shown to potentiate the effect of low doses of a variety of platelet agonists.

Rare event computation in deterministic chaotic systems using genealogical particle analysis

NASA Astrophysics Data System (ADS)

Wouters, J.; Bouchet, F.

2016-09-01

In this paper we address the use of rare event computation techniques to estimate small over-threshold probabilities of observables in deterministic dynamical systems. We demonstrate that genealogical particle analysis algorithms can be successfully applied to a toy model of atmospheric dynamics, the Lorenz ’96 model. We furthermore use the Ornstein-Uhlenbeck system to illustrate a number of implementation issues. We also show how a time-dependent objective function based on the fluctuation path to a high threshold can greatly improve the performance of the estimator compared to a fixed-in-time objective function.

Analysis of a Generally Oriented Crack in a Functionally Graded Strip Sandwiched Between Two Homogeneous Half Planes

NASA Technical Reports Server (NTRS)

Shbeeb, N.; Binienda, W. K.; Kreider, K.

1999-01-01

The driving forces for a generally oriented crack embedded in a Functionally Graded strip sandwiched between two half planes are analyzed using singular integral equations with Cauchy kernels, and integrated using Lobatto-Chebyshev collocation. Mixed-mode Stress Intensity Factors (SIF) and Strain Energy Release Rates (SERR) are calculated. The Stress Intensity Factors are compared for accuracy with previously published results. Parametric studies are conducted for various nonhomogeneity ratios, crack lengths. crack orientation and thickness of the strip. It is shown that the SERR is more complete and should be used for crack propagation analysis.

Molecular docking and spectroscopic investigations aided by density functional theory of Parkinson's drug 2-(3,4-dihydroxyphenyl)ethylamine

NASA Astrophysics Data System (ADS)

Sherlin, Y. Sheeba; Vijayakumar, T.; Roy, S. D. D.; Jayakumar, V. S.

2018-05-01

Molecular geometry of Parkinson's drug 2-(3,4-Dihydroxyphenyl)ethylamine hydrochloride (Dopamine, DA) has been evaluated and compared with experimental XRD data. Molecular docking and vibrational spectral analysis of DA have been carried out using FT-Raman and FT-IR spectra aided by Density Functional Theory at B3LYP/6-311++G(d,p). The present investigation deals with the analysis of structural and spectral features responsible for drug activities, nature of hydrogen bonding interactions of the molecule and the correlation of Parkinson's nature with its molecular structural features.

Neurobiological changes of schizotypy: evidence from both volume-based morphometric analysis and resting-state functional connectivity.

PubMed

Wang, Yi; Yan, Chao; Yin, Da-zhi; Fan, Ming-xia; Cheung, Eric F C; Pantelis, Christos; Chan, Raymond C K

2015-03-01

The current study sought to examine the underlying brain changes in individuals with high schizotypy by integrating networks derived from brain structural and functional imaging. Individuals with high schizotypy (n = 35) and low schizotypy (n = 34) controls were screened using the Schizotypal Personality Questionnaire and underwent brain structural and resting-state functional magnetic resonance imaging on a 3T scanner. Voxel-based morphometric analysis and graph theory-based functional network analysis were conducted. Individuals with high schizotypy showed reduced gray matter (GM) density in the insula and the dorsolateral prefrontal gyrus. The graph theoretical analysis showed that individuals with high schizotypy showed similar global properties in their functional networks as low schizotypy individuals. Several hubs of the functional network were identified in both groups, including the insula, the lingual gyrus, the postcentral gyrus, and the rolandic operculum. More hubs in the frontal lobe and fewer hubs in the occipital lobe were identified in individuals with high schizotypy. By comparing the functional connectivity between clusters with abnormal GM density and the whole brain, individuals with high schizotypy showed weaker functional connectivity between the left insula and the putamen, but stronger connectivity between the cerebellum and the medial frontal gyrus. Taken together, our findings suggest that individuals with high schizotypy present changes in terms of GM and resting-state functional connectivity, especially in the frontal lobe. © The Author 2014. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Quantifying Individual Brain Connectivity with Functional Principal Component Analysis for Networks.

PubMed

Petersen, Alexander; Zhao, Jianyang; Carmichael, Owen; Müller, Hans-Georg

2016-09-01

In typical functional connectivity studies, connections between voxels or regions in the brain are represented as edges in a network. Networks for different subjects are constructed at a given graph density and are summarized by some network measure such as path length. Examining these summary measures for many density values yields samples of connectivity curves, one for each individual. This has led to the adoption of basic tools of functional data analysis, most commonly to compare control and disease groups through the average curves in each group. Such group differences, however, neglect the variability in the sample of connectivity curves. In this article, the use of functional principal component analysis (FPCA) is demonstrated to enrich functional connectivity studies by providing increased power and flexibility for statistical inference. Specifically, individual connectivity curves are related to individual characteristics such as age and measures of cognitive function, thus providing a tool to relate brain connectivity with these variables at the individual level. This individual level analysis opens a new perspective that goes beyond previous group level comparisons. Using a large data set of resting-state functional magnetic resonance imaging scans, relationships between connectivity and two measures of cognitive function-episodic memory and executive function-were investigated. The group-based approach was implemented by dichotomizing the continuous cognitive variable and testing for group differences, resulting in no statistically significant findings. To demonstrate the new approach, FPCA was implemented, followed by linear regression models with cognitive scores as responses, identifying significant associations of connectivity in the right middle temporal region with both cognitive scores.

Functional capacity following univentricular repair--midterm outcome.

PubMed

Sen, Supratim; Bandyopadhyay, Biswajit; Eriksson, Peter; Chattopadhyay, Amitabha

2012-01-01

Previous studies have seldom compared functional capacity in children following Fontan procedure alongside those with Glenn operation as destination therapy. We hypothesized that Fontan circulation enables better midterm submaximal exercise capacity as compared to Glenn physiology and evaluated this using the 6-minute walk test. Fifty-seven children aged 5-18 years with Glenn (44) or Fontan (13) operations were evaluated with standard 6-minute walk protocols. Baseline SpO(2) was significantly lower in Glenn patients younger than 10 years compared to Fontan counterparts and similar in the two groups in older children. Postexercise SpO(2) fell significantly in Glenn patients compared to the Fontan group. There was no statistically significant difference in baseline, postexercise, or postrecovery heart rates (HRs), or 6-minute walk distances in the two groups. Multiple regression analysis revealed lower resting HR, higher resting SpO(2) , and younger age at latest operation to be significant determinants of longer 6-minute walk distance. Multiple regression analysis also established that younger age at operation, higher resting SpO(2) , Fontan operation, lower resting HR, and lower postexercise HR were significant determinants of higher postexercise SpO(2) . Younger age at operation and exercise, lower resting HR and postexercise HR, higher resting SpO(2) and postexercise SpO(2) , and dominant ventricular morphology being left ventricular or indeterminate/mixed had significant association with better 6-minute work on multiple regression analysis. Lower resting HR had linear association with longer 6-minute walk distances in the Glenn patients. Compared to Glenn physiology, Fontan operation did not have better submaximal exercise capacity assessed by walk distance or work on multiple regression analysis. Lower resting HR, higher resting SpO(2) , and younger age at operation were factors uniformly associated with better submaximal exercise capacity. © 2012 Wiley Periodicals, Inc.

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices.

PubMed

Lindsay, Richard J; Siess, Jan; Lohry, David P; McGee, Trevor S; Ritchie, Jordan S; Johnson, Quentin R; Shen, Tongye

2018-01-14

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

NASA Astrophysics Data System (ADS)

Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

2018-01-01

We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

The Relationship Between Body Image and Sexual Function in Middle-Aged Women.

PubMed

Afshari, Poorandokht; Houshyar, Zeinab; Javadifar, Nahid; Pourmotahari, Fatemeh; Jorfi, Maryam

2016-11-01

An individual's social and marital function, interpersonal relationships, and quality of life may, sometimes be affected by negative body image. This study is aimed at determining the relationship between body image and sexual function in middle-aged women. In this cross-sectional study, 437 middle-aged women, who were referred to various public healthcare centers in Ahvaz, Iran during 2014-2015, were selected. The Female Sexual Function Index (FSFI) and Body Shape Questionnaire (BSQ) were used for data collection. Chi-square, one-way analysis of variance, Spearman's correlation test, and logistic regression analysis were performed for statistical analysis. Approximately 58% of the participants expressed satisfaction with their body image, 35% were mildly dissatisfied, and 7% were moderately dissatisfied with their body image. Body image had a significant negative relationship with sexual satisfaction and sexual function (p=0.005). Furthermore, there was a significant relationship between body image and sexual desire (p=0.022), pain (p=0.001), sexual arousal (p<0.0005), sexual orgasm (p=0.001), and sexual satisfaction (p<0.0005). As the results indicated, body image is an important aspect of sexual health. In this study, women with a positive body image had higher sexual function valuation, compared to women with a negative body image. Also, body shape satisfaction was a predictor of sexual function.

Template based rotation: A method for functional connectivity analysis with a priori templates☆

PubMed Central

Schultz, Aaron P.; Chhatwal, Jasmeer P.; Huijbers, Willem; Hedden, Trey; van Dijk, Koene R.A.; McLaren, Donald G.; Ward, Andrew M.; Wigman, Sarah; Sperling, Reisa A.

2014-01-01

Functional connectivity magnetic resonance imaging (fcMRI) is a powerful tool for understanding the network level organization of the brain in research settings and is increasingly being used to study large-scale neuronal network degeneration in clinical trial settings. Presently, a variety of techniques, including seed-based correlation analysis and group independent components analysis (with either dual regression or back projection) are commonly employed to compute functional connectivity metrics. In the present report, we introduce template based rotation,1 a novel analytic approach optimized for use with a priori network parcellations, which may be particularly useful in clinical trial settings. Template based rotation was designed to leverage the stable spatial patterns of intrinsic connectivity derived from out-of-sample datasets by mapping data from novel sessions onto the previously defined a priori templates. We first demonstrate the feasibility of using previously defined a priori templates in connectivity analyses, and then compare the performance of template based rotation to seed based and dual regression methods by applying these analytic approaches to an fMRI dataset of normal young and elderly subjects. We observed that template based rotation and dual regression are approximately equivalent in detecting fcMRI differences between young and old subjects, demonstrating similar effect sizes for group differences and similar reliability metrics across 12 cortical networks. Both template based rotation and dual-regression demonstrated larger effect sizes and comparable reliabilities as compared to seed based correlation analysis, though all three methods yielded similar patterns of network differences. When performing inter-network and sub-network connectivity analyses, we observed that template based rotation offered greater flexibility, larger group differences, and more stable connectivity estimates as compared to dual regression and seed based analyses. This flexibility owes to the reduced spatial and temporal orthogonality constraints of template based rotation as compared to dual regression. These results suggest that template based rotation can provide a useful alternative to existing fcMRI analytic methods, particularly in clinical trial settings where predefined outcome measures and conserved network descriptions across groups are at a premium. PMID:25150630

The impact of slow graft function on graft outcome is comparable to delayed graft function in deceased donor kidney transplantation.

PubMed

Shin, Jung-Ho; Koo, Eun Hee; Ha, Sung Hae; Park, Ji Hyeon; Jang, Hye Ryoun; Lee, Jung Eun; Park, Jae-Berm; Kim, Sung Joo; Jung, Sin-Ho; Kim, Yoon-Goo; Kim, Dae Joong; Oh, Ha Young; Huh, Wooseong

2016-03-01

Slow graft function (SGF) can influence overall prognosis in patients receiving deceased donor kidney transplantation (DKT). However, the impact of SGF on renal function remains uncertain. We investigated retrospectively renal function in cases with SGF compared with early graft function (EGF) and delayed graft function (DGF). Renal function after transplantation was analyzed in 199 patients who underwent DKT. Patients were classified into 130 (65.3 %) cases with EGF, 27 (13.6 %) cases with SGF, 6 (3.0 %) cases with DGF and one dialysis (DGF1), and 36 (18.1 %) cases with DGF and two or more dialyses (DGF2). The 1-year estimated glomerular filtration rate (eGFR) in the SGF group was lower than that in the EGF group (P = 0.027), but the rate of eGFR decline did not differ between the groups. The risk factors for renal function were evaluated using the area under the eGFR curve over 3 years (AUCeGFR). Donor age was negatively, and recipient age and the number of HLA matches were positively correlated with the AUCeGFR (all P < 0.05). A multivariate analysis revealed that the AUCeGFR was lower in cases of younger recipient age, older donor age, and acute rejection (all P < 0.05). The AUCeGFR was significantly lower in the SGF and DGF2 groups compared with the EGF group (P = 0.031 and 0.006, respectively). SGF may be an independent risk factor for poor renal function after DKT. Moreover, it was comparable to DGF. Efforts should be dedicated to minimizing the development of SGF and DGF.

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

PubMed Central

Fong, Christine; Rohmer, Laurence; Radey, Matthew; Wasnick, Michael; Brittnacher, Mitchell J

2008-01-01

Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client side software setup or installation required. Source code is freely available to researchers interested in setting up a local version of PSAT for analysis of genomes not available through the public server. Access to the public web server and instructions for obtaining source code can be found at . PMID:18366802

Residual effects of cannabis use in adolescent and adult brains - A meta-analysis of fMRI studies.

PubMed

Blest-Hopley, Grace; Giampietro, Vincent; Bhattacharyya, Sagnik

2018-05-01

While numerous studies have investigated the residual effects of cannabis use on human brain function, results of these studies have been inconsistent. Using meta-analytic approaches we summarize the effects of prolonged cannabis exposure on human brain function as measured using task-based functional MRI (fMRI) across studies employing a range of cognitive activation tasks comparing regular cannabis users with non-users. Separate meta-analyses were carried out for studies investigating adult and adolescent cannabis users. Systematic literature search identified 20 manuscripts (13 adult and 7 adolescent studies) meeting study inclusion criteria. Adult analyses compared 530 cannabis users to 580 healthy controls while adolescent analyses compared 219 cannabis users to 224 healthy controls. In adult cannabis users brain activation was increased in the superior and posterior transverse temporal and inferior frontal gyri and decreased in the striate area, insula and middle temporal gyrus. In adolescent cannabis users, activation was increased in the inferior parietal gyrus and putamen compared to healthy controls. Functional alteration in these areas may reflect compensatory neuroadaptive changes in cannabis users. Copyright © 2018 Elsevier Ltd. All rights reserved.

PLAZA 3.0: an access point for plant comparative genomics

PubMed Central

Proost, Sebastian; Van Bel, Michiel; Vaneechoutte, Dries; Van de Peer, Yves; Inzé, Dirk; Mueller-Roeber, Bernd; Vandepoele, Klaas

2015-01-01

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms. PMID:25324309

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

Boroun, G. R., E-mail: grboroun@gmail.com, E-mail: boroun@razi.ac.ir; Zarrin, S.

We derive a general scheme for the evolution of the nonsinglet structure function at the leadingorder (LO) and next-to-leading-order (NLO) by using the Laplace-transform technique. Results for the nonsinglet structure function are compared with MSTW2008, GRV, and CKMT parameterizations and also EMC experimental data in the LO and NLO analysis. The results are in good agreement with the experimental data and other parameterizations in the low- and large-x regions.

Bidirectional reflectance distribution function measurements and analysis of retroreflective materials.

PubMed

Belcour, Laurent; Pacanowski, Romain; Delahaie, Marion; Laville-Geay, Aude; Eupherte, Laure

2014-12-01

We compare the performance of various analytical retroreflecting bidirectional reflectance distribution function (BRDF) models to assess how they reproduce accurately measured data of retroreflecting materials. We introduce a new parametrization, the back vector parametrization, to analyze retroreflecting data, and we show that this parametrization better preserves the isotropy of data. Furthermore, we update existing BRDF models to improve the representation of retroreflective data.

Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function

PubMed Central

2009-01-01

Background A central task in contemporary biosciences is the identification of biological processes showing response in genome-wide differential gene expression experiments. Two types of analysis are common. Either, one generates an ordered list based on the differential expression values of the probed genes and examines the tail areas of the list for over-representation of various functional classes. Alternatively, one monitors the average differential expression level of genes belonging to a given functional class. So far these two types of method have not been combined. Results We introduce a scoring function, Gene Set Z-score (GSZ), for the analysis of functional class over-representation that combines two previous analysis methods. GSZ encompasses popular functions such as correlation, hypergeometric test, Max-Mean and Random Sets as limiting cases. GSZ is stable against changes in class size as well as across different positions of the analysed gene list in tests with randomized data. GSZ shows the best overall performance in a detailed comparison to popular functions using artificial data. Likewise, GSZ stands out in a cross-validation of methods using split real data. A comparison of empirical p-values further shows a strong difference in favour of GSZ, which clearly reports better p-values for top classes than the other methods. Furthermore, GSZ detects relevant biological themes that are missed by the other methods. These observations also hold when comparing GSZ with popular program packages. Conclusion GSZ and improved versions of earlier methods are a useful contribution to the analysis of differential gene expression. The methods and supplementary material are available from the website http://ekhidna.biocenter.helsinki.fi/users/petri/public/GSZ/GSZscore.html. PMID:19775443

The Impact of Massage Therapy on Function in Pain Populations—A Systematic Review and Meta-Analysis of Randomized Controlled Trials: Part II, Cancer Pain Populations

PubMed Central

Boyd, Courtney; Crawford, Cindy; Paat, Charmagne F; Price, Ashley; Xenakis, Lea; Zhang, Weimin; Buckenmaier, Chester; Buckenmaier, Pamela; Cambron, Jerrilyn; Deery, Christopher; Schwartz, Jan; Werner, Ruth; Whitridge, Pete

2016-01-01

Abstract Purpose Pain is multi-dimensional and may be better addressed through a holistic, biopsychosocial approach. Massage therapy is commonly practiced among patients seeking pain management; however, its efficacy is unclear. This systematic review and meta-analysis is the first to rigorously assess the quality of massage therapy research and evidence for its efficacy in treating pain, function-related and health-related quality of life in cancer populations. Methods Key databases were searched from inception through February 2014. Eligible randomized controlled trials were assessed for methodological quality using the SIGN 50 Checklist. Meta-analysis was applied at the outcome level. A diverse steering committee interpreted the results to develop recommendations. Results Twelve high quality and four low quality studies were subsequently included in the review. Results demonstrate massage therapy is effective for treating pain compared to no treatment [standardized mean difference (SMD)  = −.20] and active (SMD = −0.55) comparators. Compared to active comparators, massage therapy was also found to be beneficial for treating fatigue (SMD = −1.06) and anxiety (SMD = −1.24). Conclusion Based on the evidence, weak recommendations are suggested for massage therapy, compared to an active comparator, for the treatment of pain, fatigue, and anxiety. No recommendations were suggested for massage therapy compared to no treatment or sham control based on the available literature to date. This review addresses massage therapy safety, research challenges, how to address identified research gaps, and necessary next steps for implementing massage therapy as a viable pain management option for cancer pain populations. PMID:27165967

The Impact of Massage Therapy on Function in Pain Populations-A Systematic Review and Meta-Analysis of Randomized Controlled Trials: Part II, Cancer Pain Populations.

PubMed

Boyd, Courtney; Crawford, Cindy; Paat, Charmagne F; Price, Ashley; Xenakis, Lea; Zhang, Weimin

2016-08-01

Pain is multi-dimensional and may be better addressed through a holistic, biopsychosocial approach. Massage therapy is commonly practiced among patients seeking pain management; however, its efficacy is unclear. This systematic review and meta-analysis is the first to rigorously assess the quality of massage therapy research and evidence for its efficacy in treating pain, function-related and health-related quality of life in cancer populations. Key databases were searched from inception through February 2014. Eligible randomized controlled trials were assessed for methodological quality using the SIGN 50 Checklist. Meta-analysis was applied at the outcome level. A diverse steering committee interpreted the results to develop recommendations. Twelve high quality and four low quality studies were subsequently included in the review. Results demonstrate massage therapy is effective for treating pain compared to no treatment [standardized mean difference (SMD)  = -.20] and active (SMD = -0.55) comparators. Compared to active comparators, massage therapy was also found to be beneficial for treating fatigue (SMD = -1.06) and anxiety (SMD = -1.24). Based on the evidence, weak recommendations are suggested for massage therapy, compared to an active comparator, for the treatment of pain, fatigue, and anxiety. No recommendations were suggested for massage therapy compared to no treatment or sham control based on the available literature to date. This review addresses massage therapy safety, research challenges, how to address identified research gaps, and necessary next steps for implementing massage therapy as a viable pain management option for cancer pain populations. © 2016 American Academy of Pain Medicine.

Neuropsychological function after endovascular and neurosurgical treatment of subarachnoid hemorrhage: a systematic review and meta-analysis.

PubMed

Egeto, Peter; Loch Macdonald, R; Ornstein, Tisha J; Schweizer, Tom A

2018-03-01

OBJECTIVE Subarachnoid hemorrhage (SAH) is treated with either surgical clipping or endovascular coiling, though the latter is the preferred treatment method given its more favorable functional outcomes. However, neuropsychological functioning after treatment is rarely taken into account. In this meta-analysis, the authors synthesized relevant data from the literature and compared neuropsychological functioning in patients after coiling and clipping of SAH. They hypothesized that the coiled patients would outperform the clipped patients; that group differences would be greater with higher posterior circulation rupture rates, in older patients, and in more recent publications; that group differences would be smaller with greater rates of middle cerebral artery (MCA) rupture; and that anterior communicating artery (ACoA) rupture rates would not influence effect sizes. METHODS The MEDLINE, Embase, and PsycINFO databases were searched for clinical studies that compared neuropsychological functioning after either endovascular coiling or surgical clipping for SAH. Hedge's g and 95% confidence intervals were calculated using random effects models. Patients who had undergone coiling or clipping were compared on test performance in 8 neuropsychological domains: executive functions, language, attention/processing speed, verbal memory, visual memory, spatial memory, visuospatial functions, and intelligence. Patients were also compared with healthy controls, and meta-regressions were used to explore the relation between effect sizes and publication year, delay between treatment and neuropsychological testing, mean patient age, and rates of posterior circulation, ACoA, and MCA ruptures. RESULTS Thirteen studies with 396 clipped cases, 314 coiled cases, and 169 healthy controls were included in the study. The coil-treated patients outperformed the clip-treated patients on executive function (g = 0.17, 95% CI 0.08-0.25) and language tests (g = 0.23, 95% CI 0.07-0.39), and all patients were impaired relative to healthy controls (g ranged from -0.93 to -0.29). Coiled patients outperformed clipped patients to a greater degree in more recent publications, over longer posttreatment testing delays, and among older patients. Higher rates of posterior circulation and MCA aneurysms were associated with smaller group differences, while ACoA rupture rates did not influence effect sizes. CONCLUSIONS Coiling of SAH may promote superior neuropsychological functioning under certain circumstances and could have applications for the specialized care of SAH patients.

Determinants of self-rated health: could health status explain the association between self-rated health and mortality?

PubMed

Murata, Chiyoe; Kondo, Takaaki; Tamakoshi, Koji; Yatsuya, Hiroshi; Toyoshima, Hideaki

2006-01-01

The purpose of this study was to investigate factors related to self-rated health and to mortality among 2490 community-living elderly. Respondents were followed for 7.3 years for all-cause mortality. To compare the relative impact of each variable, we employed logistic regression analysis for self-rated health and Cox hazard analysis for mortality. Cox analysis stratified by gender, follow-up periods, age group, and functional status was also employed. Series of analysis found that factors associated with self-rated health and with mortality were not identical. Psychological factors such as perceived isolation at home or 'ikigai (one aspect of psychological well-being)' were associated with self-rated health only. Age, functional status, and social relations were associated both with self-rated health and mortality after controlling for possible confounders. Illnesses and functional status accounted for 35-40% of variances in the fair/poor self-rated health. Differences by gender and functional status were observed in the factors related to self-rated health. Overall, self-rated health effect on mortality was stronger for people with no functional impairment, for shorter follow-up period, and for young-old age group. Although, illnesses and functional status were major determinants of self-rated health, economical, psychological, and social factors were also related to self-rated health.

Detecting phase separation of freeze-dried binary amorphous systems using pair-wise distribution function and multivariate data analysis.

PubMed

Chieng, Norman; Trnka, Hjalte; Boetker, Johan; Pikal, Michael; Rantanen, Jukka; Grohganz, Holger

2013-09-15

The purpose of this study is to investigate the use of multivariate data analysis for powder X-ray diffraction-pair-wise distribution function (PXRD-PDF) data to detect phase separation in freeze-dried binary amorphous systems. Polymer-polymer and polymer-sugar binary systems at various ratios were freeze-dried. All samples were analyzed by PXRD, transformed to PDF and analyzed by principal component analysis (PCA). These results were validated by differential scanning calorimetry (DSC) through characterization of glass transition of the maximally freeze-concentrate solute (Tg'). Analysis of PXRD-PDF data using PCA provides a more clear 'miscible' or 'phase separated' interpretation through the distribution pattern of samples on a score plot presentation compared to residual plot method. In a phase separated system, samples were found to be evenly distributed around the theoretical PDF profile. For systems that were miscible, a clear deviation of samples away from the theoretical PDF profile was observed. Moreover, PCA analysis allows simultaneous analysis of replicate samples. Comparatively, the phase behavior analysis from PXRD-PDF-PCA method was in agreement with the DSC results. Overall, the combined PXRD-PDF-PCA approach improves the clarity of the PXRD-PDF results and can be used as an alternative explorative data analytical tool in detecting phase separation in freeze-dried binary amorphous systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Comparison of Optimum Interpolation and Cressman Analyses

NASA Technical Reports Server (NTRS)

Baker, W. E.; Bloom, S. C.; Nestler, M. S.

1984-01-01

The objective of this investigation is to develop a state-of-the-art optimum interpolation (O/I) objective analysis procedure for use in numerical weather prediction studies. A three-dimensional multivariate O/I analysis scheme has been developed. Some characteristics of the GLAS O/I compared with those of the NMC and ECMWF systems are summarized. Some recent enhancements of the GLAS scheme include a univariate analysis of water vapor mixing ratio, a geographically dependent model prediction error correlation function and a multivariate oceanic surface analysis.

Comparison of Optimum Interpolation and Cressman Analyses

NASA Technical Reports Server (NTRS)

Baker, W. E.; Bloom, S. C.; Nestler, M. S.

1985-01-01

The development of a state of the art optimum interpolation (O/I) objective analysis procedure for use in numerical weather prediction studies was investigated. A three dimensional multivariate O/I analysis scheme was developed. Some characteristics of the GLAS O/I compared with those of the NMC and ECMWF systems are summarized. Some recent enhancements of the GLAS scheme include a univariate analysis of water vapor mixing ratio, a geographically dependent model prediction error correlation function and a multivariate oceanic surface analysis.

Executive Functions in Students With Depression, Anxiety, and Stress Symptoms

PubMed Central

Ajilchi, Bita; Nejati, Vahid

2017-01-01

Introduction: This study aimed to investigate and compare the executive functions of students with depression, anxiety, and stress symptoms with those functions in healthy ones. Methods: This study was a comparative and non-clinical analysis. The study population comprised all students of Shahid Beheshti University, Tehran, Iran. A total of 448 students were recruited using convenience sampling method. They were also screened using the Depression Anxiety Stress Scales (DASS) test comprising 21 items. Of study participants, 30 people were depressed, 27 had anxiety, and 15 suffered from stress. Then, 50 control people were matched with them. Next, both groups were compared using the Stroop test, Wisconsin card sorting, and cognitive ability test. Results: Using MANOVA test, data analysis revealed no significant differences among 4 groups with regard to selective attention and shifting attention. Depressed group reacted rapidly as opposed to the anxiety group with regard to measures of shifting attention and cognitive abilities; it was observed that the memory, inhibition control, planning, and flexibility of the healthy group were better than those of the 3 other groups. Conclusion: The findings of this research raised specific issues in relation to the role of depression, anxiety, and stress in the disruption of the executive functions of sufferers. Selective and shifting attention and cognitive abilities are specifically affected in this regard. Meanwhile, the role of stress in impairing decision making and the major role of anxiety in impairing sustained attention was shown to be considerable. PMID:28781730

Executive Functions in Students With Depression, Anxiety, and Stress Symptoms.

PubMed

Ajilchi, Bita; Nejati, Vahid

2017-01-01

This study aimed to investigate and compare the executive functions of students with depression, anxiety, and stress symptoms with those functions in healthy ones. This study was a comparative and non-clinical analysis. The study population comprised all students of Shahid Beheshti University, Tehran, Iran. A total of 448 students were recruited using convenience sampling method. They were also screened using the Depression Anxiety Stress Scales (DASS) test comprising 21 items. Of study participants, 30 people were depressed, 27 had anxiety, and 15 suffered from stress. Then, 50 control people were matched with them. Next, both groups were compared using the Stroop test, Wisconsin card sorting, and cognitive ability test. Using MANOVA test, data analysis revealed no significant differences among 4 groups with regard to selective attention and shifting attention. Depressed group reacted rapidly as opposed to the anxiety group with regard to measures of shifting attention and cognitive abilities; it was observed that the memory, inhibition control, planning, and flexibility of the healthy group were better than those of the 3 other groups. The findings of this research raised specific issues in relation to the role of depression, anxiety, and stress in the disruption of the executive functions of sufferers. Selective and shifting attention and cognitive abilities are specifically affected in this regard. Meanwhile, the role of stress in impairing decision making and the major role of anxiety in impairing sustained attention was shown to be considerable.

Using the Oxford Foot Model to determine the association between objective measures of foot function and results of the AOFAS Ankle-Hindfoot Scale and the Foot Function Index: a prospective gait analysis study in Germany

PubMed Central

Kostuj, Tanja; Stief, Felix; Hartmann, Kirsten Anna; Schaper, Katharina; Arabmotlagh, Mohammad; Baums, Mike H; Meurer, Andrea; Krummenauer, Frank; Lieske, Sebastian

2018-01-01

Objective After cross-cultural adaption for the German translation of the Ankle-Hindfoot Scale of the American Orthopaedic Foot and Ankle Society (AOFAS-AHS) and agreement analysis with the Foot Function Index (FFI-D), the following gait analysis study using the Oxford Foot Model (OFM) was carried out to show which of the two scores better correlates with objective gait dysfunction. Design and participants Results of the AOFAS-AHS and FFI-D, as well as data from three-dimensional gait analysis were collected from 20 patients with mild to severe ankle and hindfoot pathologies. Kinematic and kinetic gait data were correlated with the results of the total AOFAS scale and FFI-D as well as the results of those items representing hindfoot function in the AOFAS-AHS assessment. With respect to the foot disorders in our patients (osteoarthritis and prearthritic conditions), we correlated the total range of motion (ROM) in the ankle and subtalar joints as identified by the OFM with values identified during clinical examination ‘translated’ into score values. Furthermore, reduced walking speed, reduced step length and reduced maximum ankle power generation during push-off were taken into account and correlated to gait abnormalities described in the scores. An analysis of correlations with CIs between the FFI-D and the AOFAS-AHS items and the gait parameters was performed by means of the Jonckheere-Terpstra test; furthermore, exploratory factor analysis was applied to identify common information structures and thereby redundancy in the FFI-D and the AOFAS-AHS items. Results Objective findings for hindfoot disorders, namely a reduced ROM, in the ankle and subtalar joints, respectively, as well as reduced ankle power generation during push-off, showed a better correlation with the AOFAS-AHS total score—as well as AOFAS-AHS items representing ROM in the ankle, subtalar joints and gait function—compared with the FFI-D score. Factor analysis, however, could not identify FFI-D items consistently related to these three indicator parameters (pain, disability and function) found in the AOFAS-AHS. Furthermore, factor analysis did not support stratification of the FFI-D into two subscales. Conclusions The AOFAS-AHS showed a good agreement with objective gait parameters and is therefore better suited to evaluate disability and functional limitations of patients suffering from foot and ankle pathologies compared with the FFI-D. PMID:29626046

Massage Therapy in Children with Asthma: A Systematic Review and Meta-Analysis.

PubMed

Wu, Ji; Yang, Xi-Wen; Zhang, Ming

2017-01-01

To systematically evaluate the efficacy of massage, a traditional treatment method of traditional Chinese medicine on children with asthma. Literatures from 5 databases using the date ranging from 1 January, 1990, to 13 December, 2016, were reviewed, which were all randomized controlled trials evaluating the efficacy on children with asthma and effect on lung function mainly by massage therapy. 14 researches with 1299 patients were included in the meta-analysis. Compared with control group, a better efficacy was found in treatment group, which focused on massage therapy. Compared with control group, there was remarkable increase on FEV1 as well as PEF in treatment group. All studies have shown that massage therapy has a significantly positive effect on children with asthma, improves the pulmonary function parameters of large airway, reduces the plasma concentrations of PAF and prostaglandin, and increases the levels of PAF-AH and DP1; therefore, it greatly improves pulmonary function. However, the limited research designs of included studies lead to high risk of bias. More randomized controlled trials with better methodological quality are needed to further confirm the effectiveness of massage.

Describing-function analysis of a ripple regulator with slew-rate limits and time delays

NASA Technical Reports Server (NTRS)

Wester, Gene W.

1990-01-01

The effects of time delays and slew-rate limits on the steady-state operating points and performance of a free-running ripple regulator are evaluated using describing-function analysis. The describing function of an ideal comparator (no time delays or slew rate limits) has no phase shift and is independent of frequency. It is found that turn-on delay and turn-off delay have different effects on gain and phase and cannot be combined. Comparator hysteresis affects both gain and phase; likewise, time delays generally affect both gain and phase. It is found that the effective time delay around the feedback loop is one half the sum of turn-on and turn-off delays, regardless of whether the delays are caused by storage time or slew rate limits. Expressions are formulated for the switching frequency, switch duty ratio, dc output, and output ripple. For the case of no hysteresis, a simple, graphical solution for the switching frequency is possible, and the resulting switching frequency is independent of first-order variations of input or load.

Siblings of children with a chronic illness: a meta-analysis.

PubMed

Sharpe, Donald; Rossiter, Lucille

2002-12-01

To review the literature pertaining to the siblings of children with a chronic illness. Fifty-one published studies and 103 effect sizes were identified and examined through meta-analysis. We found (1) a modest, negative effect size statistic existed for siblings of children with a chronic illness relative to comparison participants or normative data; (2) heterogeneity existed for those effect sizes; (3) parent reports were more negative than child self-reports; (4) psychological functioning (i.e., depression, anxiety), peer activities, and cognitive development scores were lower for siblings of children with a chronic illness compared to controls; and (5) a cluster of chronic illnesses with daily treatment regimes was associated with negative effect statistics compared to chronic illnesses that did not affect daily functioning. More methodologically sound studies investigating the psychological functioning of siblings of children with a chronic illness are needed. Clinicians need to know that siblings of children with a chronic illness are at risk for negative psychological effects. Intervention programs for the siblings and families of children with a chronic illness should be developed.

Quantum Monte Carlo analysis of a charge ordered insulating antiferromagnet: The Ti 4O 7 Magneli phase

DOE PAGES

Benali, Anouar; Shulenburger, Luke; Krogel, Jaron T.; ...

2016-06-07

The Magneli phase Ti 4O 7 is an important transition metal oxide with a wide range of applications because of its interplay between charge, spin, and lattice degrees of freedom. At low temperatures, it has non-trivial magnetic states very close in energy, driven by electronic exchange and correlation interactions. We have examined three low- lying states, one ferromagnetic and two antiferromagnetic, and calculated their energies as well as Ti spin moment distributions using highly accurate Quantum Monte Carlo methods. We compare our results to those obtained from density functional theory- based methods that include approximate corrections for exchange and correlation.more » Our results confirm the nature of the states and their ordering in energy, as compared with density-functional theory methods. However, the energy differences and spin distributions differ. Here, a detailed analysis suggests that non-local exchange-correlation functionals, in addition to other approximations such as LDA+U to account for correlations, are needed to simultaneously obtain better estimates for spin moments, distributions, energy differences and energy gaps.« less

Long-term effects of musical training and functional plasticity in salience system.

PubMed

Luo, Cheng; Tu, Shipeng; Peng, Yueheng; Gao, Shan; Li, Jianfu; Dong, Li; Li, Gujing; Lai, Yongxiu; Li, Hong; Yao, Dezhong

2014-01-01

Musicians undergoing long-term musical training show improved emotional and cognitive function, which suggests the presence of neuroplasticity. The structural and functional impacts of the human brain have been observed in musicians. In this study, we used data-driven functional connectivity analysis to map local and distant functional connectivity in resting-state functional magnetic resonance imaging data from 28 professional musicians and 28 nonmusicians. Compared with nonmusicians, musicians exhibited significantly greater local functional connectivity density in 10 regions, including the bilateral dorsal anterior cingulate cortex, anterior insula, and anterior temporoparietal junction. A distant functional connectivity analysis demonstrated that most of these regions were included in salience system, which is associated with high-level cognitive control and fundamental attentional process. Additionally, musicians had significantly greater functional integration in this system, especially for connections to the left insula. Increased functional connectivity between the left insula and right temporoparietal junction may be a response to long-term musical training. Our findings indicate that the improvement of salience network is involved in musical training. The salience system may represent a new avenue for exploration regarding the underlying foundations of enhanced higher-level cognitive processes in musicians.

Function and disability in late life: comparison of the Late-Life Function and Disability Instrument to the Short-Form-36 and the London Handicap Scale.

PubMed

Dubuc, Nicole; Haley, Stephen; Ni, Pengsheng; Kooyoomjian, Jill; Jette, Alan

2004-03-18

We evaluated the Late-Life Function and Disability Instrument's (LLFDI) concurrent validity, comprehensiveness and precision by comparing it with the Short-Form-36 physical functioning (PF-10) and the London Handicap Scale (LHS). We administered the LLFDI, PF-10 and LHS to 75 community-dwelling adults (> 60 years of age). We used Pearson correlation coefficients to examine concurrent validity and Rasch analysis to compare the item hierarchies, content ranges and precision of the PF-10 and LLFDI function domains, and the LHS and the LLFDI disability domains. LLFDI Function (lower extremity scales) and PF-10 scores were highly correlated (r = 0.74 - 0.86, p > 0.001); moderate correlations were found between the LHS and the LLFDI Disability limitation (r = 0.66, p < 0.0001) and Disability frequency (r = 0.47, p < 0.001) scores. The LLFDI had a wider range of content coverage, less ceiling effects and better relative precision across the spectrum of function and disability than the PF-10 and the LHS. The LHS had slightly more content range and precision in the lower end of the disability scale than the LLFDI. The LLFDI is a more comprehensive and precise instrument compared to the PF-10 and LHS for assessing function and disability in community-dwelling older adults.

Plasmablasts and plasma cells: reconsidering teleost immune system organization.

PubMed

Ye, Jianmin; Kaattari, Ilsa; Kaattari, Stephen

2011-12-01

Comparative immunologists have expended extensive efforts in the characterization of early fish B cell development; however, analysis of the post-antigen induction stages of antibody secreting cell (ASC) differentiation has been limited. In contrast, work with murine ASCs has resolved the physically and functionally distinct cells known as plasmablasts, the short-lived plasma cells and long-lived plasma cells. Teleost ASCs are now known to also possess comparable subpopulations, which can greatly differ in such basic functions as lifespan, antigen sensitivity, antibody secretion rate, differentiative potential, and distribution within the body. Understanding the mechanisms by which these subpopulations are produced and distributed is essential for both basic understanding in comparative immunology and practical vaccine engineering. Copyright © 2011 Elsevier Ltd. All rights reserved.

Experimental analysis of multi-attribute decision-making based on Atanassov intuitionistic fuzzy sets: a discussion of anchor dependency and accuracy functions

NASA Astrophysics Data System (ADS)

Chen, Ting-Yu

2012-06-01

This article presents a useful method for relating anchor dependency and accuracy functions to multiple attribute decision-making (MADM) problems in the context of Atanassov intuitionistic fuzzy sets (A-IFSs). Considering anchored judgement with displaced ideals and solution precision with minimal hesitation, several auxiliary optimisation models have proposed to obtain the optimal weights of the attributes and to acquire the corresponding TOPSIS (the technique for order preference by similarity to the ideal solution) index for alternative rankings. Aside from the TOPSIS index, as a decision-maker's personal characteristics and own perception of self may also influence the direction in the axiom of choice, the evaluation of alternatives is conducted based on distances of each alternative from the positive and negative ideal alternatives, respectively. This article originates from Li's [Li, D.-F. (2005), 'Multiattribute Decision Making Models and Methods Using Intuitionistic Fuzzy Sets', Journal of Computer and System Sciences, 70, 73-85] work, which is a seminal study of intuitionistic fuzzy decision analysis using deduced auxiliary programming models, and deems it a benchmark method for comparative studies on anchor dependency and accuracy functions. The feasibility and effectiveness of the proposed methods are illustrated by a numerical example. Finally, a comparative analysis is illustrated with computational experiments on averaging accuracy functions, TOPSIS indices, separation measures from positive and negative ideal alternatives, consistency rates of ranking orders, contradiction rates of the top alternative and average Spearman correlation coefficients.

DROIDS 1.20: A GUI-Based Pipeline for GPU-Accelerated Comparative Protein Dynamics.

PubMed

Babbitt, Gregory A; Mortensen, Jamie S; Coppola, Erin E; Adams, Lily E; Liao, Justin K

2018-03-13

Traditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach applied to MD would connect this very short timescale process, defined in femtoseconds, to one of the longest in the universe: molecular evolution measured in millions of years. Here, we leverage advances in graphics-processing-unit-accelerated MD simulation software to develop a comparative method of MD analysis and visualization that can be applied to any two homologous Protein Data Bank structures. Our open-source pipeline, DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a "comparative computational microscope" for observing the biophysical effects of mutations and other chemical changes in proteins. DROIDS implements structural alignment and Benjamini-Hochberg-corrected Kolmogorov-Smirnov statistics to compare nanosecond-scale atom bond fluctuations on the protein backbone, color mapping the significant differences identified in protein MD with single-amino-acid resolution. DROIDS is simple to use, incorporating graphical user interface control for Amber16 MD simulations, cpptraj analysis, and the final statistical and visual representations in R graphics and UCSF Chimera. We demonstrate that DROIDS can be utilized to visually investigate molecular evolution and disease-related functional changes in MD due to genetic mutation and epigenetic modification. DROIDS can also be used to potentially investigate binding interactions of pharmaceuticals, toxins, or other biomolecules in a functional evolutionary context as well. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Altered Functional Connectivity of the Default Mode Network in Low-Empathy Subjects

PubMed Central

Kim, Seung Jun; Kim, Sung-Eun; Kim, Hyo Eun; Han, Kiwan; Jeong, Bumseok; Kim, Jae-Jin; Namkoong, Kee

2017-01-01

Empathy is the ability to identify with or make a vicariously experience of another person's feelings or thoughts based on memory and/or self-referential mental simulation. The default mode network in particular is related to self-referential empathy. In order to elucidate the possible neural mechanisms underlying empathy, we investigated the functional connectivity of the default mode network in subjects from a general population. Resting state functional magnetic resonance imaging data were acquired from 19 low-empathy subjects and 18 medium-empathy subjects. An independent component analysis was used to identify the default mode network, and differences in functional connectivity strength were compared between the two groups. The low-empathy group showed lower functional connectivity of the medial prefrontal cortex and anterior cingulate cortex (Brodmann areas 9 and 32) within the default mode network, compared to the medium-empathy group. The results of the present study suggest that empathy is related to functional connectivity of the medial prefrontal cortex/anterior cingulate cortex within the default mode network. Functional decreases in connectivity among low-empathy subjects may reflect an impairment of self-referential mental simulation. PMID:28792155

Laser System Reliability

DTIC Science & Technology

1977-03-01

system acquisition cycle since they provide necessary inputs to comparative analyses, cost/benefit trade -offs, and system simulations. In addition, the...Management Program from above performs the function of analyzing the system trade -offs with respect to reliability to determine a reliability goal...one encounters the problem of comparing present dollars with future dollars. In this analysis, we are trading off costs expended initially (or at

[The kidney transplantation from the ABO-incompatible donors].

PubMed

Goriaĭnov, V A; Kaabak, M M; Babenko, N N; Shishlo, L A; Morozova, M M; Ragimov, A A; Dashkova, N G; Salimov, É L

2012-01-01

The experience of 28 allotransplantations of ABO-incompatible kidneys was compared with the treatment results of 38 ABO-compatible renal transplantations. The transplanted kidney function, morphological changes of the transplanted kidney and the comparative analysis of actuary survival in both groups showed no significant difference. The results of the study prove the validity of the kidney transplantation from the ABO-incompatible donors.

Episodic and working memory function in Primary Progressive Aphasia: A meta-analysis.

PubMed

Eikelboom, Willem S; Janssen, Nikki; Jiskoot, Lize C; van den Berg, Esther; Roelofs, Ardi; Kessels, Roy P C

2018-06-18

The distinction between Primary Progressive Aphasia (PPA) variants remains challenging for clinicians, especially for the non-fluent (nfv-PPA) and the logopenic variants (lv-PPA). Previous research suggests that memory tests might aid this differentiation. This meta-analysis compares memory function among PPA variants. Effects sizes were extracted from 41 studies (N = 849). Random-effects models were used to compare performance on episodic and working memory tests among PPA patients and healthy controls, and between the PPA variants. Memory deficits were frequently observed in PPA compared to controls, with large effect sizes for lv-PPA (Hedges' g = -2.04 [-2.58 to -1.49]), nfv-PPA (Hedges' g = -1.34 [-1.69 to -1.00]), and the semantic variant (sv-PPA; Hedges' g = -1.23 [-1.50 to -0.97]). Sv-PPA showed primarily verbal memory deficits, whereas lv-PPA showed worse performance than nfv-PPA on both verbal and non-verbal memory tests. Memory deficits were more pronounced in lv-PPA compared to nfv-PPA. This suggests that memory tests may be helpful to distinguish between these PPA variants. Copyright © 2018. Published by Elsevier Ltd.

Electromyography function, disability degree, and pain in leprosy patients undergoing neural mobilization treatment.

PubMed

Véras, Larissa Sales Téles; Vale, Rodrigo Gomes de Souza; Mello, Danielli Braga de; Castro, José Adail Fonseca de; Lima, Vicente; Trott, Alexis; Dantas, Estélio Henrique Martin

2012-02-01

This study aimed to evaluate the effect of the neural mobilization technique on electromyography function, disability degree, and pain in patients with leprosy. A sample of 56 individuals with leprosy was randomized into an experimental group, composed of 29 individuals undergoing treatment with neural mobilization, and a control group of 27 individuals who underwent conventional treatment. In both groups, the lesions in the lower limbs were treated. In the treatment with neural mobilization, the procedure used was mobilization of the lumbosacral roots and sciatic nerve biased to the peroneal nerve that innervates the anterior tibial muscle, which was evaluated in the electromyography. Analysis of the electromyography function showed a significant increase (p<0.05) in the experimental group in both the right (Δ%=22.1, p=0.013) and the left anterior tibial muscles (Δ%=27.7, p=0.009), compared with the control group pre- and post-test. Analysis of the strength both in the movement of horizontal extension (Δ%right=11.7, p=0.003/Δ%left=27.4, p=0.002) and in the movement of back flexion (Δ%right=31.1; p=0.000/Δ%left=34.7, p=0.000) showed a significant increase (p<0.05) in both the right and the left segments when comparing the experimental group pre- and post-test. The experimental group showed a significant reduction (p=0.000) in pain perception and disability degree when the pre- and post-test were compared and when compared with the control group in the post-test. Leprosy patients undergoing the technique of neural mobilization had an improvement in electromyography function and muscle strength, reducing disability degree and pain.

Central Arterial Function Measured by Non-invasive Pulse Wave Analysis is Abnormal in Patients with Duchenne Muscular Dystrophy.

PubMed

Ryan, Thomas D; Parent, John J; Gao, Zhiqian; Khoury, Philip R; Dupont, Elizabeth; Smith, Jennifer N; Wong, Brenda; Urbina, Elaine M; Jefferies, John L

2017-08-01

Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder caused by mutation of dystrophin. Cardiovascular involvement includes dilated cardiomyopathy. Non-invasive assessment of vascular function has not been evaluated in DMD. We hypothesize arterial wave reflection is abnormal in patients with DMD. Pulse wave analysis was performed on DMD patients with a SphygmoCor SCOR-PVx System to determine central blood pressure and augmentation index (AIx) as an assessment of arterial wave reflection. Results were compared to a control group. A total of 43 patients with DMD were enrolled, and compared to 43 normal controls. Central systolic blood pressure was lower, while both AIx-75 (7.8 ± 9.6% vs. 2.1 ± 10.4%, p 0.01, DMD vs. normal) and AIx-not corrected (16.8 ± 10.1% vs. -3.6 ± 10.9, p < 0.001, DMD vs. normal) were higher in the DMD compared to control. Using multivariable linear regression model, the variables found to have a significant effect on AIx-not corrected included diagnosis of DMD, height, and heart rate (r 2  = 0.257). The current data suggest that, despite lower central systolic blood pressure, patients with DMD have higher wave reflection when compared to normal controls, which may represent increased arterial stiffness. Overall there appears to be no effect on ventricular systolic function, however the long-term consequence in this group is unknown. Further study is required to determine the mechanism of these differences, which may be related to the effects of systemic steroids or the role of dystrophin in vascular function.

A Network Meta-Analysis Comparing Effects of Various Antidepressant Classes on the Digit Symbol Substitution Test (DSST) as a Measure of Cognitive Dysfunction in Patients with Major Depressive Disorder.

PubMed

Baune, Bernhard T; Brignone, Mélanie; Larsen, Klaus Groes

2018-02-01

Major depressive disorder is a common condition that often includes cognitive dysfunction. A systematic literature review of studies and a network meta-analysis were carried out to assess the relative effect of antidepressants on cognitive dysfunction in major depressive disorder. MEDLINE, Embase, Cochrane, CDSR, and PsychINFO databases; clinical trial registries; and relevant conference abstracts were searched for randomized controlled trials assessing the effects of antidepressants/placebo on cognition. A network meta-analysis comparing antidepressants was conducted using a random effects model. The database search retrieved 11337 citations, of which 72 randomized controlled trials from 103 publications met the inclusion criteria. The review identified 86 cognitive tests assessing the effect of antidepressants on cognitive functioning. However, the Digit Symbol Substitution Test, which targets multiple domains of cognition and is recognized as being sensitive to change, was the only test that was used across 12 of the included randomized controlled trials and that allowed the construction of a stable network suitable for the network meta-analysis. The interventions assessed included selective serotonin reuptake inhibitors, serotonin-norepinephrine reuptake inhibitors, and other non-selective serotonin reuptake inhibitors/serotonin-norepinephrine reuptake inhibitors. The network meta-analysis using the Digit Symbol Substitution Test showed that vortioxetine was the only antidepressant that improved cognitive dysfunction on the Digit Symbol Substitution Test vs placebo {standardized mean difference: 0.325 (95% CI = 0.120; 0.529, P=.009}. Compared with other antidepressants, vortioxetine was statistically more efficacious on the Digit Symbol Substitution Test vs escitalopram, nortriptyline, and the selective serotonin reuptake inhibitor and tricyclic antidepressant classes. This study highlighted the large variability in measures used to assess cognitive functioning. The findings on the Digit Symbol Substitution Test indicate differential effects of various antidepressants on improving cognitive function in patients with major depressive disorder. © The Author 2017. Published by Oxford University Press on behalf of CINP.

Using the Oxford Foot Model to determine the association between objective measures of foot function and results of the AOFAS Ankle-Hindfoot Scale and the Foot Function Index: a prospective gait analysis study in Germany.

PubMed

Kostuj, Tanja; Stief, Felix; Hartmann, Kirsten Anna; Schaper, Katharina; Arabmotlagh, Mohammad; Baums, Mike H; Meurer, Andrea; Krummenauer, Frank; Lieske, Sebastian

2018-04-05

After cross-cultural adaption for the German translation of the Ankle-Hindfoot Scale of the American Orthopaedic Foot and Ankle Society (AOFAS-AHS) and agreement analysis with the Foot Function Index (FFI-D), the following gait analysis study using the Oxford Foot Model (OFM) was carried out to show which of the two scores better correlates with objective gait dysfunction. Results of the AOFAS-AHS and FFI-D, as well as data from three-dimensional gait analysis were collected from 20 patients with mild to severe ankle and hindfoot pathologies.Kinematic and kinetic gait data were correlated with the results of the total AOFAS scale and FFI-D as well as the results of those items representing hindfoot function in the AOFAS-AHS assessment. With respect to the foot disorders in our patients (osteoarthritis and prearthritic conditions), we correlated the total range of motion (ROM) in the ankle and subtalar joints as identified by the OFM with values identified during clinical examination 'translated' into score values. Furthermore, reduced walking speed, reduced step length and reduced maximum ankle power generation during push-off were taken into account and correlated to gait abnormalities described in the scores. An analysis of correlations with CIs between the FFI-D and the AOFAS-AHS items and the gait parameters was performed by means of the Jonckheere-Terpstra test; furthermore, exploratory factor analysis was applied to identify common information structures and thereby redundancy in the FFI-D and the AOFAS-AHS items. Objective findings for hindfoot disorders, namely a reduced ROM, in the ankle and subtalar joints, respectively, as well as reduced ankle power generation during push-off, showed a better correlation with the AOFAS-AHS total score-as well as AOFAS-AHS items representing ROM in the ankle, subtalar joints and gait function-compared with the FFI-D score.Factor analysis, however, could not identify FFI-D items consistently related to these three indicator parameters (pain, disability and function) found in the AOFAS-AHS. Furthermore, factor analysis did not support stratification of the FFI-D into two subscales. The AOFAS-AHS showed a good agreement with objective gait parameters and is therefore better suited to evaluate disability and functional limitations of patients suffering from foot and ankle pathologies compared with the FFI-D. © 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.

Functional changes of neural circuits in stroke patients with dysphagia: A meta-analysis.

PubMed

Liu, Lu; Xiao, Yuan; Zhang, Wenjing; Yao, Li; Gao, Xin; Chandan, Shah; Lui, Su

2017-08-01

Dysphagia is a common problem in stroke patients with unclear pathogenesis. Several recent functional magnetic resonance imaging (fMRI) studies had been carried out to explore the cerebral functional changes in dysphagic stroke patients. The aim of this study was to analysis these imaging findings using a meta-analysis. We used seed-based d mapping (SDM) to conduct a meta-analysis for dysphagic stroke patients prior to any kind of special treatment for dysphagia. A systematic search was conducted for the relevant studies. SDM meta-analysis method was used to examine regions of increased and decreased functional activation between dysphagic stroke patients and healthy controls. Finally, six studies including 81 stroke patients with dysphagia and 78 healthy controls met the inclusion standards. When compared with healthy controls, stroke patients with dysphagia showed hyperactivation in left cingulate gyrus, left precentral gyrus and right posterior cingulate gyrus, and hypoactivation in right cuneus and left middle frontal gyrus. The hyperactivity of precentral gyrus is crucial in stroke patients with dysphagia and may be associated with the severity of stroke. Besides the motor areas, the default-mode network regions (DMN) and affective network regions (AN) circuits are also involved in dysphagia after stroke. © 2017 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

Finite element analysis of functionally graded bone plate at femur bone fracture site

NASA Astrophysics Data System (ADS)

Satapathy, Pravat Kumar; Sahoo, Bamadev; Panda, L. N.; Das, S.

2018-03-01

This paper focuses on the analysis of fractured Femur bone with functionally graded bone plate. The Femur bone is modeled by using the data from the CT (Computerized Tomography) scan and the material properties are assigned using Mimics software. The fracture fixation plate used here is composed of Functionally Graded Material (FGM). The functionally graded bone plate is considered to be composed of different layers of homogeneous materials. Finite element method approach is adopted for analysis. The volume fraction of the material is calculated by considering its variation along the thickness direction (z) according to a power law and the effective properties of the homogeneous layers are estimated. The model developed is validated by comparing numerical results available in the literature. Static analysis has been performed for the bone plate system by considering both axial compressive load and torsional load. The investigation shows that by introducing FG bone plate instead of titanium, the stress at the fracture site increases by 63 percentage and the deformation decreases by 15 percentage, especially when torsional load is taken into consideration. The present model yields better results in comparison with the commercially available bone plates.

Anchor Selection Strategies for DIF Analysis: Review, Assessment, and New Approaches

ERIC Educational Resources Information Center

Kopf, Julia; Zeileis, Achim; Strobl, Carolin

2015-01-01

Differential item functioning (DIF) indicates the violation of the invariance assumption, for instance, in models based on item response theory (IRT). For item-wise DIF analysis using IRT, a common metric for the item parameters of the groups that are to be compared (e.g., for the reference and the focal group) is necessary. In the Rasch model,…

Exponential approximations in optimal design

NASA Technical Reports Server (NTRS)

Belegundu, A. D.; Rajan, S. D.; Rajgopal, J.

1990-01-01

One-point and two-point exponential functions have been developed and proved to be very effective approximations of structural response. The exponential has been compared to the linear, reciprocal and quadratic fit methods. Four test problems in structural analysis have been selected. The use of such approximations is attractive in structural optimization to reduce the numbers of exact analyses which involve computationally expensive finite element analysis.

SIR/CAR Analysis Technique for Voluntary School Sport or Amateur Athletic Organizations. A SIR/CAR Application.

ERIC Educational Resources Information Center

Moriarty, Dick; Zarebski, John

This paper delineates the exact methodology developed by the Sports Institute for Research/Change Agent Research (SIR/CAR) for applying a systems analysis technique to a voluntary mutual benefit organization, such as a school or amateur athletic group. The functions of the technique are to compare avowed and actual behavior, to utilize group…

Functional Visual Improvement After Cataract Surgery in Eyes With Age-Related Macular Degeneration: Results of the Ophthalmic Surgical Outcomes Data Project.

PubMed

Stock, Michael V; Vollman, David E; Baze, Elizabeth F; Chomsky, Amy S; Daly, Mary K; Lawrence, Mary G

2015-04-01

To determine if cataract surgery on eyes with AMD confers as much functional visual improvement as surgery on eyes without retinal pathology. This is a retrospective analysis of 4924 cataract surgeries from the Veterans Healthcare Administration Ophthalmic Surgical Outcomes Data Project (OSOD). We included cases of eyes with AMD that had both preoperative and postoperative NEI-VFQ-25 questionnaires submitted and compared their outcomes with controls without retinal pathology. We excluded patients with other retinal pathologies (740 patients). The analyses compared changes in visual acuity and overall functional visual improvement and its subscales using t-tests, multivariate logistic regressions, and linear regression modeling. Preoperative and postoperative questionnaires were submitted by 58.3% of AMD and 63.8% of no retinal pathology cases (controls). Analysis of overall score showed that cataract surgery on eyes with AMD led to increased visual function (13.8 ± 2.4 NEI-VFQ units, P < 0.0001); however, increases were significantly less when compared with controls (-6.4 ± 2.9 NEI-VFQ units, P < 0.0001). Preoperative best-corrected visual acuity (preBCVA) in AMD was predictive of postoperative visual function (r = -0.38, P < 0.0001). In controls, postoperative visual function was only weakly associated with preBCVA (r = -0.075, P = 0.0002). Patients with AMD with vision of 20/40 or better had overall outcomes similar to controls (-2.2 ± 4.7 NEI-VFQ units, P = 0.37). Cataract surgery on eyes with AMD offers an increase in functional visual improvement; however, the amount of benefit is associated with the eye's preBCVA. For eyes with preBCVA of 20/40 or greater, the improvement is similar to that of patients without retinal pathology. However, if preBCVA is less than 20/40, the amount of improvement was shown to be significantly less and decreased with decreasing preBCVA.

CUFID-query: accurate network querying through random walk based network flow estimation.

PubMed

Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun

2017-12-28

Functional modules in biological networks consist of numerous biomolecules and their complicated interactions. Recent studies have shown that biomolecules in a functional module tend to have similar interaction patterns and that such modules are often conserved across biological networks of different species. As a result, such conserved functional modules can be identified through comparative analysis of biological networks. In this work, we propose a novel network querying algorithm based on the CUFID (Comparative network analysis Using the steady-state network Flow to IDentify orthologous proteins) framework combined with an efficient seed-and-extension approach. The proposed algorithm, CUFID-query, can accurately detect conserved functional modules as small subnetworks in the target network that are expected to perform similar functions to the given query functional module. The CUFID framework was recently developed for probabilistic pairwise global comparison of biological networks, and it has been applied to pairwise global network alignment, where the framework was shown to yield accurate network alignment results. In the proposed CUFID-query algorithm, we adopt the CUFID framework and extend it for local network alignment, specifically to solve network querying problems. First, in the seed selection phase, the proposed method utilizes the CUFID framework to compare the query and the target networks and to predict the probabilistic node-to-node correspondence between the networks. Next, the algorithm selects and greedily extends the seed in the target network by iteratively adding nodes that have frequent interactions with other nodes in the seed network, in a way that the conductance of the extended network is maximally reduced. Finally, CUFID-query removes irrelevant nodes from the querying results based on the personalized PageRank vector for the induced network that includes the fully extended network and its neighboring nodes. Through extensive performance evaluation based on biological networks with known functional modules, we show that CUFID-query outperforms the existing state-of-the-art algorithms in terms of prediction accuracy and biological significance of the predictions.

Modifications Of Discrete Ordinate Method For Computations With High Scattering Anisotropy: Comparative Analysis

NASA Technical Reports Server (NTRS)

Korkin, Sergey V.; Lyapustin, Alexei I.; Rozanov, Vladimir V.

2012-01-01

A numerical accuracy analysis of the radiative transfer equation (RTE) solution based on separation of the diffuse light field into anisotropic and smooth parts is presented. The analysis uses three different algorithms based on the discrete ordinate method (DOM). Two methods, DOMAS and DOM2+, that do not use the truncation of the phase function, are compared against the TMS-method. DOMAS and DOM2+ use the Small-Angle Modification of RTE and the single scattering term, respectively, as an anisotropic part. The TMS method uses Delta-M method for truncation of the phase function along with the single scattering correction. For reference, a standard discrete ordinate method, DOM, is also included in analysis. The obtained results for cases with high scattering anisotropy show that at low number of streams (16, 32) only DOMAS provides an accurate solution in the aureole area. Outside of the aureole, the convergence and accuracy of DOMAS, and TMS is found to be approximately similar: DOMAS was found more accurate in cases with coarse aerosol and liquid water cloud models, except low optical depth, while the TMS showed better results in case of ice cloud.

[PSYCHO PHYSIOLOGICAL MARKERS OF ACCELERATED AGING AMONG THOSE WORKING WITH OCCUPATIONAL HAZARDS].

PubMed

Bashkireva, A S; Kachan, Ye Yu; Kulapina, M E

2015-01-01

We assessed the significance of psycho physiological markers of accelerated aging of the function of attention using comparative analysis of two occupational groups in order to reveal how the working process affects mental work capacity. We revealed peculiarities of systemic structure of functions which determine mental work capacity depending on the age and length of service in lorry drivers. It was proved that decrease in the mnestic functions of lorry-drivers takes place 10-15 years earlier compared to the control group. Psycho physiological indices, reflecting the functioning of attention, decreased not only with aging but also with longer driving experience. Our results show that it is necessary to conduct further studies of psycho physiological markers of age-related decrease in short-term memory depending on the activities at work in order to prevent accelerated aging and achieve professional longevity.

Prediction and Factor Extraction of Drug Function by Analyzing Medical Records in Developing Countries.

PubMed

Hu, Min; Nohara, Yasunobu; Nakamura, Masafumi; Nakashima, Naoki

2017-01-01

The World Health Organization has declared Bangladesh one of 58 countries facing acute Human Resources for Health (HRH) crisis. Artificial intelligence in healthcare has been shown to be successful for diagnostics. Using machine learning to predict pharmaceutical prescriptions may solve HRH crises. In this study, we investigate a predictive model by analyzing prescription data of 4,543 subjects in Bangladesh. We predict the function of prescribed drugs, comparing three machine-learning approaches. The approaches compare whether a subject shall be prescribed medicine from the 21 most frequently prescribed drug functions. Receiver Operating Characteristics (ROC) were selected as a way to evaluate and assess prediction models. The results show the drug function with the best prediction performance was oral hypoglycemic drugs, which has an average AUC of 0.962. To understand how the variables affect prediction, we conducted factor analysis based on tree-based algorithms and natural language processing techniques.

Indications for quantum computation requirements from comparative brain analysis

NASA Astrophysics Data System (ADS)

Bernroider, Gustav; Baer, Wolfgang

2010-04-01

Whether or not neuronal signal properties can engage 'non-trivial', i.e. functionally significant, quantum properties, is the subject of an ongoing debate. Here we provide evidence that quantum coherence dynamics can play a functional role in ion conduction mechanism with consequences on the shape and associative character of classical membrane signals. In particular, these new perspectives predict that a specific neuronal topology (e.g. the connectivity pattern of cortical columns in the primate brain) is less important and not really required to explain abilities in perception and sensory-motor integration. Instead, this evidence is suggestive for a decisive role of the number and functional segregation of ion channel proteins that can be engaged in a particular neuronal constellation. We provide evidence from comparative brain studies and estimates of computational capacity behind visual flight functions suggestive for a possible role of quantum computation in biological systems.

New method to incorporate Type B uncertainty into least-squares procedures in radionuclide metrology.

PubMed

Han, Jubong; Lee, K B; Lee, Jong-Man; Park, Tae Soon; Oh, J S; Oh, Pil-Jei

2016-03-01

We discuss a new method to incorporate Type B uncertainty into least-squares procedures. The new method is based on an extension of the likelihood function from which a conventional least-squares function is derived. The extended likelihood function is the product of the original likelihood function with additional PDFs (Probability Density Functions) that characterize the Type B uncertainties. The PDFs are considered to describe one's incomplete knowledge on correction factors being called nuisance parameters. We use the extended likelihood function to make point and interval estimations of parameters in the basically same way as the least-squares function used in the conventional least-squares method is derived. Since the nuisance parameters are not of interest and should be prevented from appearing in the final result, we eliminate such nuisance parameters by using the profile likelihood. As an example, we present a case study for a linear regression analysis with a common component of Type B uncertainty. In this example we compare the analysis results obtained from using our procedure with those from conventional methods. Copyright © 2015. Published by Elsevier Ltd.

Toward Accurate and Quantitative Comparative Metagenomics

PubMed Central

Nayfach, Stephen; Pollard, Katherine S.

2016-01-01

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

Toward Accurate and Quantitative Comparative Metagenomics.

PubMed

Nayfach, Stephen; Pollard, Katherine S

2016-08-25

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

Comparing rainfall patterns between regions in Peninsular Malaysia via a functional data analysis technique

NASA Astrophysics Data System (ADS)

Suhaila, Jamaludin; Jemain, Abdul Aziz; Hamdan, Muhammad Fauzee; Wan Zin, Wan Zawiah

2011-12-01

SummaryNormally, rainfall data is collected on a daily, monthly or annual basis in the form of discrete observations. The aim of this study is to convert these rainfall values into a smooth curve or function which could be used to represent the continuous rainfall process at each region via a technique known as functional data analysis. Since rainfall data shows a periodic pattern in each region, the Fourier basis is introduced to capture these variations. Eleven basis functions with five harmonics are used to describe the unimodal rainfall pattern for stations in the East while five basis functions which represent two harmonics are needed to describe the rainfall pattern in the West. Based on the fitted smooth curve, the wet and dry periods as well as the maximum and minimum rainfall values could be determined. Different rainfall patterns are observed among the studied regions based on the smooth curve. Using the functional analysis of variance, the test results indicated that there exist significant differences in the functional means between each region. The largest differences in the functional means are found between the East and Northwest regions and these differences may probably be due to the effect of topography and, geographical location and are mostly influenced by the monsoons. Therefore, the same inputs or approaches might not be useful in modeling the hydrological process for different regions.

Structural and functional changes in the somatosensory cortex in euthymic females with bipolar disorder.

PubMed

Minuzzi, Luciano; Syan, Sabrina K; Smith, Mara; Hall, Alexander; Hall, Geoffrey Bc; Frey, Benicio N

2017-12-01

Current evidence from neuroimaging data suggests possible dysfunction of the fronto-striatal-limbic circuits in individuals with bipolar disorder. Somatosensory cortical function has been implicated in emotional recognition, risk-taking and affective responses through sensory modalities. This study investigates anatomy and function of the somatosensory cortex in euthymic bipolar women. In total, 68 right-handed euthymic women (bipolar disorder = 32 and healthy controls = 36) between 16 and 45 years of age underwent high-resolution anatomical and functional magnetic resonance imaging during the mid-follicular menstrual phase. The somatosensory cortex was used as a seed region for resting-state functional connectivity analysis. Voxel-based morphometry was used to evaluate somatosensory cortical gray matter volume between groups. We found increased resting-state functional connectivity between the somatosensory cortex and insular cortex, inferior prefrontal gyrus and frontal orbital cortex in euthymic bipolar disorder subjects compared to healthy controls. Voxel-based morphometry analysis showed decreased gray matter in the left somatosensory cortex in the bipolar disorder group. Whole-brain voxel-based morphometry analysis controlled by age did not reveal any additional significant difference between groups. This study is the first to date to evaluate anatomy and function of the somatosensory cortex in a well-characterized sample of euthymic bipolar disorder females. Anatomical and functional changes in the somatosensory cortex in this population might contribute to the pathophysiology of bipolar disorder.

[Autism and attention deficit hyperactivity disorder: similarities and differences in executive functioning and theory of mind].

PubMed

Miranda-Casas, Ana; Baixauli-Fortea, Immaculada; Colomer-Diago, Carla; Roselló-Miranda, Belén

2013-09-06

Although the DSM-IV-TR diagnostic criteria do not overlap, the presence of attention deficit hyperactivity disorder (ADHD) symptoms in individuals with a clinical diagnosis of autism is quite high. At the same time, children with ADHD can have autistic traits, the most prevalent being social and communication difficulties. The analysis of the combination of executive functions and theory of mind (ToM) deficits could help to explain the overlap and differentiation between the two disorders. To review the findings of empirical studies in which children with ADHD and autism have been compared on indicators of executive functions and ToM. The literature review suggests the existence of distinct patterns in autism spectrum disorders (ASD) and ADHD when the executive functioning is segmented by components. Children with ADHD experience deficits in inhibitory control, while children with ASD have problems with cognitive flexibility and planning. Regarding the domain of the mentalist skills, there are developmental differences, as well as differences in their severity. Younger children with ASD have greater deficiencies in the ToM compared to children with ADHD, and a primary deficit in social orientation. Although important progress has been made, some issues remain to be clarified, among which we can highlight the analysis of how ToM development affects poor executive functions development, using longitudinal studies that analyze the developmental paths of children with ASD and children with ADHD.

Aerodynamic design optimization using sensitivity analysis and computational fluid dynamics

NASA Technical Reports Server (NTRS)

Baysal, Oktay; Eleshaky, Mohamed E.

1991-01-01

A new and efficient method is presented for aerodynamic design optimization, which is based on a computational fluid dynamics (CFD)-sensitivity analysis algorithm. The method is applied to design a scramjet-afterbody configuration for an optimized axial thrust. The Euler equations are solved for the inviscid analysis of the flow, which in turn provides the objective function and the constraints. The CFD analysis is then coupled with the optimization procedure that uses a constrained minimization method. The sensitivity coefficients, i.e. gradients of the objective function and the constraints, needed for the optimization are obtained using a quasi-analytical method rather than the traditional brute force method of finite difference approximations. During the one-dimensional search of the optimization procedure, an approximate flow analysis (predicted flow) based on a first-order Taylor series expansion is used to reduce the computational cost. Finally, the sensitivity of the optimum objective function to various design parameters, which are kept constant during the optimization, is computed to predict new optimum solutions. The flow analysis of the demonstrative example are compared with the experimental data. It is shown that the method is more efficient than the traditional methods.

Short-bearing approximation for full journal bearings

NASA Technical Reports Server (NTRS)

Ocvirk, F W

1952-01-01

A short-bearing approximation of pressure distribution in the oil film is presented which is an extension of the pressure-distribution function of Michell and Cardullo and includes end-leakage effects. Equations giving applied load, attitude angle, location and magnitude of peak film pressure, friction, and required oil flow rate as functions of the eccentricity ratio are also given. The capacity number, a basic non dimensional quantity resulting from this analysis is the product of the Sommerfeld number and the square of the length-diameter ratio. Curves determined by this analysis are compared with previously published experimental data and theoretical curves of Sommerfeld and Cameron and Wood. Conclusions reached indicate that this approximation is of practical value for analysis of short bearings.

About normal distribution on SO(3) group in texture analysis

NASA Astrophysics Data System (ADS)

Savyolova, T. I.; Filatov, S. V.

2017-12-01

This article studies and compares different normal distributions (NDs) on SO(3) group, which are used in texture analysis. Those NDs are: Fisher normal distribution (FND), Bunge normal distribution (BND), central normal distribution (CND) and wrapped normal distribution (WND). All of the previously mentioned NDs are central functions on SO(3) group. CND is a subcase for normal CLT-motivated distributions on SO(3) (CLT here is Parthasarathy’s central limit theorem). WND is motivated by CLT in R 3 and mapped to SO(3) group. A Monte Carlo method for modeling normally distributed values was studied for both CND and WND. All of the NDs mentioned above are used for modeling different components of crystallites orientation distribution function in texture analysis.

A correlational analysis of the effects of changing environmental conditions on the NR atomic hydrogen maser

NASA Technical Reports Server (NTRS)

Dragonette, Richard A.; Suter, Joseph J.

1992-01-01

An extensive statistical analysis has been undertaken to determine if a correlation exists between changes in an NR atomic hydrogen maser's frequency offset and changes in environmental conditions. Correlation analyses have been performed comparing barometric pressure, humidity, and temperature with maser frequency offset as a function of time for periods ranging from 5.5 to 17 days. Semipartial correlation coefficients as large as -0.9 have been found between barometric pressure and maser frequency offset. Correlation between maser frequency offset and humidity was small compared to barometric pressure and unpredictable. Analysis of temperature data indicates that in the most current design, temperature does not significantly affect maser frequency offset.

Dataset of potential targets for Mycobacterium tuberculosis H37Rv through comparative genome analysis.

PubMed

Asif, Siddiqui M; Asad, Amir; Faizan, Ahmad; Anjali, Malik S; Arvind, Arya; Neelesh, Kapoor; Hirdesh, Kumar; Sanjay, Kumar

2009-12-31

Mycobacterium tuberculosis is the causative agent of the disease, tuberculosis and H37Rv is the most studied clinical strain. We use comparative genome analysis of Mycobacterium tuberculosis H37Rv and human for the identification of potential targets dataset. We used DEG (Database of Essential Genes) to identify essential genes in the H37Rv strain. The analysis shows that 628 of the 3989 genes in Mycobacterium tuberculosis H37Rv were found to be essential of which 324 genes lack similarity to the human genome. Subsequently hypothetical proteins were removed through manual curation. This further resulted in a dataset of 135 proteins with essential function and no homology to human.

SPECT and PET analysis of subthalamic stimulation in Parkinson's disease: analysis using a manual segmentation.

PubMed

Haegelen, Claire; García-Lorenzo, Daniel; Le Jeune, Florence; Péron, Julie; Gibaud, Bernard; Riffaud, Laurent; Brassier, Gilles; Barillot, Christian; Vérin, Marc; Morandi, Xavier

2010-03-01

The subthalamic nucleus (STN) has become an effective target of deep-brain stimulation (DBS) in severely disabled patients with advanced Parkinson's disease (PD). Clinical studies have reported DBS-induced adverse effects on cognitive functions, mood, emotion and behavior. STN DBS seems to interfere with the limbic functions of the basal ganglia, but the limbic effects of STN DBS are controversial. We measured prospectively resting regional cerebral metabolism (rCMb) with 18-fluorodeoxyglucose and PET, and resting regional cerebral blood flow (rCBF) with HMPAO and SPECT in six patients with Parkinson's disease. We compared PET and SPECT 1 month before and 3 months after STN DBS. On cerebral MRI, 13 regions of interest (ROI) were manually delineated slice by slice in frontal and limbic lobes. We obtained mean rCBF and rCMb values for each ROI and the whole brain. We normalized rCBF and rCMB values to ones for the whole brain volume, which we compared before and following STN DBS. No significant difference emerged in the SPECT analysis. PET analysis revealed a significant decrease in rCMb following STN DBS in the superior frontal gyri and left and right dorsolateral prefrontal cortex (p < 0.05). A non-significant decrease in rCMb in the left anterior cingulate gyrus appeared following STN DBS (p = 0.075). Our prospective SPECT and PET study revealed significantly decreased glucose metabolism of the two superior frontal gyri without any attendant perfusion changes following STN DBS. These results suggest that STN DBS may change medial prefrontal function and therefore the integration of limbic information, either by disrupting emotional processes within the STN, or by hampering the normal function of a limbic circuit.

Empirical Likelihood in Nonignorable Covariate-Missing Data Problems.

PubMed

Xie, Yanmei; Zhang, Biao

2017-04-20

Missing covariate data occurs often in regression analysis, which frequently arises in the health and social sciences as well as in survey sampling. We study methods for the analysis of a nonignorable covariate-missing data problem in an assumed conditional mean function when some covariates are completely observed but other covariates are missing for some subjects. We adopt the semiparametric perspective of Bartlett et al. (Improving upon the efficiency of complete case analysis when covariates are MNAR. Biostatistics 2014;15:719-30) on regression analyses with nonignorable missing covariates, in which they have introduced the use of two working models, the working probability model of missingness and the working conditional score model. In this paper, we study an empirical likelihood approach to nonignorable covariate-missing data problems with the objective of effectively utilizing the two working models in the analysis of covariate-missing data. We propose a unified approach to constructing a system of unbiased estimating equations, where there are more equations than unknown parameters of interest. One useful feature of these unbiased estimating equations is that they naturally incorporate the incomplete data into the data analysis, making it possible to seek efficient estimation of the parameter of interest even when the working regression function is not specified to be the optimal regression function. We apply the general methodology of empirical likelihood to optimally combine these unbiased estimating equations. We propose three maximum empirical likelihood estimators of the underlying regression parameters and compare their efficiencies with other existing competitors. We present a simulation study to compare the finite-sample performance of various methods with respect to bias, efficiency, and robustness to model misspecification. The proposed empirical likelihood method is also illustrated by an analysis of a data set from the US National Health and Nutrition Examination Survey (NHANES).

The Efficacy of Liposomal Bupivacaine Using Periarticular Injection in Total Knee Arthroplasty: A Systematic Review and Meta-Analysis.

PubMed

Kuang, Ming-Jie; Du, Yuren; Ma, Jian-Xiong; He, Weiwei; Fu, Lin; Ma, Xin-Long

2017-04-01

Total knee arthroplasty (TKA) is gradually emerging as the treatment of choice for end-stage osteoarthritis. In the past, the method of liposomal bupivacaine by periarticular injection (PAI) showed better effects on pain reduction and opioid consumption after surgery. However, some recent studies have reported that liposomal bupivacaine by PAI did not improve pain control and functional recovery in patients undergoing TKA. Therefore, this meta-analysis was conducted to determine whether liposomal bupivacaine provides better pain relief and functional recovery after TKA. Web of Science, PubMed, Embase, and the Cochrane Library were comprehensively searched. Randomized controlled trials, controlled clinical trials, and cohort studies were included in our meta-analysis. Eleven studies that compared liposomal bupivacaine using the PAI technique with the conventional PAI method were included in our meta-analysis. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines and Cochrane Handbook were applied to assess the quality of the results published in all included studies to ensure that the results of our meta-analysis were reliable and veritable. Our pooled data analysis demonstrated that liposomal bupivacaine was as effective as the control group in terms of visual analog scale score at 24 hours (P = .46), 48 hours (P = .43), 72 hours (P = .21), total amount of opioid consumption (P = .25), range of motion (P = .28), length of hospital stay (P = .53), postoperative nausea (P = .34), and ambulation distance (P = .07). Compared with the conventional PAI method, liposomal bupivacaine shows similar pain control and functional recovery after TKA. Considering the cost for pain control, liposomal bupivacaine is not worthy of being recommended as a long-acting alternative analgesic agent using the PAI method. Copyright © 2016 Elsevier Inc. All rights reserved.

Site term from single-station sigma analysis of S-waves in western Turkey

NASA Astrophysics Data System (ADS)

Akyol, Nihal

2018-05-01

The main aim of this study is to obtain site terms from single-station sigma analysis and to compare them with the site functions resulting from different techniques. The dataset consists of 1764 records from 322 micro- and moderate-size local earthquakes recorded by 29 stations in western Turkey. Median models were derived from S-wave Fourier amplitude spectra for selected 22 frequencies, by utilizing the MLR procedure which performs the maximum likelihood (ML) estimation of mixed models where the fixed effects are treated as random (R) effects with infinite variance. At this stage, b (geometrical spreading coefficient) and Q (quality factor) values were decomposed, simultaneously. The residuals of the median models were examined by utilizing the single-station sigma analysis to obtain the site terms of 29 stations. Sigma for the median models is about 0.422 log10 units and decreases to about 0.308, when the site terms from the single-station sigma analysis were considered (27% reduction). The event-corrected within-event standard deviations for each frequency are rather stable, in the range 0.19-0.23 log10 units with an average value of 0.20 (± 0.01). The site terms from single-station sigma analysis were compared with the site function estimates from the horizontal-to-vertical-spectral-ratio (HVSR) and generalized inversion (INV) techniques by Akyol et al. (2013) and Kurtulmuş and Akyol (2015), respectively. Consistency was observed between the single-station sigma site terms and the INV site transfer functions. The results imply that the single-station sigma analysis could separate the site terms with respect to the median models.

Network analysis of functional brain connectivity in borderline personality disorder using resting-state fMRI

PubMed Central

Xu, Tingting; Cullen, Kathryn R.; Mueller, Bryon; Schreiner, Mindy W.; Lim, Kelvin O.; Schulz, S. Charles; Parhi, Keshab K.

2016-01-01

Borderline personality disorder (BPD) is associated with symptoms such as affect dysregulation, impaired sense of self, and self-harm behaviors. Neuroimaging research on BPD has revealed structural and functional abnormalities in specific brain regions and connections. However, little is known about the topological organizations of brain networks in BPD. We collected resting-state functional magnetic resonance imaging (fMRI) data from 20 patients with BPD and 10 healthy controls, and constructed frequency-specific functional brain networks by correlating wavelet-filtered fMRI signals from 82 cortical and subcortical regions. We employed graph-theory based complex network analysis to investigate the topological properties of the brain networks, and employed network-based statistic to identify functional dysconnections in patients. In the 0.03–0.06 Hz frequency band, compared to controls, patients with BPD showed significantly larger measures of global network topology, including the size of largest connected graph component, clustering coefficient, small-worldness, and local efficiency, indicating increased local cliquishness of the functional brain network. Compared to controls, patients showed lower nodal centrality at several hub nodes but greater centrality at several non-hub nodes in the network. Furthermore, an interconnected subnetwork in 0.03–0.06 Hz frequency band was identified that showed significantly lower connectivity in patients. The links in the subnetwork were mainly long-distance connections between regions located at different lobes; and the mean connectivity of this subnetwork was negatively correlated with the increased global topology measures. Lastly, the key network measures showed high correlations with several clinical symptom scores, and classified BPD patients against healthy controls with high accuracy based on linear discriminant analysis. The abnormal topological properties and connectivity found in this study may add new knowledge to the current understanding of functional brain networks in BPD. However, due to limitation of small sample sizes, the results of the current study should be viewed as exploratory and need to be validated on large samples in future works. PMID:26977400

Network analysis of functional brain connectivity in borderline personality disorder using resting-state fMRI.

PubMed

Xu, Tingting; Cullen, Kathryn R; Mueller, Bryon; Schreiner, Mindy W; Lim, Kelvin O; Schulz, S Charles; Parhi, Keshab K

2016-01-01

Borderline personality disorder (BPD) is associated with symptoms such as affect dysregulation, impaired sense of self, and self-harm behaviors. Neuroimaging research on BPD has revealed structural and functional abnormalities in specific brain regions and connections. However, little is known about the topological organizations of brain networks in BPD. We collected resting-state functional magnetic resonance imaging (fMRI) data from 20 patients with BPD and 10 healthy controls, and constructed frequency-specific functional brain networks by correlating wavelet-filtered fMRI signals from 82 cortical and subcortical regions. We employed graph-theory based complex network analysis to investigate the topological properties of the brain networks, and employed network-based statistic to identify functional dysconnections in patients. In the 0.03-0.06 Hz frequency band, compared to controls, patients with BPD showed significantly larger measures of global network topology, including the size of largest connected graph component, clustering coefficient, small-worldness, and local efficiency, indicating increased local cliquishness of the functional brain network. Compared to controls, patients showed lower nodal centrality at several hub nodes but greater centrality at several non-hub nodes in the network. Furthermore, an interconnected subnetwork in 0.03-0.06 Hz frequency band was identified that showed significantly lower connectivity in patients. The links in the subnetwork were mainly long-distance connections between regions located at different lobes; and the mean connectivity of this subnetwork was negatively correlated with the increased global topology measures. Lastly, the key network measures showed high correlations with several clinical symptom scores, and classified BPD patients against healthy controls with high accuracy based on linear discriminant analysis. The abnormal topological properties and connectivity found in this study may add new knowledge to the current understanding of functional brain networks in BPD. However, due to limitation of small sample sizes, the results of the current study should be viewed as exploratory and need to be validated on large samples in future works.

Gene expression profiling in whole blood of patients with coronary artery disease

PubMed Central

Taurino, Chiara; Miller, William H.; McBride, Martin W.; McClure, John D.; Khanin, Raya; Moreno, María U.; Dymott, Jane A.; Delles, Christian; Dominiczak, Anna F.

2010-01-01

Owing to the dynamic nature of the transcriptome, gene expression profiling is a promising tool for discovery of disease-related genes and biological pathways. In the present study, we examined gene expression in whole blood of 12 patients with CAD (coronary artery disease) and 12 healthy control subjects. Furthermore, ten patients with CAD underwent whole-blood gene expression analysis before and after the completion of a cardiac rehabilitation programme following surgical coronary revascularization. mRNA and miRNA (microRNA) were isolated for expression profiling. Gene expression analysis identified 365 differentially expressed genes in patients with CAD compared with healthy controls (175 up- and 190 down-regulated in CAD), and 645 in CAD rehabilitation patients (196 up- and 449 down-regulated post-rehabilitation). Biological pathway analysis identified a number of canonical pathways, including oxidative phosphorylation and mitochondrial function, as being significantly and consistently modulated across the groups. Analysis of miRNA expression revealed a number of differentially expressed miRNAs, including hsa-miR-140-3p (control compared with CAD, P=0.017), hsa-miR-182 (control compared with CAD, P=0.093), hsa-miR-92a and hsa-miR-92b (post- compared with pre-exercise, P<0.01). Global analysis of predicted miRNA targets found significantly reduced expression of genes with target regions compared with those without: hsa-miR-140-3p (P=0.002), hsa-miR-182 (P=0.001), hsa-miR-92a and hsa-miR-92b (P=2.2×10−16). In conclusion, using whole blood as a ‘surrogate tissue’ in patients with CAD, we have identified differentially expressed miRNAs, differentially regulated genes and modulated pathways which warrant further investigation in the setting of cardiovascular function. This approach may represent a novel non-invasive strategy to unravel potentially modifiable pathways and possible therapeutic targets in cardiovascular disease. PMID:20528768

Altered hippocampal volume and functional connectivity in males with Internet gaming disorder comparing to those with alcohol use disorder.

PubMed

Yoon, Eun Jin; Choi, Jung-Seok; Kim, Heejung; Sohn, Bo Kyung; Jung, Hee Yeon; Lee, Jun-Young; Kim, Dai-Jin; Park, Sun-Won; Kim, Yu Kyeong

2017-07-18

Internet gaming disorder (IGD) has been conceptualized as a behavioral addiction and shares clinical, neuropsychological, and personality characteristics with alcohol use disorder (AUD), but IGD dose not entail brain exposure to toxic agents, which renders it different from AUD. To achieve a clear understanding of the neurobiological features of IGD, we aimed to identify morphological and functional changes in IGD and compare them with those in AUD. Individuals with IGD showed larger volume in the hippocampus/amygdala and precuneus than healthy controls (HCs). The volume in the hippocampus positively correlated with the symptom severity of IGD. Moreover, functional connectivity analysis with the hippocampus/amygdala cluster revealed that the left ventromedial prefrontal cortex showed stronger functional connectivity in individuals with IGD compared to those with AUD. In contrast, individuals with AUD exhibited the smaller cerebellar volume and thinner medial frontal cortex than HCs. The volume in the cerebellum correlated with impaired working memory function as well as duration of illness in AUD group. Findings suggested that altered volume and functional connectivity in the hippocampus/amygdala in IGD might be associated with abnormally enhanced memory process of gaming-related cues, while abnormal cortical changes and cognitive impairments in AUD might be associated with neurotoxic effects of alcohol.

A Bayesian sequential design using alpha spending function to control type I error.

PubMed

Zhu, Han; Yu, Qingzhao

2017-10-01

We propose in this article a Bayesian sequential design using alpha spending functions to control the overall type I error in phase III clinical trials. We provide algorithms to calculate critical values, power, and sample sizes for the proposed design. Sensitivity analysis is implemented to check the effects from different prior distributions, and conservative priors are recommended. We compare the power and actual sample sizes of the proposed Bayesian sequential design with different alpha spending functions through simulations. We also compare the power of the proposed method with frequentist sequential design using the same alpha spending function. Simulations show that, at the same sample size, the proposed method provides larger power than the corresponding frequentist sequential design. It also has larger power than traditional Bayesian sequential design which sets equal critical values for all interim analyses. When compared with other alpha spending functions, O'Brien-Fleming alpha spending function has the largest power and is the most conservative in terms that at the same sample size, the null hypothesis is the least likely to be rejected at early stage of clinical trials. And finally, we show that adding a step of stop for futility in the Bayesian sequential design can reduce the overall type I error and reduce the actual sample sizes.

Large Scale Comparative Visualisation of Regulatory Networks with TRNDiff

DOE PAGES

Chua, Xin-Yi; Buckingham, Lawrence; Hogan, James M.; ...

2015-06-01

The advent of Next Generation Sequencing (NGS) technologies has seen explosive growth in genomic datasets, and dense coverage of related organisms, supporting study of subtle, strain-specific variations as a determinant of function. Such data collections present fresh and complex challenges for bioinformatics, those of comparing models of complex relationships across hundreds and even thousands of sequences. Transcriptional Regulatory Network (TRN) structures document the influence of regulatory proteins called Transcription Factors (TFs) on associated Target Genes (TGs). TRNs are routinely inferred from model systems or iterative search, and analysis at these scales requires simultaneous displays of multiple networks well beyond thosemore » of existing network visualisation tools [1]. In this paper we describe TRNDiff, an open source system supporting the comparative analysis and visualization of TRNs (and similarly structured data) from many genomes, allowing rapid identification of functional variations within species. The approach is demonstrated through a small scale multiple TRN analysis of the Fur iron-uptake system of Yersinia, suggesting a number of candidate virulence factors; and through a larger study exploiting integration with the RegPrecise database (http://regprecise.lbl.gov; [2]) - a collection of hundreds of manually curated and predicted transcription factor regulons drawn from across the entire spectrum of prokaryotic organisms.« less

LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

PubMed

Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

2017-10-01

Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

Structural Connectivity Changes Underlying Altered Working Memory Networks in Mild Cognitive Impairment: A Three-Way Image Fusion Analysis.

PubMed

Teipel, Stefan; Ehlers, Inga; Erbe, Anna; Holzmann, Carsten; Lau, Esther; Hauenstein, Karlheinz; Berger, Christoph

2015-01-01

Working memory impairment is among the earliest signs of cognitive decline in Alzheimer's disease (AD) and mild cognitive impairment (MCI). We aimed to study the functional and structural substrate of working memory impairment in early AD dementia and MCI. We studied a group of 12 MCI and AD subjects compared to 12 age- and gender-matched healthy elderly controls using diffusion tensor imaging (DTI), and functional magnetic resonance imaging (fMRI) during a 2-back versus 1-back letter recognition task. We performed a three-way image fusion analysis with joint independent component analysis of cortical activation during working memory, and DTI derived measures of fractional anisotropy (FA) and the mode of anisotropy. We found significant hypoactivation in posterior brain areas and relative hyperactivation in anterior brain areas during working memory in AD/MCI subjects compared to controls. Corresponding independent components from DTI data revealed reduced FA and reduced mode of anisotropy in intracortical projecting fiber tracts with posterior predominance and increased FA and increased mode along the corticospinal tract in AD/MCI compared to controls. Our findings suggest that impairments of structural fiber tract integrity accompany breakdown of posterior and relatively preserved anterior cortical activation during working memory performance in MCI/AD subjects. Copyright © 2014 by the American Society of Neuroimaging.

A comparative gene expression analysis of iron-limited cultures of Chaetoceros socialis and Pseudo-nitzschia arenysensis using newly developed iron assays

NASA Astrophysics Data System (ADS)

Abdala, Z. M.; Powell, K.; Cronin, D.; Chappell, D.

2016-02-01

A comparative gene expression analysis of iron-limited cultures of Chaetoceros socialis and Pseudo-nitzschia arenysensisusing newly developed iron assays Zuzanna M. Abdala, Kimberly Powell, Dylan P. Cronin, P. Dreux Chappell Diatoms, accounting for about 40% of the primary production in marine ecosystems, play a vital role in the dynamics of marine systems. Iron availability is understood to be a driving factor controlling productivity of many marine phytoplankton, including diatoms, as it functions as a cofactor for many proteins including several involved with photosynthetic processes. Previous work examining transcriptomes of diatoms of the Thalassiosira genus grown in controlled laboratory settings has identified genes whose expression can be used as sensitive markers of iron status. Data mining publically available diatom transcriptome data for these genes enables development of additional iron status assays for environmentally-relevant diatoms. For the present study, gene expression analysis of iron-limited laboratory cultures of Chaetoceros socialis and Pseudo-nitzschia arenysensis grown in continuous light was done using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). C. socialis and P. arenysensis serve as comparative models for analyzing gene expression in iron limitation in different ecological community assemblages. These data may ultimately assist to illuminate the function of iron in photosynthetic activity in diatoms.

Phenotype–genotype correlation in Hirschsprung disease is illuminated by comparative analysis of the RET protein sequence

PubMed Central

Kashuk, Carl S.; Stone, Eric A.; Grice, Elizabeth A.; Portnoy, Matthew E.; Green, Eric D.; Sidow, Arend; Chakravarti, Aravinda; McCallion, Andrew S.

2005-01-01

The ability to discriminate between deleterious and neutral amino acid substitutions in the genes of patients remains a significant challenge in human genetics. The increasing availability of genomic sequence data from multiple vertebrate species allows inclusion of sequence conservation and physicochemical properties of residues to be used for functional prediction. In this study, the RET receptor tyrosine kinase serves as a model disease gene in which a broad spectrum (≥116) of disease-associated mutations has been identified among patients with Hirschsprung disease and multiple endocrine neoplasia type 2. We report the alignment of the human RET protein sequence with the orthologous sequences of 12 non-human vertebrates (eight mammalian, one avian, and three teleost species), their comparative analysis, the evolutionary topology of the RET protein, and predicted tolerance for all published missense mutations. We show that, although evolutionary conservation alone provides significant information to predict the effect of a RET mutation, a model that combines comparative sequence data with analysis of physiochemical properties in a quantitative framework provides far greater accuracy. Although the ability to discern the impact of a mutation is imperfect, our analyses permit substantial discrimination between predicted functional classes of RET mutations and disease severity even for a multigenic disease such as Hirschsprung disease. PMID:15956201

Sparse dictionary learning for resting-state fMRI analysis

NASA Astrophysics Data System (ADS)

Lee, Kangjoo; Han, Paul Kyu; Ye, Jong Chul

2011-09-01

Recently, there has been increased interest in the usage of neuroimaging techniques to investigate what happens in the brain at rest. Functional imaging studies have revealed that the default-mode network activity is disrupted in Alzheimer's disease (AD). However, there is no consensus, as yet, on the choice of analysis method for the application of resting-state analysis for disease classification. This paper proposes a novel compressed sensing based resting-state fMRI analysis tool called Sparse-SPM. As the brain's functional systems has shown to have features of complex networks according to graph theoretical analysis, we apply a graph model to represent a sparse combination of information flows in complex network perspectives. In particular, a new concept of spatially adaptive design matrix has been proposed by implementing sparse dictionary learning based on sparsity. The proposed approach shows better performance compared to other conventional methods, such as independent component analysis (ICA) and seed-based approach, in classifying the AD patients from normal using resting-state analysis.

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples.

PubMed

Tan, Boonfei; Fowler, S Jane; Abu Laban, Nidal; Dong, Xiaoli; Sensen, Christoph W; Foght, Julia; Gieg, Lisa M

2015-09-01

Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate- and H2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities.

Vibration analysis and transient response of a functionally graded piezoelectric curved beam with general boundary conditions

NASA Astrophysics Data System (ADS)

Su, Zhu; Jin, Guoyong; Ye, Tiangui

2016-06-01

The paper presents a unified solution for free and transient vibration analyses of a functionally graded piezoelectric curved beam with general boundary conditions within the framework of Timoshenko beam theory. The formulation is derived by means of the variational principle in conjunction with a modified Fourier series which consists of standard Fourier cosine series and supplemented functions. The mechanical and electrical properties of functionally graded piezoelectric materials (FGPMs) are assumed to vary continuously in the thickness direction and are estimated by Voigt’s rule of mixture. The convergence, accuracy and reliability of the present formulation are demonstrated by comparing the present solutions with those from the literature and finite element analysis. Numerous results for FGPM beams with different boundary conditions, geometrical parameters as well as material distributions are given. Moreover, forced vibration of the FGPM beams subjected to dynamic loads and general boundary conditions are also investigated.

Diverse types of genetic variation converge on functional gene networks involved in schizophrenia.

PubMed

Gilman, Sarah R; Chang, Jonathan; Xu, Bin; Bawa, Tejdeep S; Gogos, Joseph A; Karayiorgou, Maria; Vitkup, Dennis

2012-12-01

Despite the successful identification of several relevant genomic loci, the underlying molecular mechanisms of schizophrenia remain largely unclear. We developed a computational approach (NETBAG+) that allows an integrated analysis of diverse disease-related genetic data using a unified statistical framework. The application of this approach to schizophrenia-associated genetic variations, obtained using unbiased whole-genome methods, allowed us to identify several cohesive gene networks related to axon guidance, neuronal cell mobility, synaptic function and chromosomal remodeling. The genes forming the networks are highly expressed in the brain, with higher brain expression during prenatal development. The identified networks are functionally related to genes previously implicated in schizophrenia, autism and intellectual disability. A comparative analysis of copy number variants associated with autism and schizophrenia suggests that although the molecular networks implicated in these distinct disorders may be related, the mutations associated with each disease are likely to lead, at least on average, to different functional consequences.

Quantum phase space with a basis of Wannier functions

NASA Astrophysics Data System (ADS)

Fang, Yuan; Wu, Fan; Wu, Biao

2018-02-01

A quantum phase space with Wannier basis is constructed: (i) classical phase space is divided into Planck cells; (ii) a complete set of Wannier functions are constructed with the combination of Kohn’s method and Löwdin method such that each Wannier function is localized at a Planck cell. With these Wannier functions one can map a wave function unitarily onto phase space. Various examples are used to illustrate our method and compare it to Wigner function. The advantage of our method is that it can smooth out the oscillations in wave functions without losing any information and is potentially a better tool in studying quantum-classical correspondence. In addition, we point out that our method can be used for time-frequency analysis of signals.

[Brain function recovery after prolonged posttraumatic coma].

PubMed

Klimash, A V; Zhanaidarov, Z S

2016-01-01

To explore the characteristics of brain function recovery in patients after prolonged posttraumatic coma and with long-unconscious states. Eighty-seven patients after prolonged posttraumatic coma were followed-up for two years. An analysis of a clinical/neurological picture after a prolonged episode of coma was based on the dynamics of vital functions, neurological status and patient's reactions to external stimuli. Based on the dynamics of the clinical/neurological picture that shows the recovery of functions of the certain brain areas, three stages of brain function recovery after a prolonged episode of coma were singled out: brain stem areas, diencephalic areas and telencephalic areas. These functional/anatomic areas of brain function recovery after prolonged coma were compared to the present classifications.

Multimethod Investigation of Interpersonal Functioning in Borderline Personality Disorder

PubMed Central

Stepp, Stephanie D.; Hallquist, Michael N.; Morse, Jennifer Q.; Pilkonis, Paul A.

2011-01-01

Even though interpersonal functioning is of great clinical importance for patients with borderline personality disorder (BPD), the comparative validity of different assessment methods for interpersonal dysfunction has not yet been tested. This study examined multiple methods of assessing interpersonal functioning, including self- and other-reports, clinical ratings, electronic diaries, and social cognitions in three groups of psychiatric patients (N=138): patients with (1) BPD, (2) another personality disorder, and (3) Axis I psychopathology only. Using dominance analysis, we examined the predictive validity of each method in detecting changes in symptom distress and social functioning six months later. Across multiple methods, the BPD group often reported higher interpersonal dysfunction scores compared to other groups. Predictive validity results demonstrated that self-report and electronic diary ratings were the most important predictors of distress and social functioning. Our findings suggest that self-report scores and electronic diary ratings have high clinical utility, as these methods appear most sensitive to change. PMID:21808661

Extracellular Enzyme Composition and Functional Characteristics of Aspergillus niger An-76 Induced by Food Processing Byproducts and Based on Integrated Functional Omics.

PubMed

Liu, Lin; Gong, Weili; Sun, Xiaomeng; Chen, Guanjun; Wang, Lushan

2018-02-07

Byproducts of food processing can be utilized for the production of high-value-added enzyme cocktails. In this study, we utilized integrated functional omics technology to analyze composition and functional characteristics of extracellular enzymes produced by Aspergillus niger grown on food processing byproducts. The results showed that oligosaccharides constituted by arabinose, xylose, and glucose in wheat bran were able to efficiently induce the production of extracellular enzymes of A. niger. Compared with other substrates, wheat bran was more effective at inducing the secretion of β-glucosidases from GH1 and GH3 families, as well as >50% of proteases from A1-family aspartic proteases. Compared with proteins induced by single wheat bran or soybean dregs, the protein yield induced by their mixture was doubled, and the time required to reach peak enzyme activity was shortened by 25%. This study provided a technical platform for the complex formulation of various substrates and functional analysis of extracellular enzymes.

Effects of onboard insecticide use on airline flight attendants.

PubMed

Kilburn, Kaye H

2004-06-01

Flight attendants (FAs) exposed to insecticide spray in an aircraft were compared with unexposed subjects for neurobehavioral function, pulmonary function, mood states, and symptoms. The 33 symptomatic FAs were self-selected, and 5 had retired for disability. Testing procedures included balance, reaction time, color discrimination, visual fields, grip strength, verbal recall, problem solving, attention and discrimination functions, and long-term memory functions. Measurements were expressed as a percentage of their predicted values (derived from unexposed controls), and the author compared the means of the percentage predicted values by analysis of variance. Symptom frequencies and Profile of Mood States (POMS) scores were assessed. FAs were significantly more impaired than controls with respect to balance with eyes closed, grip strength, and color discrimination. Nearly half had 3 or more abnormal neurobehavioral functions, after adjustment was made for age, sex, and education level. Neither elevated POMS scores nor frequencies of average symptoms correlated with their numbers of abnormal measurements. Occupational exposure to synthetic pyrethrin insecticides on airliners was associated with neurobehavioral impairment and disability retirement.

Child Adjustment and Parent Functioning: Considering the Role of Child Driven Effects

PubMed Central

Yan, Ni; Ansari, Arya

2016-01-01

Based on 13,694 mother-child dyads from the Early Childhood Longitudinal Kindergarten Cohort (ECLS-K), this study examined the bidirectional relations between parental and child functioning from kindergarten through third grade. Results from the cross-lagged models demonstrated that child-driven effects co-occurred with parental effects and these effects were comparable in size. At the same time, however, results from the latent profile analysis revealed idiosyncratic patterns of parent and child functioning. Compared with children in the least optimal functioning profiles, those in the average and above average profiles elicited greater improvements in parents’ functioning over time. Although children characterized by poor academic performance at kindergarten appeared to precede parents characterized by harsh parenting at third grade, there was a threshold in the evolving strength of the overall child-driven effects. Taken together, the results from this study underscore the importance of considering reciprocal processes in the parent-child dynamic while also underscoring individual differences in these processes across the early to middle childhood years. PMID:26866838

Comparison of Regression Analysis and Transfer Function in Estimating the Parameters of Central Pulse Waves from Brachial Pulse Wave.

PubMed

Chai, Rui; Xu, Li-Sheng; Yao, Yang; Hao, Li-Ling; Qi, Lin

2017-01-01

This study analyzed ascending branch slope (A_slope), dicrotic notch height (Hn), diastolic area (Ad) and systolic area (As) diastolic blood pressure (DBP), systolic blood pressure (SBP), pulse pressure (PP), subendocardial viability ratio (SEVR), waveform parameter (k), stroke volume (SV), cardiac output (CO), and peripheral resistance (RS) of central pulse wave invasively and non-invasively measured. Invasively measured parameters were compared with parameters measured from brachial pulse waves by regression model and transfer function model. Accuracy of parameters estimated by regression and transfer function model, was compared too. Findings showed that k value, central pulse wave and brachial pulse wave parameters invasively measured, correlated positively. Regression model parameters including A_slope, DBP, SEVR, and transfer function model parameters had good consistency with parameters invasively measured. They had same effect of consistency. SBP, PP, SV, and CO could be calculated through the regression model, but their accuracies were worse than that of transfer function model.

Estimation of the auto frequency response function at unexcited points using dummy masses

NASA Astrophysics Data System (ADS)

Hosoya, Naoki; Yaginuma, Shinji; Onodera, Hiroshi; Yoshimura, Takuya

2015-02-01

If structures with complex shapes have space limitations, vibration tests using an exciter or impact hammer for the excitation are difficult. Although measuring the auto frequency response function at an unexcited point may not be practical via a vibration test, it can be obtained by assuming that the inertia acting on a dummy mass is an external force on the target structure upon exciting a different excitation point. We propose a method to estimate the auto frequency response functions at unexcited points by attaching a small mass (dummy mass), which is comparable to the accelerometer mass. The validity of the proposed method is demonstrated by comparing the auto frequency response functions estimated at unexcited points in a beam structure to those obtained from numerical simulations. We also consider random measurement errors by finite element analysis and vibration tests, but not bias errors. Additionally, the applicability of the proposed method is demonstrated by applying it to estimate the auto frequency response function of the lower arm in a car suspension.

Aromatherapy for Sexual Problems in Menopausal Women: A Systematic Review and Meta-analysis

PubMed Central

Khadivzadeh, Talat; Najafi, Mona Najaf; Irani, Morvarid; Dizavandi, Fatemeh Rajab; Shariati, Khatereh

2018-01-01

Objectives The aim of the present systematic review and meta-analysis is the exploration of the potential evidence of the effectiveness of aromatherapy products on the sexual function of menopausal women. Methods From inception to December 2017, the search process was performed using the MEDLINE and Scopus databases and the Cochrane Library regarding the trials on the effectiveness of herbal-medicine aromatherapy on the sexual function of menopausal women. Results Three of the trials comprise suitable data for inclusion in the meta-analysis. According to the meta-analysis, it is possible to improve the standardized mean difference (SMD) of the sexual desire up to 0.56 in the aromatherapy group compared with the control group (SMD = 0.56; P < 0.001; heterogeneity; I2 = 42%; P = 0.141). According to one of the trials, the serum-estrogen level of two different doses did not change in the neroli oil inhalation group compared with the almond-oil group. Conclusions Both aromatherapy with neroli oil or lavender (monopreparation) and combined-oil aromatherapy with lavender, fennel, geranium, and rose significantly improved human sexual function; however, a significant change of the serum-estrogen level was not detected. The findings of the present review should be presented cautiously because of the corresponding limitations such as the lack of a standardized tool, the lack of intention-to-treat reporting, the low study amount, and the short-term follow-up. PMID:29765928

Horizontal gene transfer in silkworm, Bombyx mori

PubMed Central

2011-01-01

Background The domesticated silkworm, Bombyx mori, is the model insect for the order Lepidoptera, has economically important values, and has gained some representative behavioral characteristics compared to its wild ancestor. The genome of B. mori has been fully sequenced while function analysis of BmChi-h and BmSuc1 genes revealed that horizontal gene transfer (HGT) maybe bestow a clear selective advantage to B. mori. However, the role of HGT in the evolutionary history of B. mori is largely unexplored. In this study, we compare the whole genome of B. mori with those of 382 prokaryotic and eukaryotic species to investigate the potential HGTs. Results Ten candidate HGT events were defined in B. mori by comprehensive sequence analysis using Maximum Likelihood and Bayesian method combining with EST checking. Phylogenetic analysis of the candidate HGT genes suggested that one HGT was plant-to- B. mori transfer while nine were bacteria-to- B. mori transfer. Furthermore, functional analysis based on expression, coexpression and related literature searching revealed that several HGT candidate genes have added important characters, such as resistance to pathogen, to B. mori. Conclusions Results from this study clearly demonstrated that HGTs play an important role in the evolution of B. mori although the number of HGT events in B. mori is in general smaller than those of microbes and other insects. In particular, interdomain HGTs in B. mori may give rise to functional, persistent, and possibly evolutionarily significant new genes. PMID:21595916

Smoothing spline analysis of variance models: A new tool for the analysis of cyclic biomechanical data.

PubMed

Helwig, Nathaniel E; Shorter, K Alex; Ma, Ping; Hsiao-Wecksler, Elizabeth T

2016-10-03

Cyclic biomechanical data are commonplace in orthopedic, rehabilitation, and sports research, where the goal is to understand and compare biomechanical differences between experimental conditions and/or subject populations. A common approach to analyzing cyclic biomechanical data involves averaging the biomechanical signals across cycle replications, and then comparing mean differences at specific points of the cycle. This pointwise analysis approach ignores the functional nature of the data, which can hinder one׳s ability to find subtle differences between experimental conditions and/or subject populations. To overcome this limitation, we propose using mixed-effects smoothing spline analysis of variance (SSANOVA) to analyze differences in cyclic biomechanical data. The SSANOVA framework makes it possible to decompose the estimated function into the portion that is common across groups (i.e., the average cycle, AC) and the portion that differs across groups (i.e., the contrast cycle, CC). By partitioning the signal in such a manner, we can obtain estimates of the CC differences (CCDs), which are the functions directly describing group differences in the cyclic biomechanical data. Using both simulated and experimental data, we illustrate the benefits of using SSANOVA models to analyze differences in noisy biomechanical (gait) signals collected from multiple locations (joints) of subjects participating in different experimental conditions. Using Bayesian confidence intervals, the SSANOVA results can be used in clinical and research settings to reliably quantify biomechanical differences between experimental conditions and/or subject populations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessment of functional outcomes by Sheehan Disability Scale in patients with major depressive disorder treated with duloxetine versus selective serotonin reuptake inhibitors.

PubMed

Sheehan, David V; Mancini, Michele; Wang, Jianing; Berggren, Lovisa; Cao, Haijun; Dueñas, Héctor José; Yue, Li

2016-01-01

We compared functional impairment outcomes assessed with Sheehan Disability Scale (SDS) after treatment with duloxetine versus selective serotonin reuptake inhibitors (SSRIs) in patients with major depressive disorder. Data were pooled from four randomized studies comparing treatment with duloxetine and SSRIs (three double blind and one open label). Analysis of covariance, with last-observation-carried-forward approach for missing data, explored treatment differences between duloxetine and SSRIs on SDS changes during 8 to 12 weeks of acute treatment for the intent-to-treat population. Logistic regression analysis examined the predictive capacity of baseline patient characteristics for remission in functional impairment (SDS total score ≤ 6 and SDS item scores ≤ 2) at endpoint. Included were 2193 patients (duloxetine n = 1029; SSRIs n = 835; placebo n = 329). Treatment with duloxetine and SSRIs resulted in significantly (p < 0.01) greater improvements in the SDS total score versus treatment with placebo. Higher SDS (p < 0.0001) or 17-item Hamilton Depression Rating Scale baseline scores (p < 0.01) predicted lower probability of functional improvement after treatment with duloxetine or SSRIs. Female gender (p ≤ 0.05) predicted higher probability of functional improvement after treatment with duloxetine or SSRIs. Treatment with SSRIs and duloxetine improved functional impairment in patients with major depressive disorder. Higher SDS or 17-item Hamilton Depression Rating Scale baseline scores predicted less probability of SDS improvement; female gender predicted better improvement in functional impairment at endpoint. © 2015 The Authors. Human Psychopharmacology: Clinical and Experimental published by John Wiley & Sons, Ltd.

Longitudinal Analysis of Music Education on Executive Functions in Primary School Children

PubMed Central

Jaschke, Artur C.; Honing, Henkjan; Scherder, Erik J. A.

2018-01-01

Background: Research on the effects of music education on cognitive abilities has generated increasing interest across the scientific community. Nonetheless, longitudinal studies investigating the effects of structured music education on cognitive sub-functions are still rare. Prime candidates for investigating a relationship between academic achievement and music education appear to be executive functions such as planning, working memory, and inhibition. Methods: One hundred and forty-seven primary school children, Mage = 6.4 years, SD = 0.65 were followed for 2.5 years. Participants were randomized into four groups: two music intervention groups, one active visual arts group, and a no arts control group. Neuropsychological tests assessed verbal intelligence and executive functions. Additionally, a national pupil monitor provided data on academic performance. Results: Children in the visual arts group perform better on visuospatial memory tasks as compared to the three other conditions. However, the test scores on inhibition, planning and verbal intelligence increased significantly in the two music groups over time as compared to the visual art and no arts controls. Mediation analysis with executive functions and verbal IQ as mediator for academic performance have shown a possible far transfer effect from executive sub-function to academic performance scores. Discussion: The present results indicate a positive influence of long-term music education on cognitive abilities such as inhibition and planning. Of note, following a two-and-a-half year long visual arts program significantly improves scores on a visuospatial memory task. All results combined, this study supports a far transfer effect from music education to academic achievement mediated by executive sub-functions. PMID:29541017