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https://www.readbyqxmd.com/read/28343169/a-bayesian-semiparametric-factor-analysis-model-for-subtype-identification
#1
Jiehuan Sun, Joshua L Warren, Hongyu Zhao
Disease subtype identification (clustering) is an important problem in biomedical research. Gene expression profiles are commonly utilized to infer disease subtypes, which often lead to biologically meaningful insights into disease. Despite many successes, existing clustering methods may not perform well when genes are highly correlated and many uninformative genes are included for clustering due to the high dimensionality. In this article, we introduce a novel subtype identification method in the Bayesian setting based on gene expression profiles...
March 25, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28343059/internal-cycling-not-external-loading-decides-the-nutrient-limitation-in-eutrophic-lake-a-dynamic-model-with-temporal-bayesian-hierarchical-inference
#2
Zhen Wu, Yong Liu, Zhongyao Liang, Sifeng Wu, Huaicheng Guo
Lake eutrophication is associated with excessive anthropogenic nutrients (mainly nitrogen (N) and phosphorus (P)) and unobserved internal nutrient cycling. Despite the advances in understanding the role of external loadings, the contribution of internal nutrient cycling is still an open question. A dynamic mass-balance model was developed to simulate and measure the contributions of internal cycling and external loading. It was based on the temporal Bayesian Hierarchical Framework (BHM), where we explored the seasonal patterns in the dynamics of nutrient cycling processes and the limitation of N and P on phytoplankton growth in hyper-eutrophic Lake Dianchi, China...
March 19, 2017: Water Research
https://www.readbyqxmd.com/read/28342962/intellectual-evaluation-of-children-exposed-to-phthalate-tainted-products-after-the-2011-taiwan-phthalate-episode
#3
Po-Chin Huang, Chih-Hsin Tsai, Chu-Chih Chen, Ming-Tsang Wu, Mei-Lien Chen, Shu-Li Wang, Bai-Hsiun Chen, Ching-Chang Lee, Jouni J K Jaakkola, Wen-Chiu Wu, Min-Kung Chen, Chao A Hsiung, Rapit Group
INTRODUCTION: Phthalate exposure may reduce intellectual development in young children. In 2011, numerous Taiwanese children had been reported to have consumed phthalate-tainted products. We investigated the effects of phthalate exposure on the intellectual development of these children after the 2011 Taiwan di-2-ethylhexyl phthalate (DEHP) episode. METHODS: We recruited 204 children, aged 3-12 y, from 3 hospitals in Taiwan between 2012 and 2013. First-morning urine samples were collected for analyzing 5 phthalate metabolites...
March 23, 2017: Environmental Research
https://www.readbyqxmd.com/read/28340415/uncertainty-analysis-for-effluent-trading-planning-using-a-bayesian-estimation-based-simulation-optimization-modeling-approach
#4
J L Zhang, Y P Li, G H Huang, B W Baetz, J Liu
In this study, a Bayesian estimation-based simulation-optimization modeling approach (BESMA) is developed for identifying effluent trading strategies. BESMA incorporates nutrient fate modeling with soil and water assessment tool (SWAT), Bayesian estimation, and probabilistic-possibilistic interval programming with fuzzy random coefficients (PPI-FRC) within a general framework. Based on the water quality protocols provided by SWAT, posterior distributions of parameters can be analyzed through Bayesian estimation; stochastic characteristic of nutrient loading can be investigated which provides the inputs for the decision making...
March 6, 2017: Water Research
https://www.readbyqxmd.com/read/28340274/regularized-quantile-regression-applied-to-genome-enabled-prediction-of-quantitative-traits
#5
M Nascimento, F F E Silva, M D V de Resende, C D Cruz, A C C Nascimento, J M S Viana, C F Azevedo, L M A Barroso
Genomic selection (GS) is a variant of marker-assisted selection, in which genetic markers covering the whole genome predict individual genetic merits for breeding. GS increases the accuracy of breeding values (BV) prediction. Although a variety of statistical models have been proposed to estimate BV in GS, few methodologies have examined statistical challenges based on non-normal phenotypic distributions, e.g., skewed distributions. Traditional GS models estimate changes in the phenotype distribution mean, i...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28339723/leveraging-molecular-datasets-for-biomarker-based-clinical-trial-design-in-glioblastoma
#6
Shyam K Tanguturi, Lorenzo Trippa, Shakti H Ramkissoon, Kristine Pelton, David Knoff, David Sandak, Neal I Lindeman, Azra H Ligon, Rameen Beroukhim, Giovanni Parmigiani, Patrick Y Wen, Keith L Ligon, Brian M Alexander
Background.: Biomarkers can improve clinical trial efficiency, but designing and interpreting biomarker-driven trials require knowledge of relationships among biomarkers, clinical covariates, and endpoints. We investigated these relationships across genomic subgroups of glioblastoma (GBM) within our institution (DF/BWCC), validated results in The Cancer Genome Atlas (TCGA), and demonstrated potential impacts on clinical trial design and interpretation. Methods.: We identified genotyped patients at DF/BWCC, and clinical associations across 4 common GBM genomic biomarker groups were compared along with overall survival (OS), progression-free survival (PFS), and survival post-progression (SPP)...
February 20, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339547/effectiveness-of-the-strengthening-families-programme-10-14-in-poland-cluster-randomized-controlled-trial
#7
David R Foxcroft, Howard Callen, Emma L Davies, Katarzyna Okulicz-Kozaryn
: The Strengthening Families Programme for youth aged 10-14 and parents/carers (SFP10-14) is a family-based prevention intervention with positive results in trials in the United States. We assessed the effectiveness of SFP10-14 for preventing substance misuse in Poland. : Cluster randomized controlled trial with 20 communities (511 families; 614 young people) were allocated to SFP10-14 or a control arms. Primary outcomes were alcohol, smoking and other drug use. Secondary outcomes included parenting practices, parent-child relations, and child problem behaviour...
October 24, 2016: European Journal of Public Health
https://www.readbyqxmd.com/read/28339220/experimental-bayesian-quantum-phase-estimation-on-a-silicon-photonic-chip
#8
S Paesani, A A Gentile, R Santagati, J Wang, N Wiebe, D P Tew, J L O'Brien, M G Thompson
Quantum phase estimation is a fundamental subroutine in many quantum algorithms, including Shor's factorization algorithm and quantum simulation. However, so far results have cast doubt on its practicability for near-term, nonfault tolerant, quantum devices. Here we report experimental results demonstrating that this intuition need not be true. We implement a recently proposed adaptive Bayesian approach to quantum phase estimation and use it to simulate molecular energies on a silicon quantum photonic device...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28338966/a-comparison-of-sensitivity-specificity-imputation-direct-imputation-and-fully-bayesian-analysis-to-adjust-for-exposure-misclassification-when-validation-data-are-unavailable
#9
Marine Corbin, Stephen Haslett, Neil Pearce, Milena Maule, Sander Greenland
Purpose: Measurement error is an important source of bias in epidemiological studies. We illustrate three approaches to sensitivity analysis for the effect of measurement error: imputation of the 'true' exposure based on specifying the sensitivity and specificity of the measured exposure (SS); direct imputation (DI) using a regression model for the predictive values; and adjustment based on a fully Bayesian analysis. Methods: We deliberately misclassify smoking status in data from a case-control study of lung cancer...
March 14, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/28338960/organellar-genomes-from-a-%C3%A2-5-000-years-old-archaeological-maize-sample-are-closely-related-to-nb-genotype
#10
Bernardo Pérez-Zamorano, Miguel Vallebueno-Estrada, Javier Martínez González, Angel García Cook, Rafael Montiel, Jean-Philippe Vielle-Calzada, Luis Delaye
The story of how pre-Columbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, México. Accelerator mass spectrometry dated the maize sample to be 5,040 to 5,300 years before present (95% probability). Phylogenetic analysis of the mitochondrial genome shows that the archaeological sample branches basal to the other Zea mays genomes, as expected...
March 17, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338643/geographical-correlations-between-indoor-radon-concentration-and-risks-of-lung-cancer-non-hodgkin-s-lymphoma-and-leukemia-during-1999-2008-in-korea
#11
Mina Ha, Seung-Sik Hwang, Sungchan Kang, No-Wook Park, Byung-Uck Chang, Yongjae Kim
Indoor radon is the second most important risk factor for lung cancer and may also be a risk factor for hematopoietic cancers, particularly in children and adolescents. The present study measured indoor radon concentration nationwide at 5553 points during 1989-2009 and spatially interpolated using lognormal kriging. The incidences of lung cancer, non-Hodgkin's lymphoma (NHL), and leukemia, stratified by sex and five-year age groups in each of the 234 administrative regions in the country during 1999-2008, were obtained from the National Cancer Registry and used to calculate the standardized incidence ratios...
March 24, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28337862/bayesian-sensitivity-analysis-of-a-1d-vascular-model-with-gaussian-process-emulators
#12
A Melis, R H Clayton, A Marzo
One-dimensional models of the cardiovascular system can capture the physics of pulse waves, but involve many parameters. Since these may vary among individuals, patient-specific models are difficult to construct. Sensitivity analysis can be used to rank model parameters by their effect on outputs, and to quantify how uncertainty in parameters influences output uncertainty. This type of analysis is often conducted with a Monte Carlo method, where large numbers of model runs are used to assess input-output relations...
March 24, 2017: International Journal for Numerical Methods in Biomedical Engineering
https://www.readbyqxmd.com/read/28337122/cerebrospinal-fluid-cortisol-mediates-brain-derived-neurotrophic-factor-relationships-to-mortality-after-severe-tbi-a-prospective-cohort-study
#13
Miranda J Munoz, Raj G Kumar, Byung-Mo Oh, Yvette P Conley, Zhensheng Wang, Michelle D Failla, Amy K Wagner
Distinct regulatory signaling mechanisms exist between cortisol and brain derived neurotrophic factor (BDNF) that may influence secondary injury cascades associated with traumatic brain injury (TBI) and predict outcome. We investigated concurrent CSF BDNF and cortisol relationships in 117 patients sampled days 0-6 after severe TBI while accounting for BDNF genetics and age. We also determined associations between CSF BDNF and cortisol with 6-month mortality. BDNF variants, rs6265 and rs7124442, were used to create a gene risk score (GRS) in reference to previously published hypothesized risk for mortality in "younger patients" (<48 years) and hypothesized BDNF production/secretion capacity with these variants...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28336737/comparative-effectiveness-of-different-wound-dressings-for-patients-with-partial-thickness-burns-study-protocol-of-a-systematic-review-and-a-bayesian-framework-network-meta-analysis
#14
Qiong Jiang, Zhao-Hong Chen, Shun-Bin Wang, Xiao-Dong Chen
INTRODUCTION: Selecting a suitable wound dressing for patients with partial-thickness burns (PTBs) is important in wound care. However, the comparative effectiveness of different dressings has not been studied. We report the protocol of a network meta-analysis designed to combine direct and indirect evidence of wound dressings in the management of PTB. METHODS AND ANALYSIS: We will search for randomised controlled trials (RCTs) evaluating the wound-healing effect of a wound dressing in the management of PTB...
March 22, 2017: BMJ Open
https://www.readbyqxmd.com/read/28336478/an-extended-protocol-for-usability-validation-of-medical-devices-research-design-and-reference-model
#15
Martin Schmettow, Raphaela Schnittker, Jan Maarten Schraagen
This paper proposes and demonstrates an extended protocol for usability validation testing of medical devices. A review of currently used methods for the usability evaluation of medical devices revealed two main shortcomings. Firstly, the lack of methods to closely trace the interaction sequences and derive performance measures. Secondly, a prevailing focus on cross-sectional validation studies, ignoring the issues of learnability and training. The U.S. Federal Drug and Food Administration's recent proposal for a validation testing protocol for medical devices is then extended to address these shortcomings: (1) a novel process measure 'normative path deviations' is introduced that is useful for both quantitative and qualitative usability studies and (2) a longitudinal, completely within-subject study design is presented that assesses learnability, training effects and allows analysis of diversity of users...
March 21, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28336402/post-operative-efficacy-predictability-safety-and-visual-quality-of-laser-corneal-refractive-surgery-a-network-meta-analysis
#16
Daizong Wen, Colm McAlinden, Ian Flitcroft, Ruixue Tu, Qinmei Wang, Jorge Alió, John Marshall, Yingying Huang, Benhao Song, Liang Hu, Yune Zhao, Senmiao Zhu, Rongrong Gao, Fangjun Bao, Ayong Yu, Ye Yu, Hengli Lian, Jinhai Huang
PURPOSE: To compare the post-operative efficacy, predictability, safety and visual quality of all major forms of laser corneal refractive surgeries for correcting myopia. DESIGN: Systematic review and network meta-analysis. METHODS: MEDLINE, EMBASE, Cochrane Library and the US trial registry was conducted up to November 2015. Randomized controlled trials (RCT) reporting in accordance with the eligibility criteria were included in this review...
March 20, 2017: American Journal of Ophthalmology
https://www.readbyqxmd.com/read/28335713/erratum-to-an-integrative-bayesian-dirichlet-multinomial-regression-model-for-the-analysis-of-taxonomic-abundances-in-microbiome-data
#17
W Duncan Wadsworth, Raffaele Argiento, Michele Guindani, Jessica Galloway-Pena, Samuel A Shelburne, Marina Vannucci
No abstract text is available yet for this article.
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28335525/the-history-of-clotting-factor-concentrates-pharmacokinetics
#18
REVIEW
Massimo Morfini
Clotting factor concentrates (CFCs) underwent tremendous modifications during the last forty years. Plasma-derived concentrates made the replacement therapy feasible not only in the hospital but also at patients' home by on-demand or prophylactic regimen. Virucidal methods, implemented soon after hepatitis and AIDS outbreak, and purification by Mabs made the plasma-derived concentrates safer and purer. CFCs were considered equivalent to the other drugs and general rules and methods of pharmacokinetics (PK) were applied to their study...
March 20, 2017: Journal of Clinical Medicine
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#19
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334312/efficient-inference-for-genetic-association-studies-with-multiple-outcomes
#20
Helene Ruffieux, Anthony C Davison, Jorg Hager, Irina Irincheeva
Combined inference for heterogeneous high-dimensional data is critical in modern biology, where clinical and various kinds of molecular data may be available from a single study. Classical genetic association studies regress a single clinical outcome on many genetic variants one by one, but there is an increasing demand for joint analysis of many molecular outcomes and genetic variants in order to unravel functional interactions. Unfortunately, most existing approaches to joint modeling are either too simplistic to be powerful or are impracticable for computational reasons...
March 16, 2017: Biostatistics
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