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Bayesian probability

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https://www.readbyqxmd.com/read/28230712/updating-evidence-for-using-hypothermia-in-pediatric-severe-traumatic-brain-injury-conventional-and-bayesian-meta-analytic-perspectives
#1
Robert C Tasker, Frederick W Vonberg, Elizabeth D Ulano, Alireza Akhondi-Asl
OBJECTIVE: To evaluate clinical trials of hypothermia management on outcome in pediatric patients with severe traumatic brain injury using conventional and Bayesian meta-analyses. DATA SOURCES: Screening of PubMed and other databases to identify randomized controlled trials of hypothermia for pediatric severe traumatic brain injury published before September 2016. STUDY SELECTION: Four investigators assessed and reviewed randomized controlled trial data...
February 20, 2017: Pediatric Critical Care Medicine
https://www.readbyqxmd.com/read/28228750/evolutionary-roots-and-diversification-of-the-genus-aeromonas
#2
Ariadna Sanglas, Vicenta Albarral, Maribel Farfán, J G Lorén, M C Fusté
Despite the importance of diversification rates in the study of prokaryote evolution, they have not been quantitatively assessed for the majority of microorganism taxa. The investigation of evolutionary patterns in prokaryotes constitutes a challenge due to a very scarce fossil record, limited morphological differentiation and frequently complex taxonomic relationships, which make even species recognition difficult. Although the speciation models and speciation rates in eukaryotes have traditionally been established by analyzing the fossil record data, this is frequently incomplete, and not always available...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28226784/parameter-estimation-for-gene-regulatory-networks-a-two-stage-mcmc-bayesian-approach
#3
Niannan Xue, Wei Pan, Yike Guo, Niannan Xue, Wei Pan, Yike Guo, Wei Pan, Yike Guo, Niannan Xue
Genetic regulatory networks have emerged as a useful way to elucidate the biochemical pathways for biological functions. Yet, determination of the exact parametric forms for these models remain a major challenge. In this paper, we present a novel computational approach implemented in C++ to solve this inverse problem. This takes the form of an optimization stage first after which Bayesian filtering takes place. The key advantage of such a flexible, general and robust approach is that it provides us with a joint probability distribution of the model parameters instead of single estimates, which we can propagate to final predictions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226754/pixel-based-skin-segmentation-in-psoriasis-images
#4
Y George, M Aldeen, R Garnavi, Y George, M Aldeen, R Garnavi, M Aldeen, Y George, R Garnavi
In this paper, we present a detailed comparison study of skin segmentation methods for psoriasis images. Different techniques are modified and then applied to a set of psoriasis images acquired from the Royal Melbourne Hospital, Melbourne, Australia, with aim of finding the best technique suited for application to psoriasis images. We investigate the effect of different colour transformations on skin detection performance. In this respect, explicit skin thresholding is evaluated with three different decision boundaries (CbCr, HS and rgHSV)...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28222151/bayesian-stock-assessment-of-pacific-herring-in-prince-william-sound-alaska
#5
Melissa L Muradian, Trevor A Branch, Steven D Moffitt, Peter-John F Hulson
The Pacific herring (Clupea pallasii) population in Prince William Sound, Alaska crashed in 1993 and has yet to recover, affecting food web dynamics in the Sound and impacting Alaskan communities. To help researchers design and implement the most effective monitoring, management, and recovery programs, a Bayesian assessment of Prince William Sound herring was developed by reformulating the current model used by the Alaska Department of Fish and Game. The Bayesian model estimated pre-fishery spawning biomass of herring age-3 and older in 2013 to be a median of 19,410 mt (95% credibility interval 12,150-31,740 mt), with a 54% probability that biomass in 2013 was below the management limit used to regulate fisheries in Prince William Sound...
2017: PloS One
https://www.readbyqxmd.com/read/28216881/specific-pcr-identification-between-peucedanum-praeruptorum-and-angelica-decursiva-and-identification-between-them-and-adulterant-using-dna-barcode
#6
Bang-Xing Han, Yuan Yuan, Lu-Qi Huang, Qun Zhao, Ling-Ling Tan, Xiang-Wen Song, Xiao-Mei He, Tao Xu, Feng Liu, Jian Wang
BACKGROUND: The traditional Chinese medicine (TCM) Qianhu and Zihuaqianhu are the dried roots of Peucedanum praeruptorum and Angelica decursiva, respectively. Since the plant sources of Qianhu and Zihuaqianhu are more complex, the chemical compositions of P. praeruptorum and A. decursiva are significantly different, and many adulterants exist because of the differences in traditional understanding and medication habits. Therefore, the rapid and accurate identification methods are required...
January 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28215350/species-delimitation-and-phylogeography-of-the-pectenia-species-complex-a-misunderstood-case-of-species-pairs-in-lichenized-fungi-where-reproduction-mode-does-not-delimit-lineages
#7
Mónica A G Otálora, Isabel Martínez, Gregorio Aragón, Mats Wedin
The main goal of this work was to study species boundaries in the genus Pectenia and elucidate the biogeographic history of the four currently accepted species. To accomplish this, we included 92 specimens across the range of Pectenia in Europe and northern Africa. We used three nuclear loci and assessed species circumscription using two Bayesian coalescent-based methods and the Bayes Factor approach. We reviewed the value of reproductive mode and other morphological features as predictors of monophyletic groups...
March 2017: Fungal Biology
https://www.readbyqxmd.com/read/28213206/selected-aspects-of-prior-and-likelihood-information-for-a-bayesian-classifier-in-a-road-safety-analysis
#8
Marzena Nowakowska
The development of the Bayesian logistic regression model classifying the road accident severity is discussed. The already exploited informative priors (method of moments, maximum likelihood estimation, and two-stage Bayesian updating), along with the original idea of a Boot prior proposal, are investigated when no expert opinion has been available. In addition, two possible approaches to updating the priors, in the form of unbalanced and balanced training data sets, are presented. The obtained logistic Bayesian models are assessed on the basis of a deviance information criterion (DIC), highest probability density (HPD) intervals, and coefficients of variation estimated for the model parameters...
February 14, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28209373/cost-utility-of-first-line-disease-modifying-treatments-for-relapsing-remitting-multiple-sclerosis
#9
Erkki Soini, Jaana Joutseno, Marja-Liisa Sumelahti
PURPOSE: This study evaluated the cost-effectiveness of first-line treatments of relapsing-remitting multiple sclerosis (RRMS) (dimethyl fumarate [DMF] 240 mg PO BID, teriflunomide 14 mg once daily, glatiramer acetate 20 mg SC once daily, interferon [IFN]-β1a 44 µg TIW, IFN-β1b 250 µg EOD, and IFN-β1a 30 µg IM QW) and best supportive care (BSC) in the health care payer setting in Finland. METHODS: The primary outcome was the modeled incremental cost-effectiveness ratio (ICER; €/quality-adjusted life-year [QALY] gained, 3%/y discounting)...
February 13, 2017: Clinical Therapeutics
https://www.readbyqxmd.com/read/28202004/a-phase-ii-study-to-evaluate-ly2603618-in-combination-with-gemcitabine-in-pancreatic-cancer-patients
#10
Berta Laquente, Jose Lopez-Martin, Donald Richards, Gerald Illerhaus, David Z Chang, George Kim, Philip Stella, Dirk Richel, Cezary Szcylik, Stefano Cascinu, G L Frassineti, Tudor Ciuleanu, Karla Hurt, Scott Hynes, Ji Lin, Aimee Bence Lin, Daniel Von Hoff, Emiliano Calvo
BACKGROUND: The aim of this study was to determine whether checkpoint kinase 1 inihibitor (CHK1), LY2603618, and gemcitabine prolong overall survival (OS) compared to gemcitabine alone in patients with unresectable pancreatic cancer. METHODS: Patients with Stage II-IV locally advanced or metastatic pancreatic cancer were randomized (2:1) to either 230 mg of LY2603618/1000 mg/m(2) gemcitabine combined or 1000 mg/m(2) gemcitabine alone. OS was assessed using both a Bayesian augment control model and traditional frequentist analysis for inference...
February 15, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28199179/experienced-probabilities-increase-understanding-of-diagnostic-test-results-in-younger-and-older-adults
#11
Bonnie Armstrong, Julia Spaniol
BACKGROUND: With advancing age, the frequency of medical screening increases. Interpreting the results of medical tests involves estimation of posterior probabilities such as positive predictive values (PPVs) and negative predictive values (NPVs). Both laypeople and experts are typically poor at estimating posterior probabilities when the relevant statistics are communicated descriptively. The current study examined whether an experience format would improve posterior probability judgments in younger and older adults, relative to a description format...
February 1, 2017: Medical Decision Making: An International Journal of the Society for Medical Decision Making
https://www.readbyqxmd.com/read/28197852/stereospecific-assignment-of-the-asparagine-and-glutamine-sidechain-amide-protons-in-proteins-from-chemical-shift-analysis
#12
Tobias Harsch, Philipp Schneider, Bärbel Kieninger, Harald Donaubauer, Hans Robert Kalbitzer
Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB)...
February 15, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28197115/application-and-evaluation-of-an-expert-judgment-elicitation-procedure-for-correlations
#13
Mariëlle Zondervan-Zwijnenburg, Wenneke van de Schoot-Hubeek, Kimberley Lek, Herbert Hoijtink, Rens van de Schoot
The purpose of the current study was to apply and evaluate a procedure to elicit expert judgments about correlations, and to update this information with empirical data. The result is a face-to-face group elicitation procedure with as its central element a trial roulette question that elicits experts' judgments expressed as distributions. During the elicitation procedure, a concordance probability question was used to provide feedback to the experts on their judgments. We evaluated the elicitation procedure in terms of validity and reliability by means of an application with a small sample of experts...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28188878/towards-a-higher-level-ensifera-phylogeny-inferred-from-mitogenome-sequences
#14
Zhijun Zhou, Ling Zhao, Nian Liu, Huifang Guo, Bei Guan, Juanxia Di, Fuming Shi
Although mitogenomes are useful tools for inferring evolutionary history, only a few representative ones can be used for most Ensifera lineages. Thirty-two ensiferan mitogenomes were determined using ABI Sanger sequencing and standard primer walking of 2-3 overlapping Long-PCR fragments, or Illumina® HiSeq2000 for "shotgun" sequenced long-PCR-amplified mitochondrial or total genomic DNA. Six patterns of gene arrangements, including the novel trnR-trnS(AGN)-trnA-trnN-trnG-nad3 in Lipotactes tripyrga (Lipotactinae), were identified from 59 ensiferan mitogenomes...
February 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28185228/failures-of-cognitive-control-or-attention-the-case-of-stop-signal-deficits-in-schizophrenia
#15
Dora Matzke, Matthew Hughes, Johanna C Badcock, Patricia Michie, Andrew Heathcote
We used Bayesian cognitive modelling to identify the underlying causes of apparent inhibitory deficits in the stop-signal paradigm. The analysis was applied to stop-signal data reported by Badcock et al. (Psychological Medicine 32: 87-297, 2002) and Hughes et al. (Biological Psychology 89: 220-231, 2012), where schizophrenia patients and control participants made rapid choice responses, but on some trials were signalled to stop their ongoing response. Previous research has assumed an inhibitory deficit in schizophrenia, because estimates of the mean time taken to react to the stop signal are longer in patients than controls...
February 9, 2017: Attention, Perception & Psychophysics
https://www.readbyqxmd.com/read/28179182/chloroplast-and-its-phylogenies-to-understand-the-evolutionary-history-of-southern-south-american-azorella-laretia-and-mulinum-azorelloideae-apiaceae
#16
Martina Fernández, Cecilia Ezcurra, Carolina I Calviño
Azorella, Laretia and Mulinum are taxonomically complex, and good candidates to study evolutionary radiations in the Andes and the importance of hybridizations. Previous phylogenetic studies of subfamily Azorelloideae agree that Azorella and Mulinum as currently conceived are not monophyletic, and hence a revision of their circumscription is necessary. However, these phylogenies were based only on chloroplast DNA sequence data. Here, phylogenetic relationships within Azorelloideae were inferred using sequence data from five chloroplast DNA (rps16 intron, trnQ-rps16, rps16-trnK(UUU) 5' -exon, trnG(GCC)-trnS(GCU) and rpL32-trnL(UAG)), and from nuclear rDNA ITS regions to assess the monophyly of Azorella and Mulinum and discuss generic re-circumscriptions, determine hybridization and radiation events, identify and characterize important lineages, and propose hypotheses on evolution of key morphological characters...
February 4, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28178947/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 Shelbourne, Marina Vannucci
BACKGROUND: The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer. Integrative approaches which aim at associating the composition of the human microbiome with other available information, such as clinical covariates and environmental predictors, are paramount to develop a more complete understanding of the role of microbiome in disease development...
February 8, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28178876/designing-fecal-microbiota-transplant-trials-that-account-for-differences-in-donor-stool-efficacy
#18
Scott W Olesen, Thomas Gurry, Eric J Alm
Fecal microbiota transplantation is a highly effective intervention for patients suffering from recurrent Clostridium difficile, a common hospital-acquired infection. Fecal microbiota transplantation's success as a therapy for C. difficile has inspired interest in performing clinical trials that experiment with fecal microbiota transplantation as a therapy for other conditions like inflammatory bowel disease, obesity, diabetes, and Parkinson's disease. Results from clinical trials that use fecal microbiota transplantation to treat inflammatory bowel disease suggest that, for at least one condition beyond C...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28170397/bayesian-phylogeography-of-influenza-a-h3n2-for-the-2014-15-season-in-the-united-states-using-three-frameworks-of-ancestral-state-reconstruction
#19
Daniel Magee, Marc A Suchard, Matthew Scotch
Ancestral state reconstructions in Bayesian phylogeography of virus pandemics have been improved by utilizing a Bayesian stochastic search variable selection (BSSVS) framework. Recently, this framework has been extended to model the transition rate matrix between discrete states as a generalized linear model (GLM) of genetic, geographic, demographic, and environmental predictors of interest to the virus and incorporating BSSVS to estimate the posterior inclusion probabilities of each predictor. Although the latter appears to enhance the biological validity of ancestral state reconstruction, there has yet to be a comparison of phylogenies created by the two methods...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28168017/out-of-africa-biogeography-and-diversification-of-the-pantropical-pond-skater-genus-limnogonus-st%C3%A3-l-1868-hemiptera-gerridae
#20
Zhen Ye, Yahui Zhen, Yanyan Zhou, Wenjun Bu
Gondwanan vicariance, long-distance dispersal (LDD), and boreotropical migration have been proposed as alternative hypotheses explaining the pantropical distribution pattern of organisms. In this study, the historical biogeography of the pond skater genus Limnogonus was reconstructed to evaluate the impact of biogeographical scenarios in shaping their modern transoceanic disjunction. We sampled almost 65% of recognized Limnogonus species. Four DNA fragments including 69 sequences were used to reconstruct a phylogram...
February 2017: Ecology and Evolution
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