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Bayesian modeling

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https://www.readbyqxmd.com/read/28530654/allele-specific-expression-reveals-interactions-between-genetic-variation-and-environment
#1
David A Knowles, Joe R Davis, Hilary Edgington, Anil Raj, Marie-Julie Favé, Xiaowei Zhu, James B Potash, Myrna M Weissman, Jianxin Shi, Douglas F Levinson, Philip Awadalla, Sara Mostafavi, Stephen B Montgomery, Alexis Battle
Identifying interactions between genetics and the environment (GxE) remains challenging. We have developed EAGLE, a hierarchical Bayesian model for identifying GxE interactions based on associations between environmental variables and allele-specific expression. Combining whole-blood RNA-seq with extensive environmental annotations collected from 922 human individuals, we identified 35 GxE interactions, compared with only four using standard GxE interaction testing. EAGLE provides new opportunities for researchers to identify GxE interactions using functional genomic data...
May 22, 2017: Nature Methods
https://www.readbyqxmd.com/read/28530231/constraining-climate-sensitivity-and-continental-versus-seafloor-weathering-using-an-inverse-geological-carbon-cycle-model
#2
Joshua Krissansen-Totton, David C Catling
The relative influences of tectonics, continental weathering and seafloor weathering in controlling the geological carbon cycle are unknown. Here we develop a new carbon cycle model that explicitly captures the kinetics of seafloor weathering to investigate carbon fluxes and the evolution of atmospheric CO2 and ocean pH since 100 Myr ago. We compare model outputs to proxy data, and rigorously constrain model parameters using Bayesian inverse methods. Assuming our forward model is an accurate representation of the carbon cycle, to fit proxies the temperature dependence of continental weathering must be weaker than commonly assumed...
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28529731/a-bayesian-supervised-dual-dimensionality-reduction-model-for-simultaneous-decoding-of-lfp-and-spike-train-signals
#3
Andrew Holbrook, Alexander Vandenberg-Rodes, Norbert Fortin, Babak Shahbaba
Neuroscientists are increasingly collecting multimodal data during experiments and observational studies. Different data modalities-such as EEG, fMRI, LFP, and spike trains-offer different views of the complex systems contributing to neural phenomena. Here, we focus on joint modeling of LFP and spike train data, and present a novel Bayesian method for neural decoding to infer behavioral and experimental conditions. This model performs supervised dual-dimensionality reduction: it learns low-dimensional representations of two different sources of information that not only explain variation in the input data itself, but also predict extra-neuronal outcomes...
2017: Stat: the ISI's Journal for Rapid Dissemination of Statistics Research
https://www.readbyqxmd.com/read/28528587/persistent-infections-support-maintenance-of-a-coronavirus-in-a-population-of-australian-bats-myotis-macropus
#4
J Jeong, C S Smith, A J Peel, R K Plowright, D H Kerlin, J McBroom, H McCallum
Understanding viral transmission dynamics within populations of reservoir hosts can facilitate greater knowledge of the spillover of emerging infectious diseases. While bat-borne viruses are of concern to public health, investigations into their dynamics have been limited by a lack of longitudinal data from individual bats. Here, we examine capture-mark-recapture (CMR) data from a species of Australian bat (Myotis macropus) infected with a putative novel Alphacoronavirus within a Bayesian framework. Then, we developed epidemic models to estimate the effect of persistently infectious individuals (which shed viruses for extensive periods) on the probability of viral maintenance within the study population...
May 22, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28527793/prevalence-of-non-aureus-staphylococcus-species-causing-intramammary-infections-in-canadian-dairy-herds
#5
Larissa A Z Condas, Jeroen De Buck, Diego B Nobrega, Domonique A Carson, Sohail Naushad, Sarne De Vliegher, Ruth N Zadoks, John R Middleton, Simon Dufour, John P Kastelic, Herman W Barkema
Non-aureus staphylococci (NAS), the microorganisms most frequently isolated from bovine milk worldwide, are a heterogeneous group of numerous species. To establish their importance as a group, the distribution of individual species needs to be determined. In the present study, NAS intramammary infection (IMI) was defined as a milk sample containing ≥1,000 cfu/mL in pure or mixed culture that was obtained from a cohort of cows assembled by the Canadian Bovine Mastitis Research Network. Overall, 6,213 (6.3%) of 98,233 quarter-milk samples from 5,149 cows and 20,305 udder quarters were associated with an NAS IMI...
May 17, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28524851/extended-fisheries-recovery-timelines-in-a-changing-environment
#6
Gregory L Britten, Michael Dowd, Lisa Kanary, Boris Worm
Rebuilding depleted fish stocks is an international policy goal and a 2020 Aichi target under the Convention on Biological Diversity. However, stock productivity may shift with future climate change, with unknown consequences for sustainable harvesting, biomass targets and recovery timelines. Here we develop a stochastic modelling framework to characterize variability in the intrinsic productivity parameter (r) and carrying capacity (K) for 276 global fish stocks worldwide. We use models of dynamic stock productivity fitted via Bayesian inference to forecast rebuilding timelines for depleted stocks...
May 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28523791/genetic-assessment-of-the-effects-of-streamscape-succession-on-coho-salmon-oncorhynchus-kisutch-colonization-in-recently-deglaciated-streams
#7
K T Scribner, C Soiseth, J McGuire, G K Sage, L Thorsteinson, J L Nielsen, E Knudsen
Measures of genetic diversity within and among populations and historical geomorphological data on stream landscapes were used in model simulations based on approximate Bayesian computation (ABC) to examine hypotheses of the relative importance of stream features (geomorphology and age) associated with colonization events and gene flow for coho salmon Oncorhynchus kisutch breeding in recently deglaciated streams (50-240 years b.p.) in Glacier Bay National Park (GBNP), Alaska. Population estimates of genetic diversity including heterozygosity and allelic richness declined significantly and monotonically from the oldest and largest to youngest and smallest GBNP streams...
May 19, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28520893/using-bayesian-modeling-in-frequentist-adaptive-enrichment-designs
#8
Noah Simon, Richard Simon
Our increased understanding of the mechanistic heterogeneity of diseases has pushed the development of targeted therapeutics. We do not expect all patients with a given disease to benefit from a targeted drug; only those in the target population. That is, those with sufficient dysregulation in the biomolecular pathway targeted by treatment. However, due to complexity of the pathway, and/or technical issues with our characterizing assay, it is often hard to characterize the target population until well into large-scale clinical trials...
May 17, 2017: Biostatistics
https://www.readbyqxmd.com/read/28518405/setting-ambitious-yet-achievable-targets-using-probabilistic-projections-meeting-demand-for-family-planning
#9
Vladimíra Kantorová, Jin Rou New, Ann Biddlecom, Leontine Alkema
In 2015, governments adopted 17 internationally agreed goals to ensure progress and well-being in the economic, social, and environmental dimensions of sustainable development. These new goals present a challenge for countries to set empirical targets that are ambitious yet achievable and that can account for different starting points and rates of progress. We used probabilistic projections of family planning indicators, based on a global data set and Bayesian hierarchical modeling, to generate illustrative targets at the country level...
May 18, 2017: Studies in Family Planning
https://www.readbyqxmd.com/read/28516763/first-assessment-of-nox-sources-at-a-regional-background-site-in-north-china-using-isotopic-analysis-linked-with-modeling
#10
Zheng Zong, Xiaoping Wang, Chongguo Tian, Yingjun Chen, Yunting Fang, Fan Zhang, Cheng Li, Jianzhong Sun, Jun Li, Gan Zhang
Nitrogen oxides (NOx, including NO and NO2) play an important role in the formation of atmospheric particles. Thus, NOx emission reduction is critical for improving air quality, especially in severely air-polluted regions (e.g., North China). In this study, the source of NOx was investigated by the isotopic composition (δ15N) of particulate nitrate (p-NO3-) at Beihuangcheng Island (BH), a regional background site in North China. It was found that the δ15N-NO3- (n = 120) values varied between -1.7 and +24...
May 18, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28515878/a-multispecies-dependent-double-observer-model-a-new-method-for-estimating-multispecies-abundance
#11
Jessie D Golding, J Joshua Nowak, Victoria J Dreitz
Conservation of biological communities requires accurate estimates of abundance for multiple species. Recent advances in estimating abundance of multiple species, such as Bayesian multispecies N-mixture models, account for multiple sources of variation, including detection error. However, false-positive errors (misidentification or double counts), which are prevalent in multispecies data sets, remain largely unaddressed. The dependent-double observer (DDO) method is an emerging method that both accounts for detection error and is suggested to reduce the occurrence of false positives because it relies on two observers working collaboratively to identify individuals...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28515497/invasion-dynamics-of-asian-hornet-vespa-velutina-hymenoptera-vespidae-a-case-study-of-a-commune-in-south-west-france
#12
Daniel N Franklin, Mike A Brown, Samik Datta, Andrew G S Cuthbertson, Giles E Budge, Matt J Keeling
Asian hornet, Vespa velutina Lepeletier nests were discovered in 2007 in Andernos-les-Bains on the south-west coast of France, 3 years after the first reported sightings in France. The number of nests increased in the commune over the following 7 years, despite local authorities enacting a destruction policy. The nests existed in close proximity to one another leading to a high density of over 10 nests per square kilometre in urban areas. New information on the chosen habitat for nests is presented, and the differences between primary and secondary locations are evident, with primary nests mostly occupying buildings and man-made structures, while secondary nests were found on trees...
2017: Applied Entomology and Zoology
https://www.readbyqxmd.com/read/28515190/interaction-of-ace-genotype-and-salt-intake-on-hypertension-among-chinese-kazakhs-results-from-a-population-based-cross-sectional-study
#13
Yuyan Wang, Biao Zhang, Lei Hou, Wei Han, Fang Xue, Yanhong Wang, Yong Tang, Shaohua Liang, Weizhi Wang, Kuliqian Asaiti, Zixing Wang, Yaoda Hu, Lei Wang, Changchun Qiu, Mingtao Zhang, Jingmei Jiang
OBJECTIVES: To explore the effect of interaction between ACE genotype and salt intake on hypertension among Chinese Kazakhs, and to compare applications of interactions between logistic model and generalised partially linear tree-based regression (GPLTR) model. DESIGN: Population-based cross-sectional study. SETTING: Hong Dun, North Xinjiang, China. PARTICIPANTS: Non-consanguineous Chinese Kazakh participants (n=916, 342 men and 574 women) aged ≥30 years...
May 17, 2017: BMJ Open
https://www.readbyqxmd.com/read/28514941/effects-of-marker-density-and-population-structure-on-the-genomic-prediction-accuracy-for-growth-trait-in-pacific-white-shrimp-litopenaeus-vannamei
#14
Quanchao Wang, Yang Yu, Jianbo Yuan, Xiaojun Zhang, Hao Huang, Fuhua Li, Jianhai Xiang
BACKGROUND: Due to the great advantages in selection accuracy and efficiency, genomic selection (GS) has been widely studied in livestock, crop and aquatic animals. Our previous study based on one full-sib family of Litopenaeus vannamei (L. vannamei) showed that GS was feasible in penaeid shrimp. However, the applicability of GS might be influenced by many factors including heritability, marker density and population structure etc. Therefore it is necessary to evaluate the major factors affecting the prediction ability of GS in shrimp...
May 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28511616/bayesian-meta-analysis-the-role-of-the-between-sample-heterogeneity
#15
Elías Moreno, Francisco-José Vázquez-Polo, Miguel A Negrín
The random effect approach for meta-analysis was motivated by a lack of consistent assessment of homogeneity of treatment effect before pooling. The random effect model assumes that the distribution of the treatment effect is fully heterogenous across the experiments. However, other models arising by grouping some of the experiments are plausible. We illustrate on simulated binary experiments that the fully heterogenous model gives a poor meta-inference when fully heterogeneity is not the true model and that the knowledge of the true cluster model considerably improves the inference...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28510994/improved-detection-of-burkholderia-pseudomallei-from-non-blood-clinical-specimens-using-enrichment-culture-and-pcr-narrowing-diagnostic-gap-in-resource-constrained-settings
#16
Chaitanya Tellapragada, Tushar Shaw, Annet D'Souza, Vandana Kalwaje Eshwara, Chiranjay Mukhopadhyay
OBJECTIVES: To evaluate the diagnostic utility of enrichment culture and PCR for improved case detection rates of non-bacteremic form of melioidosis in limited resource settings. METHODS: Clinical specimens (n=525) obtained from patients presenting at a tertiary care hospital of south India with clinical symptoms suggestive of community-acquired pneumonia, lower respiratory tract infections, superficial or internal abscesses, chronic skin ulcers and bone or joint infections were tested for the presence of Burkholderia pseudomallei using conventional culture (CC), enrichment culture (EC) and PCR...
May 16, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28510738/pharmacokinetic-pharmacodynamic-model-for-unfractionated-heparin-dosing-during-cardiopulmonary-bypass
#17
X Delavenne, E Ollier, S Chollet, F Sandri, J Lanoiselée, S Hodin, A Montmartin, J-F Fuzellier, P Mismetti, L Gergelé
Background: High-dose heparin is used during cardiopulmonary bypass (CPB) to prevent thrombosis in the circuits used for extracorporeal circulation. The aim of this study was, initially, to develop a population pharmacokinetic/pharmacodynamic (PK/PD) model to assess the variability of PK/PD parameters and their correlation with the results of the routine haemostatic test activated clotting time (ACT) and thereafter to develop a Bayesian estimator enabling an individualized dosing strategy...
May 1, 2017: British Journal of Anaesthesia
https://www.readbyqxmd.com/read/28510466/empirical-bayesian-geographical-mapping-of-occupational-accidents-among-iranian-workers
#18
Nasim Vahabi, Anoshirvan Kazemnejad, Somnath Datta
BACKGROUND: Work-related accidents are believed to be a serious preventable cause of mortality and disability worldwide. This study aimed to provide Bayesian geographical maps of occupational injury rates among workers insured by the Iranian Social Security Organization. METHODS: The participants included all insured workers in the Iranian Social Security Organization database in 2012. One of the applications of the Bayesian approach called the Poisson-Gamma model was applied to estimate the relative risk of occupational accidents...
May 2017: Archives of Iranian Medicine
https://www.readbyqxmd.com/read/28508154/estimating-loss-of-brucella-abortus-antibodies-from-age-specific-serological-data-in-elk
#19
J A Benavides, D Caillaud, B M Scurlock, E J Maichak, W H Edwards, P C Cross
Serological data are one of the primary sources of information for disease monitoring in wildlife. However, the duration of the seropositive status of exposed individuals is almost always unknown for many free-ranging host species. Directly estimating rates of antibody loss typically requires difficult longitudinal sampling of individuals following seroconversion. Instead, we propose a Bayesian statistical approach linking age and serological data to a mechanistic epidemiological model to infer brucellosis infection, the probability of antibody loss, and recovery rates of elk (Cervus canadensis) in the Greater Yellowstone Ecosystem...
May 15, 2017: EcoHealth
https://www.readbyqxmd.com/read/28507269/randomized-multicenter-trial-of-artss-2-argatroban-with-recombinant-tissue-plasminogen-activator-for-acute-stroke
#20
Andrew D Barreto, Gary A Ford, Loren Shen, Claudia Pedroza, Jon Tyson, Chunyan Cai, Mohammad H Rahbar, James C Grotta
BACKGROUND AND PURPOSE: We conducted a randomized exploratory study to assess safety and the probability of a favorable outcome with adjunctive argatroban, a direct thrombin-inhibitor, administered to recombinant tissue-type plasminogen activator (r-tPA)-treated ischemic stroke patients. METHODS: Patients treated with standard-dose r-tPA, not receiving endovascular therapy, were randomized to receive no argatroban or argatroban (100 μg/kg bolus) followed by infusion of either 1 (low dose) or 3 μg/kg per minute (high dose) for 48 hours...
May 15, 2017: Stroke; a Journal of Cerebral Circulation
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