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variational inference

Malgorzata A Gazda, Pedro Andrade, Sandra Afonso, Jolita Dilyte, John P Archer, Ricardo J Lopes, Rui Faria, Miguel Carneiro
Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecular basis of the superior athletic and navigational capabilities of racing pigeons using whole-genome and RNA sequencing data. We inferred multiple signatures of positive selection distributed across the genome of racing pigeons...
March 13, 2018: Molecular Biology and Evolution
Yuval B Simons, Kevin Bullaughey, Richard R Hudson, Guy Sella
Human genome-wide association studies (GWASs) are revealing the genetic architecture of anthropomorphic and biomedical traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to understand how genetic architecture is shaped by basic population genetics processes-notably, by mutation, natural selection, and genetic drift. Because many quantitative traits are subject to stabilizing selection and because genetic variation that affects one trait often affects many others, we model the genetic architecture of a focal trait that arises under stabilizing selection in a multidimensional trait space...
March 16, 2018: PLoS Biology
Zhiyi Qin, Peter Stoilov, Xuegong Zhang, Yi Xing
Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ends of transcripts. We developed a computational pipeline SEASTAR that identifies first exons from RNA-seq data alone then quantifies and compares alternative first exon usage across multiple biological conditions...
March 13, 2018: Nucleic Acids Research
Joseph M Stonecypher, Lindsey C Blom, James E Johnson, Jocelyn H Bolin, Robert C Hilliard
Tripartite efficacy refers to the beliefs of the individuals within a dyad regarding personal abilities (self-efficacy), the partner's abilities (other-efficacy), or relation-inferred self-efficacy. This efficacy model has recently gained popularity in sports research (Jackson, Whipp, & Beauchamp, 2013), although there has not been any longitudinal research on efficacy beliefs and performance within this complex intra-dyad tripartite efficacy model. In a case study, we examined six individual players on a high school basketball team to explore any longitudinal changes in these tripartite efficacy beliefs through a season of play...
January 1, 2018: Psychological Reports
Ilia Korvigo, Andrey Afanasyev, Nikolay Romashchenko, Mikhail Skoblov
Many automatic classifiers were introduced to aid inference of phenotypical effects of uncategorised nsSNVs (nonsynonymous Single Nucleotide Variations) in theoretical and medical applications. Lately, several meta-estimators have been proposed that combine different predictors, such as PolyPhen and SIFT, to integrate more information in a single score. Although many advances have been made in feature design and machine learning algorithms used, the shortage of high-quality reference data along with the bias towards intensively studied in vitro models call for improved generalisation ability in order to further increase classification accuracy and handle records with insufficient data...
2018: PloS One
Pamela J Taylor, Natasha Kalebic
PURPOSE OF REVIEW: The contribution of people with psychosis to homicide statistics is small, but there is a statistically significantly higher rate of homicide among them than in the general population. Legal authorities and the wider public call for more information. Our aim was a narrative synthesis of empirical literature generated by systematic searches for the five complete years 2013-2017. RECENT FINDINGS: One article showed that people with psychosis are five times more likely to be homicide victims than those without, but focus remains on perpetrators...
March 13, 2018: Current Opinion in Psychiatry
Petri Kemppainen, Arild Husby
Genome wide association studies have contributed immensely to our understanding of the genetic basis of complex traits. One major conclusion arising from these studies is that most traits are controlled by many loci of small effect, confirming the infinitesimal model of quantitative genetics. A popular approach to test for polygenic architecture involves so called 'chromosome partitioning' where phenotypic variance explained by each chromosome is regressed on the size of the chromosome. First developed for humans, this has now been repeatedly used in other species, but there has been no evaluation of the suitability of this method in species that can differ in their genome characteristics such as number and size of chromosomes...
March 14, 2018: Molecular Ecology Resources
Nima Rostampour, Keyvan Jabbari, Mahdad Esmaeili, Mohammad Mohammadi, Shahabedin Nabavi
Background: Accurate delivery of the prescribed dose to moving lung tumors is a key challenge in radiation therapy. Tumor tracking involves real-time specifying the target and correcting the geometry to compensate for the respiratory motion, that's why tracking the tumor requires caution. This study aims to develop a markerless lung tumor tracking method with a high accuracy. Methods: In this study, four-dimensional computed tomography (4D-CT) images of 10 patients were used, and all the slices which contained the tumor were contoured for all patients...
January 2018: Journal of Medical Signals and Sensors
Marie Lopez, Athanasios Kousathanas, Hélène Quach, Christine Harmant, Patrick Mouguiama-Daouda, Jean-Marie Hombert, Alain Froment, George H Perry, Luis B Barreiro, Paul Verdu, Etienne Patin, Lluís Quintana-Murci
Understanding how deleterious genetic variation is distributed across human populations is of key importance in evolutionary biology and medical genetics. However, the impact of population size changes and gene flow on the corresponding mutational load remains a controversial topic. Here, we report high-coverage exomes from 300 rainforest hunter-gatherers and farmers of central Africa, whose distinct subsistence strategies are expected to have impacted their demographic pasts. Detailed demographic inference indicates that hunter-gatherers and farmers recently experienced population collapses and expansions, respectively, accompanied by increased gene flow...
March 12, 2018: Nature Ecology & Evolution
Yangyang Xu, Hao Cai, Gang Cao, Yu Duan, Ke Pei, Sicong Tu, Jia Zhou, Li Xie, Dongdong Sun, Jiayu Zhao, Jing Liu, Xiaoqi Wang, Lin Shen
Baizhu Shaoyao San (BSS) is a famous traditional Chinese medicinal formula widely used for the treatment of painful diarrhea, intestinal inflammation, and diarrhea-predominant irritable bowel syndrome. According to clinical medication, three medicinal herbs (Atractylodis Macrocephalae Rhizoma, Paeoniae Radix Alba, and Citri Reticulatae Pericarpium) included in BSS must be processed using some specific methods of stir-frying. On the basis of the classical theories of traditional Chinese medicine, the therapeutic effects of BSS would be significantly enhanced after processing...
March 3, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
James A Roberts, Karl J Friston, Michael Breakspear
Biological phenomena arise through interactions between an organism's intrinsic dynamics and stochastic forces-random fluctuations due to external inputs, thermal energy, or other exogenous influences. Dynamic processes in the brain derive from neurophysiology and anatomical connectivity; stochastic effects arise through sensory fluctuations, brainstem discharges, and random microscopic states such as thermal noise. The dynamic evolution of systems composed of both dynamic and random effects can be studied with stochastic dynamic models (SDMs)...
April 2017: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
Christopher S Parker, Jonathan D Clayden, M Jorge Cardoso, Roman Rodionov, John S Duncan, Catherine Scott, Beate Diehl, Sebastien Ourselin
Patients with medically-refractory focal epilepsy may be candidates for neurosurgery and some may require placement of intracranial EEG electrodes to localise seizure onset. Assessing cerebral responses to single pulse electrical stimulation (SPES) may give diagnostically useful data. SPES produces cortico-cortical evoked potentials (CCEPs), which infer effective brain connectivity. Diffusion-weighted images and tractography may be used to estimate structural brain connectivity. This combination provides the opportunity to observe seizure onset and its propagation throughout the brain, spreading contiguously along the cortex explored with electrodes, or non-contiguously...
2018: NeuroImage: Clinical
A W Tebbe, W P Weiss
Nutrient balance studies require measuring urine volume, and urinary excretion can be used to assess Mg bioavailability. A less laborious method than total collection of urine could make balance studies more feasible and expand the utility of using urinary Mg as an index of bioavailability, but the method needs to be accurate and sensitive. Sampling interval can affect accuracy because excretion must be at steady state. Two experiments were conducted to (1) determine whether urinary creatinine could be used to accurately estimate urinary output of nutrients markedly excreted via urine (N, K, Na, S, and Mg; experiment 1) and (2) determine the appropriate sampling schedule to evaluate Mg excretion after abrupt diet changes (experiment 2)...
March 7, 2018: Journal of Dairy Science
Lucas M B Yoshihara, Elizabeth P G Arêas
The coacervation of carboxymethylcellulose (CMC) and hen egg white lysozyme (HEWL) was investigated. The work focused on the effects of pH, ionic strength, I, temperature, T, and mass fraction of the macromolecular components on the coacervation process by spectrophotometry, and on characteristics of the resulting coacervate phase by rheology in the linear and non-linear regimes. Coacervation was found to be highest at HEWL mass fraction ≈0.25 with very slight dependence on pH in the range from 5 to 9. The process was favored at I < 0...
March 2, 2018: Biophysical Chemistry
Muhammad Faraz Shaikh, Zoran Salcic, Kevin I-Kai Wang, Aiguo Patrick Hu
Electrical stimulators are often prescribed to correct foot drop walking. However, commercial foot drop stimulators trigger inappropriately under certain non-gait scenarios. Past researches addressed this limitation by defining stimulation control based on automaton of a gait cycle executed by foot drop of affected limb/foot only. Since gait is a collaborative activity of both feet, this research highlights the role of normal foot for robust gait detection and stimulation triggering. A novel bipedal gait model is proposed where gait cycle is realized as an automaton based on concurrent gait sub-phases (states) from each foot...
March 10, 2018: Medical & Biological Engineering & Computing
I Maini, I Ivanovski, O Djuric, S G Caraffi, E Errichiello, M Marinelli, F Franchi, V Bizzarri, S Rosato, M Pollazzon, C Gelmini, M Malacarne, C Fusco, G Gargano, S Bernasconi, O Zuffardi, L Garavelli
BACKGROUND: Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician. METHOD: We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016...
March 9, 2018: Italian Journal of Pediatrics
Violeta Beleva Guthrie, David L Masica, Andrew Fraser, Joseph Federico, Yunfan Fan, Manel Camps, Rachel Karchin
The evolution of new biochemical activities frequently involves complex dependencies between mutations and rapid evolutionary radiation. Mutation co-occurrence and co-variation have previously been used to identify compensating mutations that are the result of physical contacts and preserve protein function and fold. Here, we model pairwise functional dependencies and higher order interactions that enable evolution of new protein functions. We use a network model to find complex dependencies between mutations resulting from evolutionary trade-offs and pleiotropic effects...
March 7, 2018: Molecular Biology and Evolution
Chantriolnt-Andreas Kapourani, Guido Sanguinetti
Motivation: High-throughput measurements of DNA methylation are increasingly becoming a mainstay of biomedical investigations. While the methylation status of individual cytosines can sometimes be informative, several recent papers have shown that the functional role of DNA methylation is better captured by a quantitative analysis of the spatial variation of methylation across a genomic region. Results: Here we present BPRMeth, a Bioconductor package which quantifies methylation profiles by generalised linear model regression (Kapourani and Sanguinetti, 2016)...
March 7, 2018: Bioinformatics
María Laura Ponssa, Jéssica Fratani, Virginia Abdala
Anurans are characterized by their saltatory mode of locomotion, which is associated with a specific morphology. The coordinated action of the muscles and bones of the pelvic girdle is key to the transmission of the force of the hindlimbs to the axial skeleton during jumping. Two features are critical for optimal locomotory performance: the cross-sectional area of muscle and the bone crest attachment sites. The first character is a proxy of the force exerted by the muscle, whereas the crests are muscle attachments sites related to muscle force...
March 8, 2018: Journal of Anatomy
Darren C Hunter, Josephine M Pemberton, Jill G Pilkington, Michael B Morrissey
In nature, selection varies across time in most environments, but we lack an understanding of how specific ecological changes drive this variation. Ecological factors can alter phenotypic selection coefficients through changes in trait distributions or individual mean fitness, even when the trait-absolute fitness relationship remains constant. We apply and extend a regression-based approach in a population of Soay sheep (Ovis aries) and suggest metrics of environment-selection relationships that can be compared across studies...
March 8, 2018: Evolution; International Journal of Organic Evolution
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