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variational inference

Scott Ferrenberg, Alexander S Martinez, Akasha M Faist
BACKGROUND: Understanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces...
2016: PeerJ
Jacques Pécréaux, Stefanie Redemann, Zahraa Alayan, Benjamin Mercat, Sylvain Pastezeur, Carlos Garzon-Coral, Anthony A Hyman, Jonathon Howard
Precise positioning of the mitotic spindle is important for specifying the plane of cell division, which in turn determines how the cytoplasmic contents of the mother cell are partitioned into the daughter cells, and how the daughters are positioned within the tissue. During metaphase in the early Caenorhabditis elegans embryo, the spindle is aligned and centered on the anterior-posterior axis by a microtubule-dependent machinery that exerts restoring forces when the spindle is displaced from the center. To investigate the accuracy and stability of centering, we tracked the position and orientation of the mitotic spindle during the first cell division with high temporal and spatial resolution...
October 18, 2016: Biophysical Journal
Wei Tong, Tae-Sung Kim, Yong-Jin Park
BACKGROUND: Chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic. RESULTS: A total of 3677 variations across the chloroplast genome were identified with an average density of 27...
December 2016: Rice
Matthew Stephens
SummaryWe introduce a new Empirical Bayes approach for large-scale hypothesis testing, including estimating false discovery rates (FDRs), and effect sizes. This approach has two key differences from existing approaches to FDR analysis. First, it assumes that the distribution of the actual (unobserved) effects is unimodal, with a mode at 0. This "unimodal assumption" (UA), although natural in many contexts, is not usually incorporated into standard FDR analysis, and we demonstrate how incorporating it brings many benefits...
October 17, 2016: Biostatistics
Olga V Popova, Kirill V Mikhailov, Mikhail A Nikitin, Maria D Logacheva, Aleksey A Penin, Maria S Muntyan, Olga S Kedrova, Nikolai B Petrov, Yuri V Panchin, Vladimir V Aleoshin
Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the early-branching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa...
2016: PloS One
Tim Friede, Christian Röver, Simon Wandel, Beat Neuenschwander
Random-effects meta-analyses are used to combine evidence of treatment effects from multiple studies. Since treatment effects may vary across trials due to differences in study characteristics, heterogeneity in treatment effects between studies must be accounted for to achieve valid inference. The standard model for random-effects meta-analysis assumes approximately normal effect estimates and a normal random-effects model. However, standard methods based on this model ignore the uncertainty in estimating the between-trial heterogeneity...
October 18, 2016: Biometrical Journal. Biometrische Zeitschrift
Anna Cho, Todd Morris, Chris Wilson, Joanna Freeland
Environmental DNA (eDNA) is emerging as a potentially powerful tool for inferring species' presence, and hence occupancy, from DNA that is shed into environmental samples such as water. Although eDNA screening has been used to detect DNA from a variety of taxonomic groups, it has not yet been used to identify DNA from species with numerous potentially sympatric confamilial species, a situation that may preclude the development of species-specific markers. There are 41 native freshwater mussel species (Unionidae) in Ontario, Canada...
July 18, 2016: Genome Génome / Conseil National de Recherches Canada
Shinnosuke Nakayama, Tobias Rapp, Robert Arlinghaus
Fast and slow life histories are proposed to covary with consistent individual differences in behaviour, but little is known whether it holds in the wild, where individuals experience natural fluctuations of the environment. We investigated whether individual differences in behaviour, such as movement traits and prey selection, are linked to variation in life-history traits in Eurasian perch (Perca fluviatilis) in the wild. Using high-resolution acoustic telemetry, we collected the positional data of fish in a whole natural lake and estimated individual movement traits by fitting a 2-state correlated random walk model...
October 17, 2016: Journal of Animal Ecology
Cécile Barbet, Guillaume Thierry
In sentence verification tasks involving under-informative statements such as Some elephants are mammals, some adults appear more tolerant to pragmatic violations than others. The underlying causes of such inter-individual variability remain however essentially unknown. Here, we investigated inter-individual variation in adults deriving the scalar inference "not all" triggered by the quantifier some. We first assessed the individual intolerance to pragmatic violations in adult participants presented with under-informative some-statements (e...
2016: Frontiers in Psychology
Namrata Dhaka, Kadambini Rout, Satish K Yadava, Yaspal Singh Sodhi, Vibha Gupta, Deepak Pental, Akshay K Pradhan
Seed weight QTL identified in different populations were synthesized into consensus QTL which were shown to harbor candidate genes by in silico mapping. Allelic variation inferred would be useful in breeding B. juncea lines with high seed weight. Seed weight is an important yield influencing trait in oilseed Brassicas and is a multigenic trait. Among the oilseed Brassicas, Brassica juncea harbors the maximum phenotypic variation wherein thousand seed weight varies from around 2.0 g to more than 7.0 g. In this study, we have undertaken quantitative trait locus/quantitative trait loci (QTL) analysis of seed weight in B...
October 15, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Monica E Ellwood-Lowe, Matthew D Sacchet, Ian H Gotlib
In the nascent field of the cognitive neuroscience of socioeconomic status (SES), researchers are using neuroimaging to examine how growing up in poverty affects children's neurocognitive development, particularly their language abilities. In this review we highlight difficulties inherent in the frequent use of reverse inference to interpret SES-related abnormalities in brain regions that support language. While there is growing evidence suggesting that SES moderates children's developing brain structure and function, no studies to date have elucidated explicitly how these neural findings are related to variations in children's language abilities, or precisely what it is about SES that underlies or contributes to these differences...
October 3, 2016: Developmental Cognitive Neuroscience
Per Bäckman, Ulrika Tehler, Bo Olsson
BACKGROUND: Exposure following oral inhalation depends on the deposition pattern of the inhaled aerosol, the extent and rate of oral and pulmonary absorption, as well as systemic distribution and clearance. For lipophilic inhaled compounds with low water solubility and high permeability, the extent and rate of pulmonary absorption can be assumed dependent on deposition pattern as well as dissolution rate. MATERIALS AND METHODS: A mechanistic model of airway deposition, mucociliary clearance, dissolution, absorption, and dissipation was applied to simulate systemic exposure of the novel selective glucocorticoid receptor modulator, AZD5423, when dosed to healthy volunteers using two different nebulizers and two different dry powder inhalers in combination with two different primary particle size distributions...
October 14, 2016: Journal of Aerosol Medicine and Pulmonary Drug Delivery
Yair Field, Evan A Boyle, Natalie Telis, Ziyue Gao, Kyle J Gaulton, David Golan, Loic Yengo, Ghislain Rocheleau, Philippe Froguel, Mark I McCarthy, Jonathan K Pritchard
Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the Singleton Density Score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2,000-3,000 years. We see strong signals of selection at lactase and the MHC, and in favor of blond hair and blue eyes. For polygenic adaptation we find that recent selection for increased height has driven allele frequency shifts across most of the genome...
October 13, 2016: Science
Panagiotis Pappas, Giorgos Dallas, Giorgos Paradisis
In research, the accurate and reliable measurement of leg and vertical stiffness could contribute to valid interpretations. The current study aimed at determining the intra-participant variability (i.e. intra-day and inter-day reliabilities) of leg and vertical stiffness, as well as related parameters, during high speed treadmill running, using the "sine-wave" method. Thirty-one males ran on a treadmill at 6.67 m∙s(-1), and the contact and flight times were measured. To determine the intra-day reliability three 10-s running bouts with 10-min recovery were performed...
October 13, 2016: Journal of Applied Biomechanics
Pieter Clauw, Frederik Coppens, Arthur Korte, Dorota Herman, Bram Slabbinck, Stijn Dhondt, Twiggy Van Daele, Liesbeth De Milde, Mattias Vermeersch, Katrien Maleux, Steven Maere, Nathalie Gonzalez, Dirk Inzé
Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under non-lethal drought conditions is lacking. Recent advances in genomics, phenomics and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The genetic architecture of the growth responses upon mild drought was investigated by subjecting the different leaf growth phenotypes to genome-wide association mapping and by characterizing the transcriptome of young developing leaves...
October 11, 2016: Plant Cell
Andrea Maria Mess, Ana Claudia Oliveira Carreira, Cláudia Marinovic de Oliveira, Paula Fratini, Phelipe Oliveira Favaron, Rodrigo da Silva Nunes Barreto, Christiane Pfarrer, Flávio Vieira Meirelles, Maria Angelica Miglino
Reproductive technologies are widely used in cattle, although many are associated with high-embryonic mortality, especially during early gestation, when the yolk sac undergoes macroscopic changes in structure. We hypothesized that vasculogenesis and angiogenesis are affected, thereby affecting embryonic and placental differentiation. To test this, we studied yolk sac development and gene expression of the vascular endothelial growth factor system (VEGF-A, VEGFR-1/Flt-1, VEGFR-2/KDR). Samples from Days 25 to 40/41 of pregnancy from control cattle (n = 8) and from pregnancies established with IVF, (n = 7) or somatic cell nuclear transfer/clones (n = 5) were examined by histology, immunohistochemistry, and quantitative reverse transcriptase PCR...
September 13, 2016: Theriogenology
M B Morrissey
Meta-analysis is increasingly used to synthesize major patterns in the large literatures within ecology and evolution. Meta-analytic methods that do not account for the process of observing data, which we may refer to as 'informal meta-analyses', may have undesirable properties. In some cases, informal meta-analyses may produce results that are unbiased, but do not necessarily make the best possible use of available data. In other cases, unbiased statistical noise in individual reports in the literature can potentially be converted into severe systematic biases in informal meta-analyses...
October 2016: Journal of Evolutionary Biology
Sindhu Ghanta, Michael I Jordan, Kivanc Kose, Dana H Brooks, Milind Rajadhyaksha, Jennifer G Dy
Segmenting objects of interest from 3D datasets is a common problem encountered in biological data. Small field of view and intrinsic biological variability combined with optically subtle changes of intensity, resolution and low contrast in images make the task of segmentation difficult, especially for microscopy of unstained living or freshly excised thick tissues. Incorporating shape information in addition to the appearance of the object of interest can often help improve segmentation performance. However, shapes of objects in tissue can be highly variable and design of a flexible shape model that encompasses these variations is challenging...
October 5, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
D E Pearse
As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of the genome under selection and extend knowledge of the genetic basis of adaptive evolution. What is far less clear, but has been the focus of active discussion, is how such information can or should transfer into conservation practice to complement more typical conservation applications of genetic data...
October 9, 2016: Journal of Fish Biology
Masouda Rahim, Sasha Mannion, Blake Klug, Hayden Hobbs, Willem van der Merwe, Michael Posthumus, Malcolm Collins, Alison V September
OBJECTIVES: The extracellular matrix (ECM) of ligaments continuously undergoes remodelling in order to maintain tissue homeostasis. Several key mediators of ECM remodelling were chosen for investigation in the present study. It is thought that polymorphisms within genes encoding signalling molecules may contribute to inter-individual variation in the responses to mechanical loading, potentially altering risk of injury. DESIGN: A genetic association study was conducted on 232 asymptomatic controls (CON) and 234 participants with surgically diagnosed anterior cruciate ligament (ACL) ruptures; of which 135 participants reported a non-contact mechanism of injury (NON subgroup)...
September 28, 2016: Journal of Science and Medicine in Sport
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