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variational inference

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https://www.readbyqxmd.com/read/27913832/general-and-specific-combining-abilities-in-a-maize-zea-mays-l-test-cross-hybrid-panel-relative-importance-of-population-structure-and-genetic-divergence-between-parents
#1
A Larièpe, L Moreau, J Laborde, C Bauland, S Mezmouk, L Décousset, T Mary-Huard, J B Fiévet, A Gallais, P Dubreuil, A Charcosset
General and specific combining abilities of maize hybrids between 288 inbred lines and three tester lines were highly related to population structure and genetic distance inferred from SNP data. Many studies have attempted to provide reliable and quick methods to identify promising parental lines and combinations in hybrid breeding programs. Since the 1950s, maize germplasm has been organized into heterotic groups to facilitate the exploitation of heterosis. Molecular markers have proven efficient tools to address the organization of genetic diversity and the relationship between lines or populations...
December 2, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27912743/str-realigner-a-realignment-method-for-short-tandem-repeat-regions
#2
Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori, Masao Nagasaki
BACKGROUND: In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27912019/dynamic-n-occupancy-models-estimating-demographic-rates-and-local-abundance-from-detection-nondetection-data
#3
Sam Rossman, Charles B Yackulic, Sarah P Saunders, Janice Reid, Ray Davis, Elise F Zipkin
Occupancy modeling is a widely used analytical technique for assessing species distributions and range dynamics. However, occupancy analyses frequently ignore variation in abundance of occupied sites, even though site abundances affect many of the parameters being estimated (e.g., extinction, colonization, detection probability). We introduce a new model ("dynamic N-occupancy") capable of providing accurate estimates of local abundance, population gains (reproduction/immigration), and apparent survival probabilities while accounting for imperfect detection using only detection/nondetection data...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911952/high-interannual-variability-in-connectivity-and-genetic-pool-of-a-temperate-clingfish-matches-oceanographic-transport-predictions
#4
Maria Klein, Sara Teixeira, Jorge Assis, Ester A Serrão, Emanuel J Gonçalves, Rita Borges
Adults of most marine benthic and demersal fish are site-attached, with the dispersal of their larval stages ensuring connectivity among populations. In this study we aimed to infer spatial and temporal variation in population connectivity and dispersal of a marine fish species, using genetic tools and comparing these with oceanographic transport. We focused on an intertidal rocky reef fish species, the shore clingfish Lepadogaster lepadogaster, along the southwest Iberian Peninsula, in 2011 and 2012. We predicted high levels of self-recruitment and distinct populations, due to short pelagic larval duration and because all its developmental stages have previously been found near adult habitats...
2016: PloS One
https://www.readbyqxmd.com/read/27907056/understanding-variation-in-sets-of-n-of-1-trials
#5
Artur Araujo, Steven Julious, Stephen Senn
A recent paper in this journal by Chen and Chen has used computer simulations to examine a number of approaches to analysing sets of n-of-1 trials. We have examined such designs using a more theoretical approach based on considering the purpose of analysis and the structure as regards randomisation that the design uses. We show that different purposes require different analyses and that these in turn may produce quite different results. Our approach to incorporating the randomisation employed when the purpose is to test a null hypothesis of strict equality of the treatment makes use of Nelder's theory of general balance...
2016: PloS One
https://www.readbyqxmd.com/read/27903894/dbsap-single-amino-acid-polymorphism-database-for-protein-variation-detection
#6
Ruifang Cao, Yan Shi, Shuangguan Chen, Yimin Ma, Jiajun Chen, Juan Yang, Geng Chen, Tieliu Shi
Millions of human single nucleotide polymorphisms (SNPs) or mutations have been identified so far, and these variants could be strongly correlated with phenotypic variations of traits/diseases. Among these variants, non-synonymous ones can result in amino-acid changes that are called single amino-acid polymorphisms (SAPs). Although some studies have tried to investigate the SAPs, only a small fraction of SAPs have been identified due to inadequately inferred protein variation database and the low coverage of mass spectrometry (MS) experiments...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903871/decline-and-recovery-of-a-large-carnivore-environmental-change-and-long-term-trends-in-an-endangered-brown-bear-population
#7
Isabel Martínez Cano, Fernando González Taboada, Javier Naves, Alberto Fernández-Gil, Thorsten Wiegand
Understanding what factors drive fluctuations in the abundance of endangered species is a difficult ecological problem but a major requirement to attain effective management and conservation success. The ecological traits of large mammals make this task even more complicated, calling for integrative approaches. We develop a framework combining individual-based modelling and statistical inference to assess alternative hypotheses on brown bear dynamics in the Cantabrian range (Iberian Peninsula). Models including the effect of environmental factors on mortality rates were able to reproduce three decades of variation in the number of females with cubs of the year (Fcoy), including the decline that put the population close to extinction in the mid-nineties, and the following increase in brown bear numbers...
November 30, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27902869/drivers-of-interannual-variability-in-virioplankton-abundance-at-the-coastal-western-antarctic-peninsula-and-the-potential-effects-of-climate-change
#8
Claire Evans, Joost Brandsma, David W Pond, Hugh J Venables, Michael P Meredith, Harry J Witte, Sharon Stammerjohn, William H Wilson, Andrew Clarke, Corina P D Brussaard
An eight year time-series in the Western Antarctic Peninsula (WAP) with an approximately weekly sampling frequency was used to elucidate changes in virioplankton abundance and their drivers in this climatically-sensitive region. Virioplankton abundances at the coastal WAP show a pronounced seasonal cycle with interannual variability in the timing and magnitude of the summer maxima. Bacterioplankton abundance is the most influential driving factor of the virioplankton, and exhibit closely coupled dynamics. Sea ice cover and duration predetermine levels of phytoplankton stock and thus, influence virioplankton by dictating the substrates available to the bacterioplankton...
November 30, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27898725/spatially-explicit-models-to-investigate-geographic-patterns-in-the-distribution-of-forensic-strs-application-to-the-north-eastern-mediterranean
#9
Francesco Messina, Andrea Finocchio, Nejat Akar, Aphrodite Loutradis, Emmanuel I Michalodimitrakis, Radim Brdicka, Carla Jodice, Andrea Novelletto
Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies...
2016: PloS One
https://www.readbyqxmd.com/read/27898704/genetic-structure-and-potential-environmental-determinants-of-local-genetic-diversity-in-japanese-honeybees-apis-cerana-japonica
#10
Teruyoshi Nagamitsu, Mika Yasuda, Fuki Saito-Morooka, Maki N Inoue, Mio Nishiyama, Koichi Goka, Shinji Sugiura, Kaoru Maeto, Kimiko Okabe, Hisatomo Taki
Declines in honeybee populations have been a recent concern. Although causes of the declines remain unclear, environmental factors may be responsible. We focused on the potential environmental determinants of local populations of wild honeybees, Apis cerana japonica, in Japan. This subspecies has little genetic variation in terms of its mitochondrial DNA sequences, and genetic variations at nuclear loci are as yet unknown. We estimated the genetic structure and environmental determinants of local genetic diversity in nuclear microsatellite genotypes of fathers and mothers, inferred from workers collected at 139 sites...
2016: PloS One
https://www.readbyqxmd.com/read/27893768/macromolecular-crowding-regulates-the-gene-expression-profile-by-limiting-diffusion
#11
Mahdi Golkaram, Stefan Hellander, Brian Drawert, Linda R Petzold
We seek to elucidate the role of macromolecular crowding in transcription and translation. It is well known that stochasticity in gene expression can lead to differential gene expression and heterogeneity in a cell population. Recent experimental observations by Tan et al. have improved our understanding of the functional role of macromolecular crowding. It can be inferred from their observations that macromolecular crowding can lead to robustness in gene expression, resulting in a more homogeneous cell population...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27891217/models-of-eucalypt-phenology-predict-bat-population-flux
#12
John R Giles, Raina K Plowright, Peggy Eby, Alison J Peel, Hamish McCallum
Fruit bats (Pteropodidae) have received increased attention after the recent emergence of notable viral pathogens of bat origin. Their vagility hinders data collection on abundance and distribution, which constrains modeling efforts and our understanding of bat ecology, viral dynamics, and spillover. We addressed this knowledge gap with models and data on the occurrence and abundance of nectarivorous fruit bat populations at 3 day roosts in southeast Queensland. We used environmental drivers of nectar production as predictors and explored relationships between bat abundance and virus spillover...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/27891163/the-visual-system-of-harvestmen-opiliones-arachnida-chelicerata-a-re-examination
#13
Tobias Lehmann, Eva Lodde-Bensch, Roland R Melzer, Martina Metz
BACKGROUND: The visual systems in chelicerates are poorly understood, even though they show strong variation in eye and visual neuropil architecture, thus may provide valuable insights for the understanding of chelicerate phylogeny and eye evolution. Comparable morphological characters are desperately sought for reconstructions of the phylogeny of Chelicerata, especially with respect to Arachnida. So far, reliable data exist only for Pycnogonida, Xiphosura, Scorpiones, and Araneae. The few earlier studies of the organisation of the visual system in harvestmen are contradictory concerning the number, morphology, and position of the visual neuropils...
2016: Frontiers in Zoology
https://www.readbyqxmd.com/read/27890039/genetic-diversity-of-infective-larvae-of-gnathostoma-spinigerum-nematoda-gnathostomatidae-in-freshwater-swamp-eels-from-thailand
#14
P Eamsobhana, D Wanachiwanawin, K Roongruangchai, S L Song, H S Yong
Human gnathostomiasis is a food-borne zoonosis caused by a tissue nematode of the genus Gnathostoma. The disease is highly endemic in Asia, including Thailand. The freshwater swamp eel (Monopterus albus), the second intermediate host of the gnathostome nematode, has an important role in transmitting the infection in Thailand. Surveys on the infective larvae of Gnathostoma spinigerum based on morphological features in freshwater swamp eels have been performed continuously and reported in Thailand. However, there is still limited molecular data on intra-species variations of the parasite...
November 28, 2016: Journal of Helminthology
https://www.readbyqxmd.com/read/27884206/large-scale-benchmarking-reveals-false-discoveries-and-count-transformation-sensitivity-in-16s-rrna-gene-amplicon-data-analysis-methods-used-in-microbiome-studies
#15
Jonathan Thorsen, Asker Brejnrod, Martin Mortensen, Morten A Rasmussen, Jakob Stokholm, Waleed Abu Al-Soud, Søren Sørensen, Hans Bisgaard, Johannes Waage
BACKGROUND: There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of 16S rRNA gene hypervariable regions, aggregating sequence-similar amplicons into operational taxonomic units (OTUs). Strategies for detecting differential relative abundance of OTUs between sample conditions include classical statistical approaches as well as a plethora of newer methods, many borrowing from the related field of RNA-seq analysis...
November 25, 2016: Microbiome
https://www.readbyqxmd.com/read/27878077/phylogeography-of-the-antilopine-wallaroo-macropus-antilopinus-across-tropical-northern-australia
#16
Jessica J Wadley, Damien A Fordham, Vicki A Thomson, Euan G Ritchie, Jeremy J Austin
The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species' range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re-examine these results to (1) determine phylogeographic patterns across the range of M...
November 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/27876654/fast-bayesian-whole-brain-fmri-analysis-with-spatial-3d-priors
#17
Per Sidén, Anders Eklund, David Bolin, Mattias Villani
Spatial whole-brain Bayesian modeling of task-related functional magnetic resonance imaging (fMRI) is a great computational challenge. Most of the currently proposed methods therefore do inference in subregions of the brain separately or do approximate inference without comparison to the true posterior distribution. A popular such method, which is now the standard method for Bayesian single subject analysis in the SPM software, is introduced in Penny et al. (2005b). The method processes the data slice-by-slice and uses an approximate variational Bayes (VB) estimation algorithm that enforces posterior independence between activity coefficients in different voxels...
November 19, 2016: NeuroImage
https://www.readbyqxmd.com/read/27875766/augmentation-of-bacterial-homeostasis-by-regulating-in-situ-buffer-capacity-significance-of-total-dissolved-salts-over-acidogenic-metabolism
#18
S Venkata Mohan, S Srikanth, G N Nikhil
During anaerobic fermentation, consequent accumulation of acidic fermented products leads to the failure of pH homeostasis. The present study aimed to comprehend the changes in buffering capacity with addition of sodium salts of hydroxide, bicarbonate and phosphate. The results showed notable augmentation in buffer capacity and cumulative hydrogen production (CHP) compared to control. The influential factor is the amount of undissociated volatile fatty acids released that affected the cell metabolism and consequently biohydrogen generation...
November 9, 2016: Bioresource Technology
https://www.readbyqxmd.com/read/27875122/inferring-individual-level-variations-in-the-functional-parcellation-of-the-cerebral-cortex
#19
Lei Nie, Paul M Matthews, Yike Guo
OBJECTIVE: Functional parcellation of the cerebral cortex is variable across different subjects or between cognitive states. Ignoring individual-or state-dependent variations in the functional parcellation may lead to inaccurate representations of individual functional connectivity, limiting the precision of interpretations of differences in individual connectivity profiles. However, it is difficult to infer the individual-level variations due to the relatively low robustness of methods for parcellation of individual subjects...
December 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27870999/sparse-bayesian-registration-of-medical-images-for-self-tuning-of-parameters-and-spatially-adaptive-parametrization-of-displacements
#20
Loïc Le Folgoc, Hervé Delingette, Antonio Criminisi, Nicholas Ayache
We extend Bayesian models of non-rigid image registration to allow not only for the automatic determination of registration parameters (such as the trade-off between image similarity and regularization functionals), but also for a data-driven, multiscale, spatially adaptive parametrization of deformations. Adaptive parametrizations have been used with success to promote both the regularity and accuracy of registration schemes, but so far on non-probabilistic grounds - either as part of multiscale heuristics, or on the basis of sparse optimization...
November 9, 2016: Medical Image Analysis
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