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variational inference

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https://www.readbyqxmd.com/read/28817531/bias-confounding-and-interaction-lions-and-tigers-and-bears-oh-my
#1
Thomas R Vetter, Edward J Mascha
Epidemiologists seek to make a valid inference about the causal effect between an exposure and a disease in a specific population, using representative sample data from a specific population. Clinical researchers likewise seek to make a valid inference about the association between an intervention and outcome(s) in a specific population, based upon their randomly collected, representative sample data. Both do so by using the available data about the sample variable to make a valid estimate about its corresponding or underlying, but unknown population parameter...
September 2017: Anesthesia and Analgesia
https://www.readbyqxmd.com/read/28816661/a-3d-reconstruction-strategy-of-vehicle-outline-based-on-single-pass-single-polarization-csar-data
#2
Leping Chen, Daoxiang An, Xiaotao Huang, Zhimin Zhou
In the last few years, interest in circular synthetic aperture radar (CSAR) acquisitions has arisen as a consequence of the potential achievement of three-dimensional (3D) reconstructions over 360° azimuth angle variation. In real-world scenarios full 3D reconstructions of arbitrary targets need multi-pass data, which makes the processing complex, money-consuming and time-expending. In this paper, we propose a processing strategy for the 3D reconstruction of vehicle, which can avoid using multi-pass data by introducing a priori information of vehicle's shape...
August 14, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28814653/natural-selection-on-thermal-preference-critical-thermal-maxima-and-locomotor-performance
#3
Anthony L Gilbert, Donald B Miles
Climate change is resulting in a radical transformation of the thermal quality of habitats across the globe. Whereas species have altered their distributions to cope with changing environments, the evidence for adaptation in response to rising temperatures is limited. However, to determine the potential of adaptation in response to thermal variation, we need estimates of the magnitude and direction of natural selection on traits that are assumed to increase persistence in warmer environments. Most inferences regarding physiological adaptation are based on interspecific analyses, and those of selection on thermal traits are scarce...
August 16, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28813039/comparative-assessment-of-ssr-and-snp-markers-for-inferring-the-population-genetic-structure-of-the-common-fungus-armillaria-cepistipes
#4
T Tsykun, C Rellstab, C Dutech, G Sipos, S Prospero
During the last years, simple sequence repeats (SSRs, also known as microsatellites) and single-nucleotide polymorphisms (SNPs) have become the most popular molecular markers for describing neutral genetic variation in populations of a wide range of organisms. However, only a limited number of studies has focused on comparing the performance of these two types of markers for describing the underlying genetic structure of wild populations. Moreover, none of these studies targeted fungi, the group of organisms with one of the most complex reproductive strategies...
August 16, 2017: Heredity
https://www.readbyqxmd.com/read/28812567/high-taxonomic-variability-despite-stable-functional-structure-across-microbial-communities
#5
Stilianos Louca, Saulo M S Jacques, Aliny P F Pires, Juliana S Leal, Diane S Srivastava, Laura Wegener Parfrey, Vinicius F Farjalla, Michael Doebeli
Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads...
December 5, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811388/hill-robertson-interference-reduces-genetic-diversity-on-a-young-plant-y-chromosome
#6
Josh Hough, Wei Wang, Spencer C H Barrett, Stephen I Wright
X and Y chromosomes differ in effective population size (Ne ), rates of recombination, and exposure to natural selection, all of which can affect patterns of genetic diversity. On Y chromosomes with suppressed recombination, natural selection is expected to eliminate linked neutral variation and lower the Ne of Y compared to X chromosomes or autosomes. However, female-biased sex ratios and high variance in male reproductive success can also reduce Y-linked Ne , making it difficult to infer the causes of low Y-diversity...
August 15, 2017: Genetics
https://www.readbyqxmd.com/read/28809923/generalized-structural-equations-improve-sexual-selection-analyses
#7
Sonia Lombardi, Giacomo Santini, Giovanni Maria Marchetti, Stefano Focardi
Sexual selection is an intense evolutionary force, which operates through competition for the access to breeding resources. There are many cases where male copulatory success is highly asymmetric, and few males are able to sire most females. Two main hypotheses were proposed to explain this asymmetry: "female choice" and "male dominance". The literature reports contrasting results. This variability may reflect actual differences among studied populations, but it may also be generated by methodological differences and statistical shortcomings in data analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28808549/characterization-of-natural-variation-in-north-american-atlantic-salmon-populations-salmonidae-salmo-salar-at-a-locus-with-a-major-effect-on-sea-age
#8
Henrik Kusche, Guillaume Côté, Cécilia Hernandez, Eric Normandeau, Damien Boivin-Delisle, Louis Bernatchez
Age at maturity is a key life-history trait of most organisms. In anadromous salmonid fishes such as Atlantic Salmon (Salmo salar), age at sexual maturity is associated with sea age, the number of years spent at sea before the spawning migration. For the first time, we investigated the presence of two nonsynonymous vgll3 polymorphisms in North American Atlantic Salmon populations that relate to sea age in European salmon and quantified the natural variation at these and two additional candidate SNPs from two other genes...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28808286/source-and-dynamics-of-a-volcanic-caldera-unrest-campi-flegrei-1983-84
#9
Luca De Siena, Giovanni Chiodini, Giuseppe Vilardo, Edoardo Del Pezzo, Mario Castellano, Simona Colombelli, Nicola Tisato, Guido Ventura
Despite their importance for eruption forecasting the causes of seismic rupture processes during caldera unrest are still poorly reconstructed from seismic images. Seismic source locations and waveform attenuation analyses of earthquakes in the Campi Flegrei area (Southern Italy) during the 1983-1984 unrest have revealed a 4-4.5 km deep NW-SE striking aseismic zone of high attenuation offshore Pozzuoli. The lateral features and the principal axis of the attenuation anomaly correspond to the main source of ground uplift during the unrest...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808018/a-genome-tree-of-life-for-the-fungi-kingdom
#10
JaeJin Choi, Sung-Hou Kim
Fungi belong to one of the largest and most diverse kingdoms of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information-based trees ("gene trees"), constructed commonly based on the degree of differences of proteins or DNA sequences of a small number of highly conserved genes common among the population by a multiple sequence alignment (MSA) method. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population depending on the subjective selection of the genes...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807930/transcriptome-association-identifies-regulators-of-wheat-spike-architecture
#11
Yuange Wang, Haopeng Yu, Caihuan Tian, Muhammad Sajjad, Caixia Gao, Yiping Tong, Xiangfeng Wang, Yuling Jiao
The architecture of wheat inflorescence and its complexity is among the most important agronomic traits that influence yield. For example, wheat spikes vary considerably in the number of spikelets, which are specialized reproductive branches, and the number of florets, which are spikelet branches that produce seeds. The large and repetitive nature of the three homologous and highly similar subgenomes of wheat has impeded attempts at using genetic approaches to uncover beneficial alleles that can be utilized for yield improvement...
August 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28807025/changes-in-tibialis-anterior-architecture-affect-the-amplitude-of-surface-electromyograms
#12
Taian M Vieira, Maria Cristina Bisi, Rita Stagni, Alberto Botter
BACKGROUND: Variations in the amplitude of surface electromyograms (EMGs) are typically considered to advance inferences on the timing and degree of muscle activation in different circumstances. Surface EMGs are however affected by factors other than the muscle neural drive. In this study, we use electrical stimulation to investigate whether architectural changes in tibialis anterior (TA), a key muscle for balance and gait, affect the amplitude of surface EMGs. METHODS: Current pulses (500 μs; 2 pps) were applied to the fibular nerve of ten participants, with the ankle at neutral, full dorsi and full plantar flexion positions...
August 14, 2017: Journal of Neuroengineering and Rehabilitation
https://www.readbyqxmd.com/read/28803038/srsf-shape-analysis-for-sequencing-data-reveal-new-differentiating-patterns
#13
Sergiusz Wesolowski, Daniel Vera, Wei Wu
MOTIVATION: Sequencing-based methods to examine fundamental features of the genome, such as gene expression and chromatin structure, rely on inferences from the abundance and distribution of reads derived from Illumina sequencing. Drawing sound inferences from such experiments relies on appropriate mathematical methods to model the distribution of reads along the genome, which has been challenging due to the scale and nature of these data. RESULTS: We propose a new framework (SRSFseq) based on square root slope functions shape analysis to analyse Illumina sequencing data...
July 27, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28802133/sorptive-removal-of-ionizable-antibiotic-sulfamethazine-from-aqueous-solution-by-graphene-oxide-coated-biochar-nanocomposites-influencing-factors-and-mechanism
#14
Danlian Huang, Xi Wang, Chen Zhang, Guangming Zeng, Zhiwei Peng, Jin Zhou, Min Cheng, Rongzhong Wang, Zhengxun Hu, Xiang Qin
Significant concerns have been raised over antibiotics pollution in aquatic environments in recent years. In this study, sorption of sulfamethazine (SMT) by novel graphene oxide-coated biochar nanocomposites (GO-BC) based on graphene oxide (GO) with bamboo sawdust biochar (BC) was investigated. In comparison with the original BC, the sorption capacity of GO-BC for SMT increased by 1.14 times. Sorption of SMT onto GO-BC was proved to be dominantly by chemisorption, and Freundlich isotherm described the sorption adequately...
July 31, 2017: Chemosphere
https://www.readbyqxmd.com/read/28802020/investigating-the-diversity-of-effector-genes-in-the-banana-pathogen-fusarium-oxysporum-f-sp-cubense-reveals-evidence-of-horizontal-gene-transfer
#15
Elizabeth Czislowski, Sam Fraser-Smith, Manuel Zander, Wayne T O'Neill, Rachel A Meldrum, Lucy T T Tran-Nguyen, Jacqueline Batley, Elizabeth A B Aitken
It is hypothesised that the virulence of phytopathogenic fungi is mediated through the secretion of small effector proteins that interfere with the defence responses of the host plant. In Fusarium oxysporum, one family of effectors, the secreted in xylem (SIX) genes, have been identified. We sought to characterise the diversity and evolution of the SIX genes in the banana-infecting lineages of F. oxysporum f.sp. cubense (Foc). Whole-genome sequencing data was generated for the 23 genetic lineages of Foc, which were subsequently queried for the 14 known SIX genes (SIX1-SIX14)...
August 12, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28795686/hdl-and-atherosclerotic-cardiovascular-disease-genetic-insights-into-complex-biology
#16
REVIEW
Robert S Rosenson, H Bryan Brewer, Philip J Barter, Johan L M Björkegren, M John Chapman, Daniel Gaudet, Daniel Seung Kim, Eric Niesor, Kerry-Anne Rye, Frank M Sacks, Jean-Claude Tardif, Robert A Hegele
Plasma levels of HDL cholesterol (HDL-C) predict the risk of cardiovascular disease at the epidemiological level, but a direct causal role for HDL in cardiovascular disease remains controversial. Studies in animal models and humans with rare monogenic disorders link only particular HDL-associated mechanisms with causality, including those mechanisms related to particle functionality rather than cholesterol content. Mendelian randomization studies indicate that most genetic variants that affect a range of pathways that increase plasma HDL-C levels are not usually associated with reduced risk of cardiovascular disease, with some exceptions, such as cholesteryl ester transfer protein variants...
August 10, 2017: Nature Reviews. Cardiology
https://www.readbyqxmd.com/read/28794409/annotating-pathogenic-non-coding-variants-in-genic-regions
#17
Sahar Gelfman, Quanli Wang, K Melodi McSweeney, Zhong Ren, Francesca La Carpia, Matt Halvorsen, Kelly Schoch, Fanni Ratzon, Erin L Heinzen, Michael J Boland, Slavé Petrovski, David B Goldstein
Identifying the underlying causes of disease requires accurate interpretation of genetic variants. Current methods ineffectively capture pathogenic non-coding variants in genic regions, resulting in overlooking synonymous and intronic variants when searching for disease risk. Here we present the Transcript-inferred Pathogenicity (TraP) score, which uses sequence context alterations to reliably identify non-coding variation that causes disease. High TraP scores single out extremely rare variants with lower minor allele frequencies than missense variants...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28794385/association-between-a-ccl17-genetic-variant-and-risk-of-coronary-artery-disease-in-a-chinese-han-population
#18
Yicong Ye, Xinglin Yang, Bo Long, Haiyu Pang, Yicheng Zhu, Shuyang Zhang
BACKGROUND: In the present study we investigated the effects of genetic variations in the C-C motif chemokine ligand 17 (CCL17) gene on serum CCL17 levels and risk of coronary artery disease (CAD).Methods and Results:A case-control study was conducted to determine causal inferences amongCCL17single-nucleotide polymorphisms (SNPs), serum CCL17 levels, and risk of CAD. Luciferase assays, electrophoretic mobility shift assays (EMSA), and allele-specific quantitative chromatin immunoprecipitation (ChIP) assays were used to assess the function of the SNPs...
August 8, 2017: Circulation Journal: Official Journal of the Japanese Circulation Society
https://www.readbyqxmd.com/read/28793353/what-thedress-reveals-about-the-role-of-illumination-priors-in-color-perception-and-color-constancy
#19
Stacey Aston, Anya Hurlbert
The disagreement between people who named #theDress (the Internet phenomenon of 2015) "blue and black" versus "white and gold" is thought to be caused by individual differences in color constancy. It is hypothesized that observers infer different incident illuminations, relying on illumination "priors" to overcome the ambiguity of the image. Different experiences may drive the formation of different illumination priors, and these may be indicated by differences in chronotype. We assess this hypothesis, asking whether matches to perceived illumination in the image and/or perceived dress colors relate to scores on the morningness-eveningness questionnaire (a measure of chronotype)...
August 1, 2017: Journal of Vision
https://www.readbyqxmd.com/read/28792649/speciation-as-a-sieve-for-ancestral-polymorphism
#20
Rafael F Guerrero, Matthew W Hahn
Because they are considered rare, balanced polymorphisms are often discounted as crucial constituents of genome-wide variation in sequence diversity. Despite its perceived rarity, however, long-term balancing selection can elevate genetic diversity and significantly affect observed divergence between species. Here, we discuss how ancestral balanced polymorphisms can be 'sieved' by the speciation process, which sorts them unequally across descendant lineages. After speciation, ancestral balancing selection is revealed by genomic regions of high divergence between species...
August 9, 2017: Molecular Ecology
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