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variational inference

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https://www.readbyqxmd.com/read/29351013/leaf-form-evolution-in-viburnum-parallels-variation-within-individual-plants
#1
Elizabeth L Spriggs, Samuel B Schmerler, Erika J Edwards, Michael J Donoghue
Few studies have critically evaluated how morphological variation within individual organisms corresponds to variation within and among species. Subindividual variation in plants facilitates such studies because their indeterminate modular growth generates multiple serially homologous structures along growing axes. Focusing on leaf form, we evaluate how subindividual trait variation relates to leaf evolution across Viburnum, a clade of woody angiosperms. In Viburnum we infer multiple independent origins of wide/lobed leaves with toothed margins from ancestors with elliptical, smooth-margined leaves...
February 2018: American Naturalist
https://www.readbyqxmd.com/read/29349517/a-novel-genomic-signature-predicting-fdg-uptake-in-diverse-metastatic-tumors
#2
Aurora Crespo-Jara, Maria Carmen Redal-Peña, Elena Maria Martinez-Navarro, Manuel Sureda, Francisco Jose Fernandez-Morejon, Francisco J Garcia-Cases, Ramon Gonzalez Manzano, Antonio Brugarolas
BACKGROUND: Building a universal genomic signature predicting the intensity of FDG uptake in diverse metastatic tumors may allow us to understand better the biological processes underlying this phenomenon and their requirements of glucose uptake. METHODS: A balanced training set (n = 71) of metastatic tumors including some of the most frequent histologies, with matched PET/CT quantification measurements and whole human genome gene expression microarrays, was used to build the signature...
January 18, 2018: EJNMMI Research
https://www.readbyqxmd.com/read/29347355/inverse-ising-problem-in-continuous-time-a-latent-variable-approach
#3
Christian Donner, Manfred Opper
We consider the inverse Ising problem: the inference of network couplings from observed spin trajectories for a model with continuous time Glauber dynamics. By introducing two sets of auxiliary latent random variables we render the likelihood into a form which allows for simple iterative inference algorithms with analytical updates. The variables are (1) Poisson variables to linearize an exponential term which is typical for point process likelihoods and (2) Pólya-Gamma variables, which make the likelihood quadratic in the coupling parameters...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29343499/a-population-phylogenetic-view-of-mitochondrial-heteroplasmy
#4
Peter R Wilton, Arslan Zaidi, Kateryna Makova, Rasmus Nielsen
The mitochondrion has recently emerged as an active player in a myriad of cellular processes. Additionally, it was recently shown that more than 200 diseases are known to be linked to variants in mitochondrial DNA or in nuclear genes interacting with mitochondria. This has reinvigorated interest in its biology and population genetics. Mitochondrial heteroplasmy, or genotypic variation of mitochondria within an individual, is now understood to be common in humans and important in human health. However, it is still not possible to make quantitative predictions about the inheritance of heteroplasmy and its proliferation within the body, partly due to the lack of an appropriate model...
January 17, 2018: Genetics
https://www.readbyqxmd.com/read/29342401/matched-placental-and-circulating-plasmodium-falciparum-parasites-are-genetically-homologous-at-the-var2csa-id1-dbl2x-locus-by-deep-sequencing
#5
Andreea Waltmann, Jaymin C Patel, Kyaw L Thwai, Nicholas J Hathaway, Christian M Parobek, Achille Massougbodji, Nadine Fievet, Jeffery A Bailey, Philippe Deloron, Jonathan J Juliano, Nicaise Tuikue Ndam, Steven R Meshnick
In pregnancy-associated malaria, infected erythrocytes accumulate in the placenta. It is unclear if in polyclonal infections this results in distinct peripheral and placental parasite populations. We used long amplicon deep sequencing of Plasmodium falciparum var2csa ID1-DBL2X from 15 matched peripheral and placental samples collected at delivery from a high transmission area to determine genetic homology. Despite substantial sequence variation and detecting 23 haplotypes, the matched pairs mostly contained the same genetic variants, with 11 pairs sharing 100% of their variants, whereas others showed some heterogeneity...
January 2018: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29342249/splice-expression-variation-analysis-seva-for-inter-tumor-heterogeneity-of-gene-isoform-usage-in-cancer
#6
Bahman Afsari, Theresa Guo, Michael Considine, Liliana Florea, Luciane T Kagohara, Genevieve L Stein-O'Brien, Dylan Kelley, Emily Flam, Kristina D Zambo, Patrick K Ha, Donald Geman, Michael F Ochs, Joseph A Califano, Daria A Gaykalova, Alexander V Favorov, Elana J Fertig
Motivation: Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in normal tissues, which have stable regulation of gene splicing. Pathological conditions, such as cancer, can have broken regulation of splicing that increases the heterogeneity of the expression of splice variants. Inferring events with such differential heterogeneity in gene isoform usage requires new statistical approaches...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342197/molecular-discrimination-of-tall-fescue-morphotypes-in-association-with-festuca-relatives
#7
Shyamal K Talukder, Perumal Azhaguvel, Konstantin Chekhovskiy, Malay C Saha
Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species used as forage and turf, and in conservation plantings. There are three morphotypes in hexaploid tall fescue: Continental, Mediterranean and Rhizomatous. This study was conducted to develop morphotype-specific molecular markers to distinguish Continental and Mediterranean tall fescues, and establish their relationships with other species of the Festuca genus for genomic inference. Chloroplast sequence variation and simple sequence repeat (SSR) polymorphism were explored in 12 genotypes of three tall fescue morphotypes and four Festuca species...
2018: PloS One
https://www.readbyqxmd.com/read/29340002/performance-changes-of-elite-paralympic-judo-athletes-during-a-paralympic-games-cycle-a-case-study-with-the-brazilian-national-team
#8
Irineu Loturco, Lucas A Pereira, Ciro Winckler, Jaime R Bragança, Roger A da Fonseca, Ronaldo Kobal, Cesar C Cal Abad, Katia Kitamura, Fabio Y Nakamura, Emerson Franchini
The aim of this study was to describe the variations in power performance of elite Paralympic judo athletes across three consecutive training cycles of preparation for the ParaPan American Games, the World Championship and the Paralympic Games. Eleven Paralympic judokas from the Brazilian National team participated in this study. They were repeatedly assessed using squat and countermovement jumps, mean propulsive power (MPP) in the jump-squat (JS), the bench press and prone bench pull at several moments of the preparation...
December 2017: Journal of Human Kinetics
https://www.readbyqxmd.com/read/29337998/cognitive-mechanisms-for-inferring-the-meaning-of-novel-signals-during-symbolisation
#9
Justin Sulik
As participants repeatedly interact using graphical signals (as in a game of Pictionary), the signals gradually shift from being iconic (or motivated) to being symbolic (or arbitrary). The aim here is to test experimentally whether this change in the form of the signal implies a concomitant shift in the inferential mechanisms needed to understand it. The results show that, during early, iconic stages, there is more reliance on creative inferential processes associated with insight problem solving, and that the recruitment of these cognitive mechanisms decreases over time...
2018: PloS One
https://www.readbyqxmd.com/read/29329302/phylogeography-and-conservation-genetics-of-the-rare-and-relict-bretschneidera-sinensis-akaniaceae
#10
Mei-Na Wang, Lei Duan, Qi Qiao, Zheng-Feng Wang, Elizabeth A Zimmer, Zhong-Chao Li, Hong-Feng Chen
Bretschneidera sinensis, a class-I protected wild plant in China, is a relic of the ancient Tertiary tropical flora endemic to Asia. However, little is known about its genetics and phylogeography. To elucidate the current phylogeographic patterns and infer the historical population dynamics of B. sinensis, and to make recommendations for its conservation, three non-coding regions of chloroplast DNA (trnQ-rps16, rps8-rps11, and trnT-trnL) were amplified and sequenced across 256 individuals from 23 populations of B...
2018: PloS One
https://www.readbyqxmd.com/read/29329053/long-term-safety-area-tracking-lt-sat-with-online-failure-detection-and-recovery-for-robotic-minimally-invasive-surgery
#11
Veronica Penza, Xiaofei Du, Danail Stoyanov, Antonello Forgione, Leonardo S Mattos, Elena De Momi
Despite the benefits introduced by robotic systems in abdominal Minimally Invasive Surgery (MIS), major complications can still affect the outcome of the procedure, such as intra-operative bleeding. One of the causes is attributed to accidental damages to arteries or veins by the surgical tools, and some of the possible risk factors are related to the lack of sub-surface visibilty. Assistive tools guiding the surgical gestures to prevent these kind of injuries would represent a relevant step towards safer clinical procedures...
December 22, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/29328224/magnetometry-using-fluorescence-of-sodium-vapor
#12
Tingwei Fan, Lei Zhang, Xuezong Yang, Shuzhen Cui, Tianhua Zhou, Yan Feng
Magnetic resonance of sodium fluorescence is studied with varying laser intensity, duty cycle, and field strength. A magnetometer based on a sodium vapor cell filled with He buffer gas is demonstrated, using a single amplitude-modulated laser beam. With a 589 nm laser tuned at the D1 or D2 line, the magnetic field is inferred from the variation of fluorescence. A magnetic field sensitivity of 150  pT/Hz is achieved at the D1 line. The work is an important step toward sensitive remote magnetometry with mesospheric sodium...
January 1, 2018: Optics Letters
https://www.readbyqxmd.com/read/29325559/pangenome-analyses-of-the-wheat-pathogen-zymoseptoria-tritici-reveal-the-structural-basis-of-a-highly-plastic-eukaryotic-genome
#13
Clémence Plissonneau, Fanny E Hartmann, Daniel Croll
BACKGROUND: Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence...
January 11, 2018: BMC Biology
https://www.readbyqxmd.com/read/29324975/strong-population-bottleneck-and-repeated-demographic-expansions-of-populus-adenopoda-salicaceae-in-subtropical-china
#14
Liqiang Fan, Honglei Zheng, Richard I Milne, Lei Zhang, Kangshan Mao
Background and Aims: Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few poplars that naturally occur in this subtropical area. Methods: Genetic variations across the range of the species in subtropical China were surveyed using ten nuclear microsatellite loci and four chloroplast fragments (matK, trnG-psbK, psbK-psbI and ndhC-trnV)...
January 6, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29324781/neuraminidase-inhibitor-susceptibility-and-neuraminidase-enzyme-kinetics-of-human-influenza-a-and-b-viruses-circulating-in-thailand-in-2010-2015
#15
Nipaporn Tewawong, Bindumadhav M Marathe, Yong Poovorawan, Sompong Vongpunsawad, Richard J Webby, Elena A Govorkova
Amino acid substitutions within or near the active site of the viral neuraminidase (NA) may affect influenza virus fitness. In influenza A(H3N2) and B viruses circulating in Thailand between 2010 and 2015, we identified several NA substitutions that were previously reported to be associated with reduced inhibition by NA inhibitors (NAIs). To study the effect of these substitutions on the enzymatic properties of NA and on virus characteristics, we generated recombinant influenza viruses possessing either a wild type (WT) NA or an NA with a single I222V, S331G, or S331R substitution [in influenza A(H3N2) viruses] or a single D342S, A395T, A395V, or A395D NA substitution (in influenza B viruses)...
2018: PloS One
https://www.readbyqxmd.com/read/29324746/the-relationship-between-observational-scale-and-explained-variance-in-benthic-communities
#16
Alison M Flanagan, Roger D Flood, Michael G Frisk, Corey D Garza, Glenn R Lopez, Nicole P Maher, Robert M Cerrato
This study addresses the impact of spatial scale on explaining variance in benthic communities. In particular, the analysis estimated the fraction of community variation that occurred at a spatial scale smaller than the sampling interval (i.e., the geographic distance between samples). This estimate is important because it sets a limit on the amount of community variation that can be explained based on the spatial configuration of a study area and sampling design. Six benthic data sets were examined that consisted of faunal abundances, common environmental variables (water depth, grain size, and surficial percent cover), and sonar backscatter treated as a habitat proxy (categorical acoustic provinces)...
2018: PloS One
https://www.readbyqxmd.com/read/29321854/phylogenetic-relationships-and-phylogeography-of-relevant-lineages-within-the-complex-campanulaceae-family-in-macaronesia
#17
Tiago Menezes, Maria M Romeiras, Miguel M de Sequeira, Mónica Moura
Macaronesia has long been recognized as a natural model for studying evolutionary processes in plant diversification. Several studies have attempted to focus on single lineages, and few have covered the diversification of a family across all the archipelagos. We used a comprehensive sample to clarify the phylogenetic relationships and the biogeographic history of the Macaronesian Campanulaceae. Hypotheses related to the colonization of these archipelagos will be used to examine the diversification patterns of different lineages...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29321847/search-and-foraging-behaviors-from-movement-data-a-comparison-of-methods
#18
Ashley Bennison, Stuart Bearhop, Thomas W Bodey, Stephen C Votier, W James Grecian, Ewan D Wakefield, Keith C Hamer, Mark Jessopp
Search behavior is often used as a proxy for foraging effort within studies of animal movement, despite it being only one part of the foraging process, which also includes prey capture. While methods for validating prey capture exist, many studies rely solely on behavioral annotation of animal movement data to identify search and infer prey capture attempts. However, the degree to which search correlates with prey capture is largely untested. This study applied seven behavioral annotation methods to identify search behavior from GPS tracks of northern gannets (Morus bassanus), and compared outputs to the occurrence of dives recorded by simultaneously deployed time-depth recorders...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29320688/coevolutionary-landscape-of-kinase-family-proteins-sequence-probabilities-and-functional-motifs
#19
Allan Haldane, William F Flynn, Peng He, Ronald M Levy
The protein kinase catalytic domain is one of the most abundant domains across all branches of life. Although kinases share a common core function of phosphoryl-transfer, they also have wide functional diversity and play varied roles in cell signaling networks, and for this reason are implicated in a number of human diseases. This functional diversity is primarily achieved through sequence variation, and uncovering the sequence-function relationships for the kinase family is a major challenge. In this study we use a statistical inference technique inspired by statistical physics, which builds a coevolutionary "Potts" Hamiltonian model of sequence variation in a protein family...
January 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29319883/trait-specific-processes-of-convergence-and-conservatism-shape-ecomorphological-evolution-in-ground-dwelling-squirrels
#20
Bryan S McLean, Kristofer M Helgen, H Thomas Goodwin, Joseph A Cook
Our understanding of mechanisms operating over deep timescales to shape phenotypic diversity often hinges on linking variation in one or few trait(s) to specific evolutionary processes. When distinct processes are capable of similar phenotypic signatures, however, identifying these drivers is difficult. We explored ecomorphological evolution across a radiation of ground-dwelling squirrels whose history includes convergence and constraint, two processes that can yield similar signatures of standing phenotypic diversity...
January 10, 2018: Evolution; International Journal of Organic Evolution
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