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https://www.readbyqxmd.com/read/28227987/incorporating-shape-prior-into-active-contours-with-a-sparse-linear-combination-of-training-shapes-application-to-corpus-callosum-segmentation
#1
Mohammad M Farhangi, Hichem Frigui, Robert Bert, Amir A Amini, Mohammad M Farhangi, Hichem Frigui, Robert Bert, Amir A Amini, Robert Bert, Mohammad M Farhangi, Amir A Amini, Hichem Frigui
In this paper, a novel method of embedding shape information into level set image segmentation is proposed. Our method is based on inferring shape variations by a sparse linear combination of instances in the shape repository. Given a sufficient number of training shapes with variations, a new shape can be approximated by a linear span of training shapes associated with those variations. At each step of curve evolution the curve is moved to minimize Chan-Vese energy functional as well as toward the best approximation based on a linear combination of training samples...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28223505/light-driven-growth-in-amazon-evergreen-forests-explained-by-seasonal-variations-of-vertical-canopy-structure
#2
Hao Tang, Ralph Dubayah
Light-regime variability is an important limiting factor constraining tree growth in tropical forests. However, there is considerable debate about whether radiation-induced green-up during the dry season is real, or an apparent artifact of the remote-sensing techniques used to infer seasonal changes in canopy leaf area. Direct and widespread observations of vertical canopy structures that drive radiation regimes have been largely absent. Here we analyze seasonal dynamic patterns between the canopy and understory layers in Amazon evergreen forests using observations of vertical canopy structure from a spaceborne lidar...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28219035/conceptualizing-agency-folkpsychological-and-folkcommunicative-perspectives-on-plants
#3
Bethany L Ojalehto, Douglas L Medin, Salino G García
The present research addresses cultural variation in concepts of agency. Across two experiments, we investigate how Indigenous Ngöbe of Panama and US college students interpret and make inferences about nonhuman agency, focusing on plants as a critical test case. In Experiment 1, participants predicted goal-directed actions for plants and other nonhuman kinds and judged their capacities for intentional agency. Goal-directed action is pervasive among living kinds and as such we expected cultural agreement on these predictions...
February 17, 2017: Cognition
https://www.readbyqxmd.com/read/28213113/a-variational-bayesian-inference-method-for-parametric-imaging-of-pet-data
#4
M Castellaro, G Rizzo, M Tonietto, M Veronese, F E Turkheimer, M A Chappell, A Bertoldo
In dynamic Positron Emission Tomography (PET) studies, compartmental models provide the richest information on the tracer kinetics of the tissue. Inverting such models at the voxel level is however quite challenging due to the low signal-to-noise ratio of the time activity curves. In this study, we propose the use of a Variational Bayesian (VB) approach to efficiently solve this issue and thus obtain robust quantitative parametric maps. VB was adapted to the non-uniform noise distribution of PET data. Moreover, we propose a novel hierarchical scheme to define the model parameter priors directly from the images in case such information are not available from the literature, as often happens with new PET tracers...
February 14, 2017: NeuroImage
https://www.readbyqxmd.com/read/28211151/phenotypic-distribution-models-corroborate-species-distribution-models-a-shift-in-the-role-and-prevalence-of-a-dominant-prairie-grass-in-response-to-climate-change
#5
Adam B Smith, Jacob Alsdurf, Mary Knapp, Sara G Baer, Loretta C Johnson
Phenotypic variation within species can vary widely across environmental gradients but forecasts of species' responses to environmental change often assume species respond homogenously across their ranges. We compared predictions from species and phenotype distribution models under future climate scenarios for Andropogon gerardii, a widely distributed, dominant grass found throughout the central United States. Phenotype data on aboveground biomass, height, leaf width, and chlorophyll content were obtained from 33 populations spanning a ~1000-km gradient that encompassed the majority of the species' environmental range...
February 17, 2017: Global Change Biology
https://www.readbyqxmd.com/read/28208453/nonparametric-bayesian-inference-of-the-microcanonical-stochastic-block-model
#6
Tiago P Peixoto
A principled approach to characterize the hidden structure of networks is to formulate generative models and then infer their parameters from data. When the desired structure is composed of modules or "communities," a suitable choice for this task is the stochastic block model (SBM), where nodes are divided into groups, and the placement of edges is conditioned on the group memberships. Here, we present a nonparametric Bayesian method to infer the modular structure of empirical networks, including the number of modules and their hierarchical organization...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208137/structural-and-referent-based-effects-on-prosodic-expression-in-russian
#7
Tatiana Luchkina, Jennifer S Cole
This study examines prosody in read productions of two published narratives by 15 Russian speakers. Two distinct sources of variation in acoustic-prosodic expression are considered: structural and referent-based. Structural effects refer to the particular linearization of words in a sentence or phrase. Referent-based effects relate to the semantic and pragmatic characteristics of the discourse referent of a word, and to grammatical roles that are partially dependent on referent characteristics. Here, we examine referent animacy and the related grammatical function of subjecthood, and the relative accessibility or information status of a word...
2016: Phonetica
https://www.readbyqxmd.com/read/28204784/a-poissonian-model-of-indel-rate-variation-for-phylogenetic-tree-inference
#8
Yongliang Zhai, Alexandre Bouchard-Côté
No abstract text is available yet for this article.
February 16, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28202728/satellite-based-assessment-of-yield-variation-and-its-determinants-in-smallholder-african-systems
#9
Marshall Burke, David B Lobell
The emergence of satellite sensors that can routinely observe millions of individual smallholder farms raises possibilities for monitoring and understanding agricultural productivity in many regions of the world. Here we demonstrate the potential to track smallholder maize yield variation in western Kenya, using a combination of 1-m Terra Bella imagery and intensive field sampling on thousands of fields over 2 y. We find that agreement between satellite-based and traditional field survey-based yield estimates depends significantly on the quality of the field-based measures, with agreement highest ([Formula: see text] up to 0...
February 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28201983/comparative-analysis-of-the-mitochondrial-genomes-of-colletotrichum-gloeosporioides-sensu-lato-insights-into-the-evolution-of-a-fungal-species-complex-interacting-with-diverse-plants
#10
Xiaofei Liang, Xianglin Tian, Wenkui Liu, Tingyu Wei, Wei Wang, Qiuyue Dong, Bo Wang, Yanan Meng, Rong Zhang, Mark L Gleason, Guangyu Sun
BACKGROUND: The fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show considerable variation in host and tissue adaptation strategies. Accurate species delimitation in C. gloeosporioides s.l. is very challenging due to nascent lineage boundaries and phenotypic plasticity, which strongly impedes studies of the complex's host-interaction biology...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198357/cgcorrect-a-method-to-correct-for-confounding-cell-cell-variation-due-to-cell-growth-in-single-cell-transcriptomics
#11
Thomas Blasi, Florian Buettner, Michael Strasser, Carsten Marr, Fabian Theis
MOTIVATION: Accessing gene expression at the single cell level has unraveled often large heterogeneity among seemingly homogeneous cells, which remained obscured in traditional population based approaches. The computational analysis of single-cell transcriptomics data, however, still imposes unresolved challenges with respect to normalization, visualization and modeling the data. One such issue are differences in cell size, which introduce additional variability into the data, for which appropriate normalization techniques are needed...
February 15, 2017: Physical Biology
https://www.readbyqxmd.com/read/28196149/climatic-and-geographic-predictors-of-life-history-variation-in-eastern-massasauga-sistrurus-catenatus-a-range-wide-synthesis
#12
Eric T Hileman, Richard B King, John M Adamski, Thomas G Anton, Robyn L Bailey, Sarah J Baker, Nickolas D Bieser, Thomas A Bell, Kristin M Bissell, Danielle R Bradke, Henry Campa, Gary S Casper, Karen Cedar, Matthew D Cross, Brett A DeGregorio, Michael J Dreslik, Lisa J Faust, Daniel S Harvey, Robert W Hay, Benjamin C Jellen, Brent D Johnson, Glenn Johnson, Brooke D Kiel, Bruce A Kingsbury, Matthew J Kowalski, Yu Man Lee, Andrew M Lentini, John C Marshall, David Mauger, Jennifer A Moore, Rori A Paloski, Christopher A Phillips, Paul D Pratt, Thomas Preney, Kent A Prior, Andrew Promaine, Michael Redmer, Howard K Reinert, Jeremy D Rouse, Kevin T Shoemaker, Scott Sutton, Terry J VanDeWalle, Patrick J Weatherhead, Doug Wynn, Anne Yagi
Elucidating how life history traits vary geographically is important to understanding variation in population dynamics. Because many aspects of ectotherm life history are climate-dependent, geographic variation in climate is expected to have a large impact on population dynamics through effects on annual survival, body size, growth rate, age at first reproduction, size-fecundity relationship, and reproductive frequency. The Eastern Massasauga (Sistrurus catenatus) is a small, imperiled North American rattlesnake with a distribution centered on the Great Lakes region, where lake effects strongly influence local conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28196110/ethnic-variation-in-medical-and-lifestyle-risk-factors-for-b-cell-non-hodgkin-lymphoma-a-case-control-study-among-israelis-and-palestinians
#13
Geffen Kleinstern, Rania Abu Seir, Riki Perlman, Areej Khatib, Ziad Abdeen, Husein Elyan, Ronit Nirel, Gail Amir, Asad Ramlawi, Fouad Sabatin, Paolo Boffetta, Eldad J Dann, Meirav Kedmi, Martin Ellis, Arnon Nagler, Dina Ben Yehuda, Ora Paltiel
BACKGROUND: Risk factors for B-cell non-Hodgkin lymphoma (B-NHL) have not been assessed among Palestinian Arabs (PA) and Israeli Jews (IJ). METHODS: In a case-control study we investigated self-reported medical and lifestyle exposures, reporting odds ratios (ORs) and 95% confidence intervals [CIs], by ethnicity, for overall B-NHL and subtypes. RESULTS: We recruited 823 cases and 808 healthy controls. Among 307 PA/516 IJ B-NHL cases (mean age at diagnosis = 51 [±17] versus 60 [±15] years, respectively) subtype distributions differed, with diffuse large B-cell lymphoma (DLBCL) being prominent among PA (71%) compared to IJ (41%); follicular lymphoma (FL), was observed in 14% versus 28%, and marginal zone lymphoma, in 2% versus 14%, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28193880/spatial-and-temporal-dynamics-of-superspreading-events-in-the-2014-2015-west-africa-ebola-epidemic
#14
Max S Y Lau, Benjamin Douglas Dalziel, Sebastian Funk, Amanda McClelland, Amanda Tiffany, Steven Riley, C Jessica E Metcalf, Bryan T Grenfell
The unprecedented scale of the Ebola outbreak in Western Africa (2014-2015) has prompted an explosion of efforts to understand the transmission dynamics of the virus and to analyze the performance of possible containment strategies. Models have focused primarily on the reproductive numbers of the disease that represent the average number of secondary infections produced by a random infectious individual. However, these population-level estimates may conflate important systematic variation in the number of cases generated by infected individuals, particularly found in spatially localized transmission and superspreading events...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28187131/genome-size-cytogenetic-data-and-transferability-of-est-ssrs-markers-in-wild-and-cultivated-species-of-the-genus-theobroma-l-byttnerioideae-malvaceae
#15
Rangeline Azevedo da Silva, Gustavo Souza, Lívia Santos Lima Lemos, Uilson Vanderlei Lopes, Nara Geórgia Ribeiro Braz Patrocínio, Rafael Moysés Alves, Lucília Helena Marcellino, Didier Clement, Fabienne Micheli, Karina Peres Gramacho
The genus Theobroma comprises several trees species native to the Amazon. Theobroma cacao L. plays a key economic role mainly in the chocolate industry. Both cultivated and wild forms are described within the genus. Variations in genome size and chromosome number have been used for prediction purposes including the frequency of interspecific hybridization or inference about evolutionary relationships. In this study, the nuclear DNA content, karyotype and genetic diversity using functional microsatellites (EST-SSR) of seven Theobroma species were characterized...
2017: PloS One
https://www.readbyqxmd.com/read/28185895/using-the-small-subunit-of-nuclear-ribosomal-dna-to-reveal-the-phylogenetic-position-of-the-plerocercoid-larvae-of-spirometra-tapeworms
#16
Xi Zhang, Jiang Yang Duan, Zhong Quan Wang, Peng Jiang, Ruo Dan Liu, Jing Cui
Although medically important, the systematics of Spirometra and the taxonomic position of S. erinaceieuropaei remain unclear. In this study, the 18S rDNA gene of S. erinaceieuropaei sparganum from naturally infected frogs caught in 14 geographical locations of China was sequenced. In addition, all available 18S sequences of the family Diphyllobothriidae in the Genbank database were included to reconstruct the phylogeny of diphyllobothriid tapeworms. The secondary structure model of the 18S rDNA was also predicated to further explore the sequence variation...
February 6, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28185551/assisted-transcriptome-reconstruction-and-splicing-orthology
#17
Samuel Blanquart, Jean-Stéphane Varré, Paul Guertin, Amandine Perrin, Anne Bergeron, Krister M Swenson
BACKGROUND: Transcriptome reconstruction, defined as the identification of all protein isoforms that may be expressed by a gene, is a notably difficult computational task. With real data, the best methods based on RNA-seq data identify barely 21 % of the expressed transcripts. While waiting for algorithms and sequencing techniques to improve - as has been strongly suggested in the literature - it is important to evaluate assisted transcriptome prediction; this is the question of how alternative transcription in one species performs as a predictor of protein isoforms in another relatively close species...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28183833/cytogeography-of-the-subalpine-marsh-marigold-polyploid-complex-caltha-leptosepala-s-l-ranunculaceae
#18
Keir M Wefferling, Sílvia Castro, João Loureiro, Mariana Castro, Daniela Tavares, Sara B Hoot
PREMISE OF THE STUDY: Unrecognized variation in ploidy level can lead to an underestimation of species richness and a misleading delineation of geographic range. Caltha leptosepala (Ranunculaceae) comprises a complex of hexaploids (6x), rare nonaploids (9x), and dodecaploids (12x), all with unknown distributions. We delineate the geographic distribution and contact zones of the cytotypes, investigate morphologies of cytotypes and subspecies, and discuss the biogeography and evolutionary history of the polyploid complex...
February 9, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28183358/genetic-diversity-and-population-structure-of-the-primary-malaria-vector-anopheles-sinensis-diptera-culicidae-in-china-inferred-by-cox1-gene
#19
Xinyu Feng, Libin Huang, Lin Lin, Manni Yang, Yajun Ma
BACKGROUND: Anopheles sinensis is a primary vector for Plasmodium vivax malaria in most regions of China. A comprehensive understanding of genetic variation and structure of the mosquito would be of benefit to the vector control and in a further attempt to contribute to malaria elimination in China. However, there is only inadequate population genetic data pertaining to An. sinensis currently. METHODS: Genetic variations and structure among populations of An. sinensis was examined and analyzed based on the nucleotide sequences of a 662 nt variable region of the mitochondrial cox1 gene among 15 populations from 20 collection sites in China...
February 10, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28177780/calculating-higher-order-moments-of-phylogenetic-stochastic-mapping-summaries-in-linear-time
#20
Amrit Dhar, Vladimir N Minin
Stochastic mapping is a simulation-based method for probabilistically mapping substitution histories onto phylogenies according to continuous-time Markov models of evolution. This technique can be used to infer properties of the evolutionary process on the phylogeny and, unlike parsimony-based mapping, conditions on the observed data to randomly draw substitution mappings that do not necessarily require the minimum number of events on a tree. Most stochastic mapping applications simulate substitution mappings only to estimate the mean and/or variance of two commonly used mapping summaries: the number of particular types of substitutions (labeled substitution counts) and the time spent in a particular group of states (labeled dwelling times) on the tree...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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