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https://www.readbyqxmd.com/read/27914203/multiple-processes-drive-genetic-structure-of-humpback-whale-megaptera-novaeangliae-populations-across-spatial-scales
#1
Francine Kershaw, Inês Carvalho, Jacqueline Loo, Cristina Pomilla, Peter B Best, Ken P Findlay, Salvatore Cerchio, Tim Collins, Marcia H Engel, Gianna Minton, Peter Ersts, Jaco Barendse, P G H Kotze, Yvette Razafindrakoto, Solange Ngouessono, Michael Meÿer, Meredith Thorton, Howard C Rosenbaum
Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3,575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample, and males and females separately, we assessed genetic diversity, tested for genetic differentiation between putative populations and isolation by distance, estimated the number of genetic clusters without a priori population information, and estimated rates of gene flow using maximum likelihood and Bayesian approaches...
December 3, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27913348/automatic-refinement-strategies-for-manual-initialization-of-object-trackers
#2
Hao Zhu, Fatih Porikli
Tracking objects across multiple frames is a wellinvestigated problem in computer vision. The majority of the existing algorithms assume an accurate initialization is readily available. However, in many real-life settings, in particular for applications where the video is streaming in real-time, the initialization has to be provided by a human operator. This limitation raises an inevitable uncertainty issue. Here, we first collect a large and new dataset of inputs that consists of more than 20K human initialization clicks, called as HIC, by several subjects under three practical user interface scenarios for the popular TB50 tracking benchmark...
December 1, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/27912022/inferring-species-interactions-from-co-occurrence-data-with-markov-networks
#3
David J Harris
Inferring species interactions from co-occurrence data is one of the most controversial tasks in community ecology. One difficulty is that a single pairwise interaction can ripple through an ecological network and produce surprising indirect consequences. For example, the negative correlation between two competing species can be reversed in the presence of a third species that outcompetes both of them. Here, I apply models from statistical physics, called Markov networks or Markov random fields, that can predict the direct and indirect consequences of any possible species interaction matrix...
December 2016: Ecology
https://www.readbyqxmd.com/read/27911851/inherited-variants-affecting-rna-editing-may-contribute-to-ovarian-cancer-susceptibility-results-from-a-large-scale-collaboration
#4
Jennifer B Permuth, Brett Reid, Madalene Earp, Y Ann Chen, Alvaro N A Monteiro, Zhihua Chen, Aocs Study Group, Georgia Chenevix-Trench, Peter A Fasching, Matthias W Beckmann, Diether Lambrechts, Adriaan Vanderstichele, Els Van Niewenhuyse, Ignace Vergote, Mary Anne Rossing, Jennifer Anne Doherty, Jenny Chang-Claude, Kirsten Moysich, Kunle Odunsi, Marc T Goodman, Yurii B Shvetsov, Lynne R Wilkens, Pamela J Thompson, Thilo Dörk, Natalia Bogdanova, Ralf Butzow, Heli Nevanlinna, Liisa Pelttari, Arto Leminen, Francesmary Modugno, Robert P Edwards, Roberta B Ness, Joseph Kelley, Florian Heitz, Beth Karlan, Jenny Lester, Susanne K Kjaer, Allan Jensen, Graham Giles, Michelle Hildebrandt, Dong Liang, Karen H Lu, Xifeng Wu, Douglas A Levine, Maria Bisogna, Andrew Berchuck, Daniel W Cramer, Kathryn L Terry, Shelley S Tworoger, Elizabeth M Poole, Elisa V Bandera, Brooke Fridley, Julie Cunningham, Stacey J Winham, Sara H Olson, Irene Orlow, Line Bjorge, Lambertus A Kiemeney, Leon Massuger, Tanja Pejovic, Melissa Moffitt, Nhu Le, Linda S Cook, Angela Brooks-Wilson, Linda E Kelemen, Jacek Gronwald, Jan Lubinski, Nicolas Wentzensen, Louise A Brinton, Jolanta Lissowska, Hanna Yang, Estrid Hogdall, Claus Hogdall, Lene Lundvall, Paul D P Pharoah, Honglin Song, Ian Campbell, Diana Eccles, Iain McNeish, Alice Whittemore, Valerie McGuire, Weiva Sieh, Joseph Rothstein, Catherine M Phelan, Harvey Risch, Steven Narod, John McLaughlin, Hoda Anton-Culver, Argyrios Ziogas, Usha Menon, Simon Gayther, Susan J Ramus, Aleksandra Gentry-Maharaj, Celeste Leigh Pearce, Anna H Wu, Jolanta Kupryjanczyk, Agnieszka Dansonka-Mieszkowska, Joellen M Schildkraut, Jin Q Cheng, Ellen L Goode, Thomas A Sellers
RNA editing in mammals is a form of post-transcriptional modification in which adenosine is converted to inosine by the adenosine deaminases acting on RNA (ADAR) family of enzymes. Based on evidence of altered ADAR expression in epithelial ovarian cancers (EOC), we hypothesized that single nucleotide polymorphisms (SNPs) in ADAR genes modify EOC susceptibility, potentially by altering ovarian tissue gene expression. Using directly genotyped and imputed data from 10,891 invasive EOC cases and 21,693 controls, we evaluated the associations of 5,303 SNPs in ADAD1, ADAR, ADAR2, ADAR3, and SND1...
July 12, 2016: Oncotarget
https://www.readbyqxmd.com/read/27911522/projections-for-measuring-the-size-of-the-solar-core-with-neutrino-electron-scattering
#5
Jonathan H Davis
We quantify the amount of data needed in order to measure the size and position of the ^{8}B neutrino production region within the solar core, for experiments looking at elastic scattering between electrons and solar neutrinos. The directions of the electrons immediately after scattering are strongly correlated with the incident directions of the neutrinos; however, this is degraded significantly by the subsequent scattering of these electrons in the detector medium. We generate distributions of such electrons for different neutrino production profiles, and use a maximum likelihood analysis to make projections for future experimental sensitivity...
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27910634/the-upgrade-of-the-thomson-scattering-system-for-measurement-on-the-c-2-c-2u-devices
#6
K Zhai, T Schindler, J Kinley, B Deng, M C Thompson
The C-2/C-2U Thomson scattering system has been substantially upgraded during the latter phase of C-2/C-2U program. A Rayleigh channel has been added to each of the three polychromators of the C-2/C-2U Thomson scattering system. Onsite spectral calibration has been applied to avoid the issue of different channel responses at different spots on the photomultiplier tube surface. With the added Rayleigh channel, the absolute intensity response of the system is calibrated with Rayleigh scattering in argon gas from 0...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27908740/molecular-phylogenetics-of-new-world-searobins-triglidae-prionotinae
#7
David S Portnoy, Stuart C Willis, Elizabeth Hunt, Dominic G Swift, John R Gold, Kevin W Conway
Phylogenetic relationships among members of the New World searobin genera Bellator and Prionotus (Family Triglidae, Subfamily Prionotinae) and among other searobins in the families Triglidae and Peristediidae were investigated using both mitochondrial and nuclear DNA sequences. Phylogenetic hypotheses derived from maximum likelihood and Bayesian methodologies supported a monophyletic Prionotinae that included four well resolved clades of uncertain relationship; three contained species in the genus Prionotus and one contained species in the genus Bellator...
November 28, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27908172/design-of-a-dual-resolution-collimator-for-preclinical-cardiac-spect-with-a-stationary-triple-detector-system
#8
Stephen C Moore, Mi-Ae Park, Zhe Liu, Morgan C Lyon, Lindsay C Johnson, Victor H Lushear, James G Westberg, Scott D Metzler
PURPOSE: One approach to preclinical single-photon emission computed tomography (SPECT) imaging that provides both high resolution and high sensitivity is based on imaging a mouse inside a collimating tube; many magnified pinhole projection images from a small target region, e.g., the heart, can be recorded simultaneously on multiple detectors with little multiplexing since each pinhole aperture's opening angle is restricted to view mostly the target organ. However, to obtain complete data for reconstruction, it may be necessary to scan the mouse through the target region of the tube...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27908169/flexible-mini-gamma-camera-reconstructions-of-extended-sources-using-step-and-shoot-and-list-mode
#9
José Gardiazabal, Philipp Matthies, Jakob Vogel, Benjamin Frisch, Nassir Navab, Sibylle Ziegler, Tobias Lasser
PURPOSE: Hand- and robot-guided mini gamma cameras have been introduced for the acquisition of single-photon emission computed tomography (SPECT) images. Less cumbersome than whole-body scanners, they allow for a fast acquisition of the radioactivity distribution, for example, to differentiate cancerous from hormonally hyperactive lesions inside the thyroid. This work compares acquisition protocols and reconstruction algorithms in an attempt to identify the most suitable approach for fast acquisition and efficient image reconstruction, suitable for localization of extended sources, such as lesions inside the thyroid...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27908152/design-of-a-model-observer-to-evaluate-calcification-detectability-in-breast-tomosynthesis-and-application-to-smoothing-prior-optimization
#10
Koen Michielsen, Johan Nuyts, Lesley Cockmartin, Nicholas Marshall, Hilde Bosmans
PURPOSE: In this work, the authors design and validate a model observer that can detect groups of microcalcifications in a four-alternative forced choice experiment and use it to optimize a smoothing prior for detectability of microcalcifications. METHODS: A channelized Hotelling observer (CHO) with eight Laguerre-Gauss channels was designed to detect groups of five microcalcifications in a background of acrylic spheres by adding the CHO log-likelihood ratios calculated at the expected locations of the five calcifications...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27907229/inferring-the-number-of-contributors-to-complex-dna-mixtures-using-three-methods-exploring-the-limits-of-low-template-dna-interpretation
#11
Lauren E Alfonse, Genesis Tejada, Harish Swaminathan, Desmond S Lun, Catherine M Grgicak
In forensic DNA casework, the interpretation of an evidentiary profile may be dependent upon the assumption on the number of individuals from whom the evidence arose. Three methods of inferring the number of contributors-NOCIt, maximum likelihood estimator, and maximum allele count, were evaluated using 100 test samples consisting of one to five contributors and 0.5-0.016 ng template DNA amplified with Identifiler(®) Plus and PowerPlex(®) 16 HS. Results indicate that NOCIt was the most accurate method of the three, requiring 0...
December 1, 2016: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/27907107/a-time-calibrated-mitogenome-phylogeny-of-catfish-teleostei-siluriformes
#12
Ilias Kappas, Spiros Vittas, Chrysoula N Pantzartzi, Elena Drosopoulou, Zacharias G Scouras
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data...
2016: PloS One
https://www.readbyqxmd.com/read/27907065/statistical-frailty-modeling-for-quantitative-analysis-of-exocytotic-events-recorded-by-live-cell-imaging-rapid-release-of-insulin-containing-granules-is-impaired-in-human-diabetic-%C3%AE-cells
#13
Giuliana Cortese, Nikhil R Gandasi, Sebastian Barg, Morten Gram Pedersen
Hormones and neurotransmitters are released when secretory granules or synaptic vesicles fuse with the cell membrane, a process denoted exocytosis. Modern imaging techniques, in particular total internal reflection fluorescence (TIRF) microscopy, allow the investigator to monitor secretory granules at the plasma membrane before and when they undergo exocytosis. However, rigorous statistical approaches for temporal analysis of such exocytosis data are still lacking. We propose here that statistical methods from time-to-event (also known as survival) analysis are well suited for the problem...
2016: PloS One
https://www.readbyqxmd.com/read/27906607/wald-tests-for-variance-adjusted-equivalence-assessment-with-normal-endpoints
#14
Yue-Ming Chen, Yu-Ting Weng, Xiaoyu Dong, Yi Tsong
Equivalence tests may be tested with mean difference against a margin adjusted for variance. The justification of using variance adjusted non-inferiority or equivalence margin is for the consideration that larger margin should be used with large measurement variability. However, under the null hypothesis, the test statistic does not follow a t-distribution or any well-known distribution even when the measurement is normally distributed. In this study, we investigate asymptotic tests for testing equivalence hypothesis...
December 1, 2016: Journal of Biopharmaceutical Statistics
https://www.readbyqxmd.com/read/27905511/crystallizing-highly-likely-subspaces-that-contain-an-unknown-quantum-state-of-light
#15
Yong Siah Teo, Dmitri Mogilevtsev, Alexander Mikhalychev, Jaroslav Řeháček, Zdeněk Hradil
In continuous-variable tomography, with finite data and limited computation resources, reconstruction of a quantum state of light is performed on a finite-dimensional subspace. In principle, the data themselves encode all information about the relevant subspace that physically contains the state. We provide a straightforward and numerically feasible procedure to uniquely determine the appropriate reconstruction subspace by extracting this information directly from the data for any given unknown quantum state of light and measurement scheme...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27902843/ridge-estimation-of-the-var-1-model-and-its-time-series-chain-graph-from-multivariate-time-course-omics-data
#16
Viktorian Miok, Saskia M Wilting, Wessel N van Wieringen
Omics experiments endowed with a time-course design may enable us to uncover the dynamic interplay among genes of cellular processes. Multivariate techniques (like VAR(1) models describing the temporal and contemporaneous relations among variates) that may facilitate this goal are hampered by the high-dimensionality of the resulting data. This is resolved by the presented ridge regularized maximum likelihood estimation procedure for the VAR(1) model. Information on the absence of temporal and contemporaneous relations may be incorporated in this procedure...
November 7, 2016: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/27901448/phylogeny-and-haplotype-analysis-of-fungi-within-the-fusarium-incarnatum-equiseti-species-complex
#17
H Ramdial, R K Latchoo, F N Hosein, S N Rampersad
Fusarium spp. are ranked among the top 10 most economically and scientifically important plant-pathogenic fungi in the world and are associated with plant diseases that include fruit decay of a number of crops. Fusarium isolates infecting bell pepper in Trinidad were identified based on sequence comparisons of the translation elongation factor gene (EF-1a) with sequences of Fusarium incarnatum-equiseti species complex (FIESC) verified in the FUSARIUM-ID database. Eighty-two isolates were identified as belonging to one of four phylogenetic species within the subclades FIESC-1, FIESC-15, FIESC-16, and FIESC-26, with the majority of isolates belonging to FIESC-15...
November 30, 2016: Phytopathology
https://www.readbyqxmd.com/read/27900633/two-phase-outcome-dependent-studies-for-failure-times-and-testing-for-effects-of-expensive-covariates
#18
J F Lawless
Two- or multi-phase study designs are often used in settings involving failure times. In most studies, whether or not certain covariates are measured on an individual depends on their failure time and status. For example, when failures are rare, case-cohort or case-control designs are used to increase the number of failures relative to a random sample of the same size. Another scenario is where certain covariates are expensive to measure, so they are obtained only for selected individuals in a cohort. This paper considers such situations and focuses on cases where we wish to test hypotheses of no association between failure time and expensive covariates...
November 29, 2016: Lifetime Data Analysis
https://www.readbyqxmd.com/read/27899070/multigene-phylogenetic-analysis-redefines-dung-beetles-relationships-and-classification-coleoptera-scarabaeidae-scarabaeinae
#19
Sergei Tarasov, Dimitar Dimitrov
BACKGROUND: Dung beetles (subfamily Scarabaeinae) are popular model organisms in ecology and developmental biology, and for the last two decades they have experienced a systematics renaissance with the adoption of modern phylogenetic approaches. Within this period 16 key phylogenies and numerous additional studies with limited scope have been published, but higher-level relationships of this pivotal group of beetles remain contentious and current classifications contain many unnatural groupings...
November 29, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27898938/effects-of-varying-floor-space-on-aggressive-behavior-and-cortisol-concentrations-in-group-housed-sows
#20
P H Hemsworth, R S Morrison, A J Tilbrook, K L Butler, M Rice, S J Moeller
Floor space is an important determinant of aggression and stress in group-housed sows, and the aim of the present experiment was to comprehensively examine the effects of floor space in the range of 1.45 to 2.90 m/sow from mixing until 27 d after insemination on aggression, stress, and reproduction of group-housed sows. A previous experiment on the effects of floor space indicated spatial variability across and along the research facility in both sow aggression and stress. To minimize this spatial variability within the research facility, similar-sized pens but with varying groups sizes (10-20) in 4 separate blocks of 3 contiguous pens within each of 9 time replicates (180 sows/replicate) were used to examine 6 space allowances (1...
November 2016: Journal of Animal Science
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