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https://www.readbyqxmd.com/read/28931087/microbial-analysis-of-zetaproteobacteria-and-co-colonizers-of-iron-mats-in-the-troll-wall-vent-field-arctic-mid-ocean-ridge
#1
Jan Vander Roost, Ingunn Hindenes Thorseth, Håkon Dahle
Over the last decade it has become increasingly clear that Zetaproteobacteria are widespread in hydrothermal systems and that they contribute to the biogeochemical cycling of iron in these environments. However, how chemical factors control the distribution of Zetaproteobacteria and their co-occurring taxa remains elusive. Here we analysed iron mats from the Troll Wall Vent Field (TWVF) located at the Arctic Mid-Ocean Ridge (AMOR) in the Norwegian-Greenland Sea. The samples were taken at increasing distances from high-temperature venting chimneys towards areas with ultraslow low-temperature venting, encompassing a large variety in geochemical settings...
2017: PloS One
https://www.readbyqxmd.com/read/28926390/misconceptions-misuses-and-misinterpretations-of-p-values-and-significance-testing
#2
Joel J Gagnier, Hal Morgenstern
The interpretation and reporting of p values and significance testing in biomedical research are fraught with misconceptions and inaccuracies. Publications of peer-reviewed research in orthopaedics are not immune to such problems. The American Statistical Association (ASA) recently published an official statement on the use, misuse, and misinterpretation of statistical testing and p values in applied research. The ASA statement discussed 6 principles: (1) "P-values can indicate how incompatible the data are with a specified statistical model...
September 20, 2017: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/28919350/crystal-structure-of-inositol-1-3-4-5-6-pentakisphosphate-2-kinase-from-cryptococcus-neoformans
#3
Juntaek Oh, Dong-Gi Lee, Yong-Sun Bahn, Sangkee Rhee
The fungal pathogen Cryptococcus neoformans is a causative agent of meningoencephalitis in humans. For its pathogenicity, the inositol polyphosphate biosynthetic pathway plays critical roles. Recently, Ipk1 from C. neoformans (CnIpk1) was identified as an inositol 1,3,4,5,6-pentakisphosphate 2-kinase that catalyzes the phosphorylation of IP5 to form IP6, a substrate for subsequent reaction to produce inositol pyrophosphates, such as PP-IP5/IP7. Furthermore, it was shown that deletion of IPK1 significantly reduces the virulence of C...
September 15, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28918281/distribution-of-vocs-in-urban-and-rural-atmospheres-of-subtropical-india-temporal-variation-source-attribution-ratios-ofp-and-risk-assessment
#4
Amit Kumar, Deepak Singh, Krishan Kumar, Braj Bihari Singh, Vinod Kumar Jain
This paper reports the first study which comprises the seasonal, diurnal variability, source characterization, ozone forming potential and risk assessment of volatile organic compounds (VOCs) at three sites (two urban and one rural) in the National Capital Territory of Delhi, India. The study was performed during three seasons of the year 2013-14 and two different categories of VOCs (aromatics and halogenated) have been selected. The study used the sampling and analytical procedures of NIOSH methods. Results showed that the mean concentration of sum of VOCs (∑VOC) is significantly higher at urban sites (110...
September 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28916222/estimating-vocal-effort-from-the-aerodynamics-of-labial-fricatives-a-feasibility-study
#5
Yohann Meynadier, Anita El Hajj, Michel Pitermann, Thierry Legou, Antoine Giovanni
OBJECTIVE AND HYPOTHESIS: Vocal effort in loud voice is produced with increased subglottal pressure during vowels and increased supraglottal pressure during consonants. In the paper, our main objective is to check whether it was supported by a parallel increase in the airflow resistance of the laryngeal articulator and of the supralaryngeal articulator, here the lips. STUDY DESIGN AND METHOD: For this comparison, our choice fell on the fricative consonants, as their production allows perfectly synchronous air pressure and airflow measurements...
September 12, 2017: Journal of Voice: Official Journal of the Voice Foundation
https://www.readbyqxmd.com/read/28915250/multi-layered-mutation-in-hedgehog-related-genes-in-gorlin-syndrome-may-affect-the-phenotype
#6
Shoko Onodera, Akiko Saito, Daigo Hasegawa, Nana Morita, Katsuhito Watanabe, Takeshi Nomura, Takahiko Shibahara, Shinsuke Ohba, Akira Yamaguchi, Toshifumi Azuma
Gorlin syndrome is a genetic disorder of autosomal dominant inheritance that predisposes the affected individual to a variety of disorders that are attributed largely to heterozygous germline patched1 (PTCH1) mutations. PTCH1 is a hedgehog (Hh) receptor as well as a repressor, mutation of which leads to constitutive activation of Hh pathway. Hh pathway encompasses a wide variety of cellular signaling cascades, which involve several molecules; however, no associated genotype-phenotype correlations have been reported...
2017: PloS One
https://www.readbyqxmd.com/read/28914457/gross-brain-morphology-of-the-armoured-catfish-rineloricaria-heteroptera-isbr%C3%A3-cker-and-nijssen-1976-siluriformes-loricariidae-loricariinae-a-descriptive-and-quantitative-approach
#7
Arturo Angulo, Francisco Langeani
The gross morphology of the brain of Rineloricaria heteroptera and its relation to the sensory/behavioural ecology of the species is described and discussed. The sexual and ontogenetic intraspecific variation in the whole brain length and mass, as well as within/between the eight different brain subdivisions volumes, is also examined and discussed. Negative allometry for the whole brain length/mass and relative growth of the telencephalon and optic tecta was observed. Positive allometry was observed for the relative growth of the olfactory bulbs and medulla oblongata...
September 15, 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28904781/sharing-is-caring-measurement-error-and-the-issues-arising-from-combining-3d-morphometric-datasets
#8
Carmelo Fruciano, Mélina A Celik, Kaylene Butler, Tom Dooley, Vera Weisbecker, Matthew J Phillips
Geometric morphometrics is routinely used in ecology and evolution and morphometric datasets are increasingly shared among researchers, allowing for more comprehensive studies and higher statistical power (as a consequence of increased sample size). However, sharing of morphometric data opens up the question of how much nonbiologically relevant variation (i.e., measurement error) is introduced in the resulting datasets and how this variation affects analyses. We perform a set of analyses based on an empirical 3D geometric morphometric dataset...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28904774/phenotypic-differentiation-of-the-solidago-virgaurea-complex-along-an-elevational-gradient-insights-from-a-common-garden-experiment-and-population-genetics
#9
Masaaki Hirano, Shota Sakaguchi, Koichi Takahashi
Plant species distributed along wide elevational or latitudinal gradients show phenotypic variation due to their heterogeneous habitats. This study investigated whether phenotypic variation in populations of the Solidago virgaurea complex along an elevational gradient is caused by genetic differentiation. A common garden experiment was based on seeds collected from nine populations of the S. virgaurea complex growing at elevations from 1,597 m to 2,779 m a.s.l. on Mt. Norikura in central Japan. Population genetic analyses with microsatellite markers were used to infer the genetic structure and levels of gene flow between populations...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28903535/modeling-the-multiple-facets-of-speciation-with-gene-flow-toward-inferring-the-divergence-history-of-lake-whitefish-species-pairs-coregonus-clupeaformis
#10
Clément Rougeux, Louis Bernatchez, Pierre-Alexandre Gagnaire
Parallel divergence across replicated species pairs occurring in similar environmental contrasts may arise through distinct evolutionary scenarios. Deciphering whether such parallelism actually reflects repeated parallel divergence driven by divergent selection or a single divergence event with subsequent gene flow needs to be ascertained. Reconstructing historical gene flow is therefore of fundamental interest to understand how demography and selection jointly shaped genomic divergence during speciation. Here, we use an extended modeling framework to explore the multiple facets of speciation-with-gene-flow with demo-genetic divergence models that capture both temporal and genomic variation in effective population size and migration rate...
August 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28900618/comparative-genomic-in-situ-hybridization-and-the-possible-role-of-retroelements-in-the-karyotypic-evolution-of-three-akodontini-species
#11
Naiara Pereira Araújo, Gustavo Campos Silva Kuhn, Flávia Nunes Vieira, Thaís Queiroz Morcatty, Adriano Pereira Paglia, Marta Svartman
South American Akodontini rodents are characterized by a large number of chromosome rearrangements. Among them, the genus Akodon has been extensively analyzed with classical and molecular cytogenetics, which allowed the identification of a large number of intra- and interspecific chromosomal variation due to Robertsonian rearrangements, pericentric inversions, and heterochromatin additions/deletions. In order to shed some light on the cause of these rearrangements, we comparatively analyzed the karyotypes of three Akodontini species, Akodon cursor (2n = 14, FN = 19), A...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28898266/translating-natural-genetic-variation-to-gene-expression-in-a-computational-model-of-the-drosophila-gap-gene-regulatory-network
#12
Vitaly V Gursky, Konstantin N Kozlov, Ivan V Kulakovskiy, Asif Zubair, Paul Marjoram, David S Lawrie, Sergey V Nuzhdin, Maria G Samsonova
Annotating the genotype-phenotype relationship, and developing a proper quantitative description of the relationship, requires understanding the impact of natural genomic variation on gene expression. We apply a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a panel of natural sequenced D. melanogaster lines. Using a thermodynamic modeling framework, we provide both analytical and computational descriptions of how single-nucleotide variants affect gene expression...
2017: PloS One
https://www.readbyqxmd.com/read/28895585/habitual-sleep-duration-and-sleep-duration-variation-are-independently-associated-with-body-mass-index
#13
X Xu, M P Conomos, O Manor, J E Rohwer, A T Magis, J C Lovejoy
BACKGROUND: Sleep plays a vital role in maintaining homeostasis and promoting health. Previous studies show that shorter sleep duration is associated with elevated body mass index (BMI) and other cardiovascular risk factors. The goal of this study was to investigate the effects of habitual sleep duration and nightly sleep duration variation based on daily device-recorded data on BMI and obesity-related biomarkers. METHOD: 748 individuals (50.6% females, 85.4% European-Americans, average age: 49...
September 12, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28894954/maternal-allocation-of-carotenoids-increases-tolerance-to-bacterial-infection-in-brown-trout
#14
Laetitia G E Wilkins, Lucas Marques da Cunha, Laure Menin, Daniel Ortiz, Véronique Vocat-Mottier, Matay Hobil, David Nusbaumer, Claus Wedekind
Life-history theory predicts that iteroparous females allocate their resources differently among different breeding seasons depending on their residual reproductive value. In iteroparous salmonids there is typically much variation in egg size, egg number, and in the compounds that females allocate to their clutch. These compounds include various carotenoids whose functions are not sufficiently understood yet. We sampled 37 female and 35 male brown trout from natural streams, collected their gametes for in vitro fertilizations, experimentally produced 185 families in 7 full-factorial breeding blocks, raised the developing embryos singly (n = 2960), and either sham-treated or infected them with Pseudomonas fluorescens...
September 11, 2017: Oecologia
https://www.readbyqxmd.com/read/28893846/comparison-of-single-genome-and-allele-frequency-data-reveals-discordant-demographic-histories
#15
Annabel C Beichman, Tanya N Phung, Kirk E Lohmueller
Inference of demographic history from genetic data is a primary goal of population genetics of model and non-model organisms. Whole genome-based approaches such as the Pairwise/Multiple Sequentially Markovian Coalescent (PSMC/MSMC) methods use genomic data from one to four individuals to infer the demographic history of an entire population, while site frequency spectrum (SFS)-based methods use the distribution of allele frequencies in a sample to reconstruct the same historical events. Although both methods are extensively used in empirical studies and perform well on data simulated under simple models, there have been only limited comparisons of them in more complex and realistic settings...
September 11, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28890416/bayesian-population-receptive-field-modelling
#16
REVIEW
Peter Zeidman, Edward Harry Silson, Dietrich Samuel Schwarzkopf, Chris Ian Baker, Will Penny
We introduce a probabilistic (Bayesian) framework and associated software toolbox for mapping population receptive fields (pRFs) based on fMRI data. This generic approach is intended to work with stimuli of any dimension and is demonstrated and validated in the context of 2D retinotopic mapping. The framework enables the experimenter to specify generative (encoding) models of fMRI timeseries, in which experimental stimuli enter a pRF model of neural activity, which in turns drives a nonlinear model of neurovascular coupling and Blood Oxygenation Level Dependent (BOLD) response...
September 7, 2017: NeuroImage
https://www.readbyqxmd.com/read/28888611/comparison-of-mammary-lipid-metabolism-in-dairy-cows-and-goats-fed-diets-supplemented-with-starch-plant-oil-or-fish-oil
#17
L Bernard, P G Toral, Y Chilliard
A direct comparison of cow and goat performance and milk fatty acid (FA) responses to diets known to induce milk fat depression in the bovine has suggested interspecies differences in rumen and mammary lipid metabolism. Thus, this study was conducted to infer some potential mechanisms responsible for the differences in mammary lipogenesis due to diet and ruminant species. To meet this objective, 12 cows and 15 goats were fed a basal diet (control), a similar diet supplemented with 2.2% fish oil (FO), or a diet containing 5...
September 6, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28888397/social-reorganization-and-biological-change-an-examination-of-stature-variation-among-iron-age-samnites-from-abruzzo-central-italy
#18
Vitale Stefano Sparacello, Giuseppe Vercellotti, Vincenzo d'Ercole, Alfredo Coppa
Stature is a sensitive indicator of overall environmental quality experienced during growth and development, and can provide insights on a population's 'well-being'. This study investigated changes in estimated adult stature in a large (N=568) sample of Samnite Iron Age (800-27 BCE) people from central Italy, during a period of increasing sociopolitical complexity. Stature was analyzed diachronically, between sexes, and across social strata inferred using the 'Status Index' based on funerary treatment. It was expected: 1) a decrease in stature from the Orientalizing-Archaic period (O-A) to the fifth century BC (V SEC) and the following Hellenistic period (ELL), due to population increase and urbanization; 2) social status to positively influence the attainment of the full stature potential; 3) sexual dimorphism to be higher in more stratified groups...
September 2017: International Journal of Paleopathology
https://www.readbyqxmd.com/read/28888158/predicting-motorcycle-crash-injury-severity-using-weather-data-and-alternative-bayesian-multivariate-crash-frequency-models
#19
Wen Cheng, Gurdiljot Singh Gill, Taha Sakrani, Mohan Dasu, Jiao Zhou
Motorcycle crashes constitute a very high proportion of the overall motor vehicle fatalities in the United States, and many studies have examined the influential factors under various conditions. However, research on the impact of weather conditions on the motorcycle crash severity is not well documented. In this study, we examined the impact of weather conditions on motorcycle crash injuries at four different severity levels using San Francisco motorcycle crash injury data. Five models were developed using Full Bayesian formulation accounting for different correlations commonly seen in crash data and then compared for fitness and performance...
September 6, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28886340/variant-interpretation-functional-assays-to-the-rescue
#20
Lea M Starita, Nadav Ahituv, Maitreya J Dunham, Jacob O Kitzman, Frederick P Roth, Georg Seelig, Jay Shendure, Douglas M Fowler
Classical genetic approaches for interpreting variants, such as case-control or co-segregation studies, require finding many individuals with each variant. Because the overwhelming majority of variants are present in only a few living humans, this strategy has clear limits. Fully realizing the clinical potential of genetics requires that we accurately infer pathogenicity even for rare or private variation. Many computational approaches to predicting variant effects have been developed, but they can identify only a small fraction of pathogenic variants with the high confidence that is required in the clinic...
September 7, 2017: American Journal of Human Genetics
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