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https://www.readbyqxmd.com/read/27910948/improved-in-cell-structure-determination-of-proteins-at-near-physiological-concentration
#1
Teppei Ikeya, Tomomi Hanashima, Saori Hosoya, Manato Shimazaki, Shiro Ikeda, Masaki Mishima, Peter Güntert, Yutaka Ito
Investigating three-dimensional (3D) structures of proteins in living cells by in-cell nuclear magnetic resonance (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. In-cell NMR provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be determined based on data derived only from in-cell NMR...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910627/bayesian-tomography-and-integrated-data-analysis-in-fusion-diagnostics
#2
Dong Li, Y B Dong, Wei Deng, Z B Shi, B Z Fu, J M Gao, T B Wang, Yan Zhou, Yi Liu, Q W Yang, X R Duan
In this article, a Bayesian tomography method using non-stationary Gaussian process for a prior has been introduced. The Bayesian formalism allows quantities which bear uncertainty to be expressed in the probabilistic form so that the uncertainty of a final solution can be fully resolved from the confidence interval of a posterior probability. Moreover, a consistency check of that solution can be performed by checking whether the misfits between predicted and measured data are reasonably within an assumed data error...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910423/uncertainty-analysis-of-signal-deconvolution-using-a-measured-instrument-response-function
#3
E P Hartouni, B Beeman, J A Caggiano, C Cerjan, M J Eckart, G P Grim, R Hatarik, A S Moore, D H Munro, T Phillips, D B Sayre
A common analysis procedure minimizes the ln-likelihood that a set of experimental observables matches a parameterized model of the observation. The model includes a description of the underlying physical process as well as the instrument response function (IRF). In the case investigated here, the National Ignition Facility (NIF) neutron time-of-flight (nTOF) spectrometers, the IRF is constructed from measurements and models. IRF measurements have a finite precision that can make significant contributions to determine the uncertainty estimate of the physical model's parameters...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27909972/can-we-estimate-short-and-intermediate-term-survival-in-patients-undergoing-surgery-for-metastatic-bone-disease
#4
Jonathan A Forsberg, Rikard Wedin, Patrick J Boland, John H Healey
BACKGROUND: Objective means of estimating survival can be used to guide surgical decision-making and to risk-stratify patients for clinical trials. Although a free, online tool ( www.pathfx.org ) can estimate 3- and 12-month survival, recent work, including a survey of the Musculoskeletal Tumor Society, indicated that estimates at 1 and 6 months after surgery also would be helpful. Longer estimates help justify the need for more durable and expensive reconstructive options, and very short estimates could help identify those who will not survive 1 month and should not undergo surgery...
December 1, 2016: Clinical Orthopaedics and related Research
https://www.readbyqxmd.com/read/27909402/upright-perception-and-ocular-torsion-change-independently-during-head-tilt
#5
Jorge Otero-Millan, Amir Kheradmand
We maintain a stable perception of the visual world despite continuous movements of our eyes, head and body. Perception of upright is a key aspect of such orientation constancy. Here we investigated whether changes in upright perception during sustained head tilt were related to simultaneous changes in torsional position of the eyes. We used a subjective visual vertical (SVV) task, modified to track changes in upright perception over time, and a custom video method to measure ocular torsion simultaneously. We tested 12 subjects in upright position, during prolonged (~15 min) lateral head tilts of 20 degrees, and also after the head returned to upright position...
2016: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/27908740/molecular-phylogenetics-of-new-world-searobins-triglidae-prionotinae
#6
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/27908590/disease-mapping-of-zero-excessive-mesothelioma-data-in-flanders
#7
Thomas Neyens, Andrew B Lawson, Russell S Kirby, Valerie Nuyts, Kevin Watjou, Mehreteab Aregay, Rachel Carroll, Tim S Nawrot, Christel Faes
PURPOSE: To investigate the distribution of mesothelioma in Flanders using Bayesian disease mapping models that account for both an excess of zeros and overdispersion. METHODS: The numbers of newly diagnosed mesothelioma cases within all Flemish municipalities between 1999 and 2008 were obtained from the Belgian Cancer Registry. To deal with overdispersion, zero inflation, and geographical association, the hurdle combined model was proposed, which has three components: a Bernoulli zero-inflation mixture component to account for excess zeros, a gamma random effect to adjust for overdispersion, and a normal conditional autoregressive random effect to attribute spatial association...
November 1, 2016: Annals of Epidemiology
https://www.readbyqxmd.com/read/27907850/automated-annotation-and-quantitative-description-of-ultrasound-videos-of-the-fetal-heart
#8
Christopher P Bridge, Christos Ioannou, J Alison Noble
Interpretation of ultrasound videos of the fetal heart is crucial for the antenatal diagnosis of congenital heart disease (CHD). We believe that automated image analysis techniques could make an important contribution towards improving CHD detection rates. However, to our knowledge, no previous work has been done in this area. With this goal in mind, this paper presents a framework for tracking the key variables that describe the content of each frame of freehand 2D ultrasound scanning videos of the healthy fetal heart...
November 19, 2016: Medical Image Analysis
https://www.readbyqxmd.com/read/27907261/fitting-state-space-integral-projection-models-to-size-structured-time-series-data-to-estimate-unknown-parameters
#9
J Wilson White, Kerry J Nickols, Daniel Malone, Mark H Carr, Richard M Starr, Flora Cordoleani, Marissa L Baskett, Alan Hastings, Louis W Botsford
Integral projection models (IPMs) have a number of advantages over matrix-model approaches for analyzing size-structured population dynamics, because the latter require parameter estimates for each age or stage transition. However, IPMs still require appropriate data. Typically they are parameterized using individual-scale relationships between body size and demographic rates, but these are not always available. We present an alternative approach for estimating demographic parameters from time series of size-structured survey data using a Bayesian state-space IPM (SSIPM)...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27907107/a-time-calibrated-mitogenome-phylogeny-of-catfish-teleostei-siluriformes
#10
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/27905953/improving-the-usefulness-of-us-mortality-data-new-methods-for-reclassification-of-underlying-cause-of-death
#11
Kyle J Foreman, Mohsen Naghavi, Majid Ezzati
BACKGROUND: Mortality data are affected by miscertification of the medical cause of death deaths and changes to cause of death classification systems. We present both mappings of ICD9 and ICD10 to a unified list of causes, and a new statistical model for reducing the impact of misclassification of cause of death. METHODS: We propose a Bayesian mixed-effects multinomial logistic model that can be run on individual record level death certificates to reclassify "garbage-coded" deaths onto causes that are more meaningful for public health purposes...
April 28, 2016: Population Health Metrics
https://www.readbyqxmd.com/read/27905886/multi-locus-phylogeny-using-topotype-specimens-sheds-light-on-the-systematics-of-niviventer-rodentia-muridae-in-china
#12
Bin Zhang, Kai He, Tao Wan, Peng Chen, Guozheng Sun, Shaoying Liu, Truong Son Nguyen, Liangkong Lin, Xuelong Jiang
BACKGROUND: Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4)...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27905871/phyinformr-phylogenetic-experimental-design-and-phylogenomic-data-exploration-in-r
#13
Alex Dornburg, J Nick Fisk, Jules Tamagnan, Jeffrey P Townsend
BACKGROUND: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27905334/the-opportunistic-screening-of-refractive-errors-in-school-going-children-by-pediatrician-using-enhanced-br%C3%A3-ckner-test
#14
Piyush Jain, Mihir T Kothari, Vaibhav Gode
AIM: The aim of this study was to compare the results of enhanced Brückner test (EBT) performed by a pediatrician and an experienced pediatric ophthalmologist. SUBJECTS AND METHODS: In this prospective double-masked cohort study, a pediatrician and a pediatric ophthalmologist performed the EBT in a classroom of a school in semi-dark lighting condition using a direct ophthalmoscope. The results of the test were compared using 2 × 2 Bayesian table and kappa statistics...
October 2016: Indian Journal of Ophthalmology
https://www.readbyqxmd.com/read/27905150/genetic-parameter-estimates-for-prenatal-and-postnatal-mortality-in-nellore-cattle
#15
L C Magalhães Silva, F Baldi, C Aboujaoude, G C Venturini, L G Albuquerque, M J R Paranhos da Costa
The aim of this study was to estimate genetic parameters for prenatal (PRE) and postnatal (POS) mortality in Nellore cattle. A total of 13 141 (PRE) and 17 818 (POS) records from Nellore females were used. PRE and POS were recorded using binary scale scores: a score of '1' was given to calves that were born alive (PRE) and those that were alive at weaning (POS), and a score of '0' was given to calves that were not alive at or around birth (PRE), as well as to those weighed at birth but not at weaning (POS)...
December 1, 2016: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/27903902/role-of-the-chromatin-landscape-and-sequence-in-determining-cell-type-specific-genomic-glucocorticoid-receptor-binding-and-gene-regulation
#16
Michael I Love, Matthew R Huska, Marcel Jurk, Robert Schöpflin, Stephan R Starick, Kevin Schwahn, Samantha B Cooper, Keith R Yamamoto, Morgane Thomas-Chollier, Martin Vingron, Sebastiaan H Meijsing
The genomic loci bound by the glucocorticoid receptor (GR), a hormone-activated transcription factor, show little overlap between cell types. To study the role of chromatin and sequence in specifying where GR binds, we used Bayesian modeling within the universe of accessible chromatin. Taken together, our results uncovered that although GR preferentially binds accessible chromatin, its binding is biased against accessible chromatin located at promoter regions. This bias can only be explained partially by the presence of fewer GR recognition sequences, arguing for the existence of additional mechanisms that interfere with GR binding at promoters...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903883/function-driven-discovery-of-disease-genes-in-zebrafish-using-an-integrated-genomics-big-data-resource
#17
Hongseok Shim, Ji Hyun Kim, Chan Yeong Kim, Sohyun Hwang, Hyojin Kim, Sunmo Yang, Ji Eun Lee, Insuk Lee
Whole exome sequencing (WES) accelerates disease gene discovery using rare genetic variants, but further statistical and functional evidence is required to avoid false-discovery. To complement variant-driven disease gene discovery, here we present function-driven disease gene discovery in zebrafish (Danio rerio), a promising human disease model owing to its high anatomical and genomic similarity to humans. To facilitate zebrafish-based function-driven disease gene discovery, we developed a genome-scale co-functional network of zebrafish genes, DanioNet (www...
November 16, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903870/sea-level-driven-glacial-age-refugia-and-post-glacial-mixing-on-subtropical-coasts-a-palaeohabitat-and-genetic-study
#18
Greer A Dolby, Ryan Hechinger, Ryan A Ellingson, Lloyd T Findley, Julio Lorda, David K Jacobs
Using a novel combination of palaeohabitat modelling and genetic mixture analyses, we identify and assess a sea-level-driven recolonization process following the Last Glacial Maximum (LGM). Our palaeohabitat modelling reveals dramatic changes in estuarine habitat distribution along the coast of California (USA) and Baja California (Mexico). At the LGM (approx. 20 kya), when sea level was approximately 130 m lower, the palaeo-shoreline was too steep for tidal estuarine habitat formation, eliminating this habitat type from regions where it is currently most abundant, and limiting such estuaries to a northern and a southern refugium separated by 1000 km...
November 30, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27903261/discrete-phenotypes-are-not-underpinned-by-genome-wide-genetic-differentiation-in-the-squat-lobster-munida-gregaria-crustacea-decapoda-munididae-a-multi-marker-study-covering-the-patagonian-shelf
#19
Chen Wang, Shobhit Agrawal, Jürgen Laudien, Vreni Häussermann, Christoph Held
BACKGROUND: DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27903059/identifying-counties-vulnerable-to-diabetes-from-obesity-prevalence-in-the-united-states-a-spatiotemporal-analysis
#20
Xiao Li, Amanda Staudt, Lung-Chang Chien
Clinical and epidemiological research has reported a strong association between diabetes and obesity. However, whether increased diabetes prevalence is more likely to appear in areas with increased obesity prevalence has not been thoroughly investigated in the United States (US). The Bayesian structured additive regression model was applied to identify whether counties with higher obesity prevalence are more likely clustered in specific regions in 48 contiguous US states. Prevalence data adopted the small area estimate from the Behavioral Risk Factor Surveillance System...
November 21, 2016: Geospatial Health
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