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https://www.readbyqxmd.com/read/29786975/a-comparison-of-one-stage-vs-two-stage-individual-patient-data-meta-analysis-methods-a-simulation-study
#1
Evangelos Kontopantelis
BACKGROUND: Individual patient data (IPD) meta-analysis allows for the exploration of heterogeneity and can identify subgroups that most benefit from an intervention (or exposure), much more successfully than meta-analysis of aggregate data. One-stage or two-stage IPD meta-analysis is possible, with the former using mixed-effects regression models and the latter obtaining study-estimates through simpler regression models before aggregating using standard meta-analysis methodology. However, a comprehensive comparison of the two methods, in practice, is lacking...
May 22, 2018: Research Synthesis Methods
https://www.readbyqxmd.com/read/29786693/hormonebase-a-population-level-database-of-steroid-hormone-levels-across-vertebrates
#2
Maren N Vitousek, Michele A Johnson, Jeremy W Donald, Clinton D Francis, Matthew J Fuxjager, Wolfgang Goymann, Michaela Hau, Jerry F Husak, Bonnie K Kircher, Rosemary Knapp, Lynn B Martin, Eliot T Miller, Laura A Schoenle, Jennifer J Uehling, Tony D Williams
Hormones are central regulators of organismal function and flexibility that mediate a diversity of phenotypic traits from early development through senescence. Yet despite these important roles, basic questions about how and why hormone systems vary within and across species remain unanswered. Here we describe HormoneBase, a database of circulating steroid hormone levels and their variation across vertebrates. This database aims to provide all available data on the mean, variation, and range of plasma glucocorticoids (both baseline and stress-induced) and androgens in free-living and un-manipulated adult vertebrates...
May 22, 2018: Scientific Data
https://www.readbyqxmd.com/read/29786689/gridded-birth-and-pregnancy-datasets-for-africa-latin-america-and-the-caribbean
#3
W H M James, N Tejedor-Garavito, S E Hanspal, A Campbell-Sutton, G M Hornby, C Pezzulo, K Nilsen, A Sorichetta, C W Ruktanonchai, A Carioli, D Kerr, Z Matthews, A J Tatem
Understanding the fine scale spatial distribution of births and pregnancies is crucial for informing planning decisions related to public health. This is especially important in lower income countries where infectious disease is a major concern for pregnant women and new-borns, as highlighted by the recent Zika virus epidemic. Despite this, the spatial detail of basic data on the numbers and distribution of births and pregnancies is often of a coarse resolution and difficult to obtain, with no co-ordination between countries and organisations to create one consistent set of subnational estimates...
May 22, 2018: Scientific Data
https://www.readbyqxmd.com/read/29786659/deep-learning-to-predict-falls-in-older-adults-based-on-daily-life-trunk-accelerometry
#4
REVIEW
Ahmed Nait Aicha, Gwenn Englebienne, Kimberley S van Schooten, Mirjam Pijnappels, Ben Kröse
Early detection of high fall risk is an essential component of fall prevention in older adults. Wearable sensors can provide valuable insight into daily-life activities; biomechanical features extracted from such inertial data have been shown to be of added value for the assessment of fall risk. Body-worn sensors such as accelerometers can provide valuable insight into fall risk. Currently, biomechanical features derived from accelerometer data are used for the assessment of fall risk. Here, we studied whether deep learning methods from machine learning are suited to automatically derive features from raw accelerometer data that assess fall risk...
May 22, 2018: Sensors
https://www.readbyqxmd.com/read/29786603/natural-levels-of-polonium-210-in-urine
#5
Alan Hodgson
This paper presents a review and analysis of available data on background levels of Polonium-210 in urine. It was established that 819 measurements could be considered to correspond to natural background levels, excluding a large number of values identified by the original investigators as potentially due to an artificial source or due to recognised enhancement of dietary intake. Almost 550 measurements were extracted from studies reported in the literature; additional measurements were contributions of previously unpublished data by authors of more recent papers...
May 22, 2018: Journal of Radiological Protection: Official Journal of the Society for Radiological Protection
https://www.readbyqxmd.com/read/29786556/assessment-of-stem-cell-differentiation-based-on-genome-wide-expression-profiles
#6
REVIEW
Patricio Godoy, Wolfgang Schmidt-Heck, Birte Hellwig, Patrick Nell, David Feuerborn, Jörg Rahnenführer, Kathrin Kattler, Jörn Walter, Nils Blüthgen, Jan G Hengstler
In recent years, protocols have been established to differentiate stem and precursor cells into more mature cell types. However, progress in this field has been hampered by difficulties to assess the differentiation status of stem cell-derived cells in an unbiased manner. Here, we present an analysis pipeline based on published data and methods to quantify the degree of differentiation and to identify transcriptional control factors explaining differences from the intended target cells or tissues. The pipeline requires RNA-Seq or gene array data of the stem cell starting population, derived 'mature' cells and primary target cells or tissue...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29786162/hospitals-and-the-generic-versus-brand-name-prescription-decision-in-the-outpatient-sector
#7
Gerald J Pruckner, Thomas Schober
Health care payers try to reduce costs by promoting the use of cheaper generic drugs. We show strong interrelations in drug prescriptions between the inpatient and outpatient sectors by using a large administrative dataset from Austria. Patients with prior hospital visits have a significantly lower probability of receiving a generic drug in the outpatient sector. The size of the effect depends on both the patient and doctor characteristics, which could be related to the differences in hospital treatment and heterogeneity in the physicians' adherence to hospital choices...
May 22, 2018: Health Economics
https://www.readbyqxmd.com/read/29786140/gender-differences-in-the-association-of-periodontitis-and-type-2-diabetes
#8
Ying Liu, Yang Yu, Jeffrey C Nickel, Laura R Iwasaki, Peipei Duan, Melanie Simmer-Beck, Laura Brown
AIMS: THE OBJECTIVE WAS TO INVESTIGATE IF GENDER DIFFERENCES EXIST IN THE ASSOCIATIONS BETWEEN PERIODONTITIS AND TYPE 2 DIABETES. DISPROPORTIONATE DISPARITIES BY GENDER WERE FOUND TO EXIST IN RATES OF BOTH PERIODONTITIS AND DIABETES WITH RESPECT TO DEMOGRAPHICS AND BEHAVIOURAL PREDICTORS THAT CANNOT BE EXPLAINED SOLELY BY THE WELL-ESTABLISHED ASSOCIATION BETWEEN THESE TWO DISEASES. MATERIALS AND METHODS: MULTIPLE DATASETS WERE EXTRACTED FROM THE NATIONAL HEALTH AND NUTRITION EXAMINATION SURVEY (NHANES) 2009-2014, WHICH USED A STRATIFIED MULTISTAGE PROBABILITY SAMPLING TO OBTAIN SAMPLES FROM ALL CIVILIAN NON-INSTITUTIONALISED PEOPLE IN THE USA...
May 22, 2018: International Dental Journal
https://www.readbyqxmd.com/read/29785689/the-impact-of-hospital-costing-methods-on-cost-effectiveness-analysis-a-case-study
#9
José Leal, Stefania Manetti, James Buchanan
BACKGROUND: Several methods exist to cost hospital contacts when estimating the cost effectiveness of a new intervention. However, the implications of choosing a particular approach remain unclear. We compare the use of the three main diagnosis-related group (DRG)-based national unit costs in England to determine whether choice of approach can impact on economic evaluation results. METHODS: A cost-utility model was developed to compare secondary fracture prevention models of care for hip fracture patients, using data from large primary and hospital care administrative datasets in England...
May 22, 2018: PharmacoEconomics
https://www.readbyqxmd.com/read/29785660/prevalence-of-hypertension-and-diabetes-after-exposure-to-extracorporeal-shock-wave-lithotripsy-in-patients-with-renal-calculi-a-retrospective-non-randomized-data-analysis
#10
Christian Daniel Fankhauser, Nilufar Mohebbi, Josias Grogg, Alexander Holenstein, Qing Zhong, Thomas Hermanns, Tullio Sulser, Johann Steurer, Poyet Cedric
PURPOSE: To evaluate the association of shock-wave lithotripsy (SWL) for kidney stones and hypertension or diabetes. METHODS: Patients with urolithiasis treated by SWL were retrospectively identified. To assess whether shock-wave application to the kidney is associated with long-term adverse effects, patients after SWL for kidney stones were selected as the main group of interest. Patients treated with shock waves for distal ureter stones only were chosen as a comparison group...
May 21, 2018: International Urology and Nephrology
https://www.readbyqxmd.com/read/29785624/longitudinal-neuroimaging-hippocampal-markers-for-diagnosing-alzheimer-s-disease
#11
Carlos Platero, Lin Lin, M Carmen Tobar
Hippocampal atrophy measures from magnetic resonance imaging (MRI) are powerful tools for monitoring Alzheimer's disease (AD) progression. In this paper, we introduce a longitudinal image analysis framework based on robust registration and simultaneous hippocampal segmentation and longitudinal marker classification of brain MRI of an arbitrary number of time points. The framework comprises two innovative parts: a longitudinal segmentation and a longitudinal classification step. The results show that both steps of the longitudinal pipeline improved the reliability and the accuracy of the discrimination between clinical groups...
May 21, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29785561/reptb-a-gene-ontology-based-drug-repurposing-approach-for-tuberculosis
#12
Anurag Passi, Neeraj Kumar Rajput, David J Wild, Anshu Bhardwaj
Tuberculosis (TB) is the world's leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function correlations among known drug-target pairs to predict novel drug-target interactions. In this study, we have created a Gene Ontology based network containing 26,404 edges, 6630 drug and 4083 target nodes...
May 21, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29785479/ngspanpipe-a-pipeline-for-pan-genome-identification-in-microbial-strains-from-experimental-reads
#13
Umay Kulsum, Arti Kapil, Harpreet Singh, Punit Kaur
Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29785435/assessing-the-performance-of-mm-pbsa-and-mm-gbsa-methods-7-entropy-effects-on-the-performance-of-end-point-binding-free-energy-calculation-approaches
#14
Huiyong Sun, Lili Duan, Fu Chen, Hui Liu, Zhe Wang, Peichen Pan, Feng Zhu, John Z H Zhang, Tingjun Hou
Entropy effects play an important role in drug-target interactions, but the entropic contribution to ligand-binding affinity is often neglected by end-point binding free energy calculation methods, such as MM/GBSA and MM/PBSA, due to the expensive computational cost of normal mode analysis (NMA). Here, we systematically investigated entropy effects on the prediction power of MM/GBSA and MM/PBSA using >1500 protein-ligand systems and six representative AMBER force fields. Two computationally efficient methods, including NMA based on truncated structures and the interaction entropy approach, were used to estimate the entropic contributions to ligand-target binding free energies...
May 22, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29785346/integrated-bioinformatic-changes-and-analysis-of-retina-with-time-in-diabetic-rats
#15
Zekai Cui, Qiaolang Zeng, Yonglong Guo, Shiwei Liu, Jiansu Chen
Diabetic retinopathy (DR) is the most common chronic complication of diabetes. It can cause impaired vision and even blindness. However, the pathological mechanism of DR is still unknown. In the present study, we use bioinformatic analysis to reveal the pathological changes of early DR in a streptozotocin (STZ) induced diabetes rat model. The dataset GSE28831 was downloaded from the Gene Expression Omnibus (GEO) database. To clarify the pathological mechanism of early DR, genes which were up-regulated (UP group) or down-regulated (DOWN group) over time were identified...
2018: PeerJ
https://www.readbyqxmd.com/read/29785177/characterization-of-new-microsatellite-markers-based-on-the-transcriptome-sequencing-of-clematis-finetiana
#16
Zhigao Liu, Weili Shao, Yamei Shen, Mengcheng Ji, Wenchao Chen, Ying Ye, Yongbao Shen
Background: Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the "Queen of the Vines". However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C...
2018: Hereditas
https://www.readbyqxmd.com/read/29785154/detection-of-coronary-artery-disease-by-reduced-features-and-extreme-learning-machine
#17
Ram Sewak Singh, Barjinder Singh Saini, Ramesh Kumar Sunkaria
Objective: Cardiovascular diseases generate the highest mortality in the globe population, mainly due to coronary artery disease (CAD) like arrhythmia, myocardial infarction and heart failure. Therefore, an early identification of CAD and diagnosis is essential. For this, we have proposed a new approach to detect the CAD patients using heart rate variability (HRV) signals. This approach is based on subspaces decomposition of HRV signals using multiscale wavelet packet (MSWP) transform and entropy features extracted from decomposed HRV signals...
2018: Clujul Medical (1957)
https://www.readbyqxmd.com/read/29785110/prefrontoparietal-dysfunction-during-emotion-regulation-in-anxiety-disorder-a-meta-analysis-of-functional-magnetic-resonance-imaging-studies
#18
Hai-Yang Wang, Xiao-Xia Zhang, Cui-Ping Si, Yang Xu, Qian Liu, He-Tao Bian, Bing-Wei Zhang, Xue-Lin Li, Zhong-Rui Yan
Objective: Impairments in emotion regulation, and more specifically in cognitive reappraisal, are thought to play a key role in the pathogenesis of anxiety disorders. However, the available evidence on such deficits is inconsistent. To further illustrate the neurobiological underpinnings of anxiety disorder, the present meta-analysis summarizes functional magnetic resonance imaging (fMRI) findings for cognitive reappraisal tasks and investigates related brain areas. Methods: We performed a comprehensive series of meta-analyses of cognitive reappraisal fMRI studies contrasting patients with anxiety disorder with healthy control (HC) subjects, employing an anisotropic effect-size signed differential mapping approach...
2018: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/29784978/genomes-of-all-known-members-of-a-plasmodium-subgenus-reveal-paths-to-virulent-human-malaria
#19
Thomas D Otto, Aude Gilabert, Thomas Crellen, Ulrike Böhme, Céline Arnathau, Mandy Sanders, Samuel O Oyola, Alain Prince Okouga, Larson Boundenga, Eric Willaume, Barthélémy Ngoubangoye, Nancy Diamella Moukodoum, Christophe Paupy, Patrick Durand, Virginie Rougeron, Benjamin Ollomo, François Renaud, Chris Newbold, Matthew Berriman, Franck Prugnolle
Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite Plasmodium praefalciparum. Little is known about the other gorilla- and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum, but none of them are capable of establishing repeated infection and transmission in humans. To elucidate underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple genomes from all known Laverania species...
May 21, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29784946/interpretable-dimensionality-reduction-of-single-cell-transcriptome-data-with-deep-generative-models
#20
Jiarui Ding, Anne Condon, Sohrab P Shah
Single-cell RNA-sequencing has great potential to discover cell types, identify cell states, trace development lineages, and reconstruct the spatial organization of cells. However, dimension reduction to interpret structure in single-cell sequencing data remains a challenge. Existing algorithms are either not able to uncover the clustering structures in the data or lose global information such as groups of clusters that are close to each other. We present a robust statistical model, scvis, to capture and visualize the low-dimensional structures in single-cell gene expression data...
May 21, 2018: Nature Communications
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