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Jarrod D Frizzell, Li Liang, Phillip J Schulte, Clyde W Yancy, Paul A Heidenreich, Adrian F Hernandez, Deepak L Bhatt, Gregg C Fonarow, Warren K Laskey
Importance: Several attempts have been made at developing models to predict 30-day readmissions in patients with heart failure, but none have sufficient discriminatory capacity for clinical use. Machine-learning (ML) algorithms represent a novel approach and may have potential advantages over traditional statistical modeling. Objective: To develop models using a ML approach to predict all-cause readmissions 30 days after discharge from a heart failure hospitalization and to compare ML model performance with models developed using "conventional" statistically based methods...
October 26, 2016: JAMA Cardiology
Erica H Craig, Jennifer R Adams, Lisette P Waits, Mark R Fuller, Diana M Whittington
Understanding the genetics of a population is a critical component of developing conservation strategies. We used archived tissue samples from golden eagles (Aquila chrysaetos canadensis) in three geographic regions of western North America to conduct a preliminary study of the genetics of the North American subspecies, and to provide data for United States Fish and Wildlife Service (USFWS) decision-making for golden eagle management. We used a combination of mitochondrial DNA (mtDNA) D-loop sequences and 16 nuclear DNA (nDNA) microsatellite loci to investigate the extent of gene flow among our sampling areas in Idaho, California and Alaska and to determine if we could distinguish birds from the different geographic regions based on their genetic profiles...
2016: PloS One
Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
This paper introduces an approach to classification of RNA-seq read counts using grey relational analysis (GRA) and Bayesian Gaussian process (GP) models. Read counts are transformed to microarray-like data to facilitate normal-based statistical methods. GRA is designed to select differentially expressed genes by integrating outcomes of five individual feature selection methods including two-sample t-test, entropy test, Bhattacharyya distance, Wilcoxon test and receiver operating characteristic curve. GRA performs as an aggregate filter method through combining advantages of the individual methods to produce significant feature subsets that are then fed into a nonparametric GP model for classification...
2016: PloS One
Ljerka Lah, Daronja Trense, Harald Benke, Per Berggren, Þorvaldur Gunnlaugsson, Christina Lockyer, Ayaka Öztürk, Bayram Öztürk, Iwona Pawliczka, Anna Roos, Ursula Siebert, Krzysztof Skóra, Gísli Víkingsson, Ralph Tiedemann
The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach...
2016: PloS One
Claudia Wultsch, Anthony Caragiulo, Isabela Dias-Freedman, Howard Quigley, Salisa Rabinowitz, George Amato
Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico...
2016: PloS One
Michael Worobey, Thomas D Watts, Richard A McKay, Marc A Suchard, Timothy Granade, Dirk E Teuwen, Beryl A Koblin, Walid Heneine, Philippe Lemey, Harold W Jaffe
The emergence of HIV-1 group M subtype B in North American men who have sex with men was a key turning point in the HIV/AIDS pandemic. Phylogenetic studies have suggested cryptic subtype B circulation in the United States (US) throughout the 1970s and an even older presence in the Caribbean. However, these temporal and geographical inferences, based upon partial HIV-1 genomes that postdate the recognition of AIDS in 1981, remain contentious and the earliest movements of the virus within the US are unknown. We serologically screened >2,000 1970s serum samples and developed a highly sensitive approach for recovering viral RNA from degraded archival samples...
October 26, 2016: Nature
Wilson Bautista-Molano, Robert B M Landewé, Cesar Serna, Rafael Valle-Oñate, Désirée van der Heijde
OBJECTIVES: To evaluate the patients' characteristics associated with the clinical decision to request SI-MRI and/or HLA-B27 in patients with SpA in daily practice. METHODS: Patients referred to a rheumatology outpatient-clinic in a national referral-centre were selected. Patients with a clinical diagnosis of SpA according to the rheumatologist were included. SI-MRI and HLA-B27 was available for patients in whom the rheumatologists had ordered these tests. Characteristics associated with ordering SI-MRI or HLA-B27 were identified with univariable analyses...
October 26, 2016: Clinical and Experimental Rheumatology
Mathieu Latutrie, Yves Bergeron, Francine Tremblay
BACKGROUND: In North America, the last ice age is the most recent event with severe consequences on boreal species' ranges. Phylogeographic patterns of range expansion in trembling aspen (Populus tremuloides) suggested that Beringia is likely to be a refugium and the "ice-free corridor" in Alberta may represent a region where small populations persisted during the last glacial maximum (LGM). The purpose of this study was to ascertain whether the origins of trembling aspen in western North America are reflected in the patterns of neutral genetic diversity and population structure...
October 26, 2016: BMC Evolutionary Biology
André E R Soares, Ben J Novak, James Haile, Tim H Heupink, Jon Fjeldså, M Thomas P Gilbert, Hendrik Poinar, George M Church, Beth Shapiro
BACKGROUND: Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context...
October 26, 2016: BMC Evolutionary Biology
Andrik Rampun, Bernie Tiddeman, Reyer Zwiggelaar, Paul Malcolm
PURPOSE: In this paper the authors propose a texton based prostate computer aided diagnosis approach which bypasses the typical feature extraction process such as filtering and convolution which can be computationally expensive. The study focuses the peripheral zone because 75% of prostate cancers start within this region and the majority of prostate cancers arising within this region are more aggressive than those arising in the transitional zone. METHODS: For the model development, square patches were extracted at random locations from malignant and benign regions...
October 2016: Medical Physics
S F Carr, R Garnett, C S Lo
Controlling molecule-surface interactions is key for chemical applications ranging from catalysis to gas sensing. We present a framework for accelerating the search for the global minimum on potential surfaces, corresponding to stable adsorbate-surface structures. We present a technique using Bayesian inference that enables us to predict converged density functional theory potential energies with fewer self-consistent field iterations. We then discuss how this technique fits in with the Bayesian Active Site Calculator, which applies Bayesian optimization to the problem...
October 21, 2016: Journal of Chemical Physics
Konrad Hinsen, Gerald R Kneller
Anomalous diffusion is characterized by its asymptotic behavior for t → ∞. This makes it difficult to detect and describe in particle trajectories from experiments or computer simulations, which are necessarily of finite length. We propose a new approach using Bayesian inference applied directly to the observed trajectories sampled at different time scales. We illustrate the performance of this approach using random trajectories with known statistical properties and then use it for analyzing the motion of lipid molecules in the plane of a lipid bilayer...
October 21, 2016: Journal of Chemical Physics
Qinxue Wang, Haobin Huang, Xiaoning Zeng, Yuan Ma, Xin Zhao, Mao Huang
BACKGROUND: The benefit of maintenance therapy has been confirmed in patients with non-progressing non-small cell lung cancer (NSCLC) after first-line therapy by many trials and meta-analyses. However, since few head-to-head trials between different regimens have been reported, clinicians still have little guidance on how to select the most efficacious single-agent regimen. Hence, we present a network meta-analysis to assess the comparative treatment efficacy of several single-agent maintenance therapy regimens for stage III/IV NSCLC...
2016: PeerJ
Jeffrey C Valentine, Sandra Jo Wilson, David Rindskopf, Timothy S Lau, Emily E Tanner-Smith, Martha Yeide, Robin LaSota, Lisa Foster
For a variety of reasons, researchers and evidence-based clearinghouses synthesizing the results of multiple studies often have very few studies that are eligible for any given research question. This situation is less than optimal for meta-analysis as it is usually practiced, that is, by employing inverse variance weights, which allows more informative studies to contribute relatively more to the analysis. This article outlines the choices available for synthesis when there are few studies to synthesize. As background, we review the synthesis practices used in several projects done at the behest of governmental agencies and private foundations...
October 25, 2016: Evaluation Review
Bruno Michel, Anne-Laure Clamens, Olivier Béthoux, Gael J Kergoat, Fabien L Condamine
In this study, we reconstruct the first time-calibrated phylogeny of the iconic antlion family, the Myrmeleontidae (Neuroptera: Myrmeleontiformia). We use maximum likelihood and Bayesian inference to analyse a molecular dataset based on seven mitochondrial and nuclear gene markers. The dataset encompasses 106 species of Neuroptera, including 94 antlion species. The resulting phylogenetic framework provides support for a myrmeleontid classification distinguishing four subfamilies: Acanthaclisinae, Myrmeleontinae, Palparinae, and Stilbopteryginae...
October 22, 2016: Molecular Phylogenetics and Evolution
Bernhard Winkler, Paul P Heinisch, Brigitta Gahl, Soheila Aghlmandi, Hans Jörg Jenni, Thierry P Carrel
The pathophysiologic side effects of cardiopulmonary bypass have already been identified. Minimally invasive extracorporeal circulation technologies (MiECT) and off-pump coronary artery bypass graft surgery (OPCABG) aim to reduce these problems. This metaanalysis provides a comparison of MiECT and OPCABG in randomized and observational studies. A fully probabilistic, Bayesian approach of primary and secondary endpoints was conducted. MiECT does not give inferior results when compared with OPCABG. However, there is a trend to borderline significantly higher blood loss in this group in randomized controlled trials...
October 22, 2016: Annals of Thoracic Surgery
Paula Ribeiro Prist, Maria Uriarte, Leandro Reverberi Tambosi, Amanda Prado, Renata Pardini, Paulo Sérgio D Andrea, Jean Paul Metzger
Hantavirus Pulmonary Syndrome (HPS) is a disease caused by Hantavirus, which are negative-sense RNA viruses in the family Bunyaviridae that are highly virulent to humans. Numerous factors modify risk of Hantavirus transmission and consequent HPS risk. Human-driven landscape change can foster transmission risk by increasing numbers of habitat generalist rodent species that serve as the principal reservoir host. Climate can also affect rodent population dynamics and Hantavirus survival, and a number of social factors can influence probability of HPS transmission to humans...
2016: PloS One
Marília Silveira de Almeida Campos, Lorena Rocha Ayres, Manuela Roque Siane Morelo, Fabiana Angelo Marques, Leonardo Régis Leira Pereira
Several newer antiepileptic drugs (AEDs) have been introduced into clinical practice, offering choices for individualizing the treatment of epilepsy since AEDs have different efficacy and tolerability profiles. In particular, questions exist regarding which AEDs are the best options for the monotherapy of focal epilepsy. Is carbamazepine (CBZ), which is considered the standard treatment for focal epilepsy, still the best option for monotherapy of focal epilepsy, despite the emergence of new AEDs? In this systematic review, we compared the relative tolerability of all available AEDs for monotherapy of all types of epilepsy as well as their efficacy in the monotherapy of focal epilepsy...
October 25, 2016: Pharmacotherapy
Neal D Goldstein, Igor Burstyn, Seth L Welles
BACKGROUND: Men who have sex with men (MSM) continue to be overrepresented for new HIV infections compared to non-MSM. This disparity becomes even more alarming when considering racial groups. We describe the race-specific effects in HIV prevalence among MSM relative to non-MSM and explore the causes of disagreement among estimates. METHODS: We used data from the National Epidemiologic Survey on Alcohol and Related Conditions, a nationally representative longitudinal survey conducted in the U...
October 21, 2016: Epidemiology
Sebastian Schneeweiss, Wesley Eddings, Robert J Glynn, Elisabetta Patorno, Jeremy Rassen, Jessica M Franklin
BACKGROUND: Data-adaptive approaches to confounding adjustment may improve performance beyond expert knowledge when analyzing electronic healthcare databases and have additional practical advantages for analyzing multiple databases in rapid cycles. Improvements seemed possible if outcome predictors were reliably identified empirically and adjusted. METHODS: In five cohort studies from diverse healthcare databases, we implemented a base-case high-dimensional propensity score algorithm with propensity score decile-adjusted outcome models to estimate treatment effects among prescription drug initiators...
October 21, 2016: Epidemiology
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