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https://www.readbyqxmd.com/read/28525607/rna-moip-prediction-of-rna-secondary-structure-and-local-3d-motifs-from-sequence-data
#1
Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldisphül
RNA structures are hierarchically organized. The secondary structure is articulated around sophisticated local three-dimensional (3D) motifs shaping the full 3D architecture of the molecule. Recent contributions have identified and organized recurrent local 3D motifs, but applications of this knowledge for predictive purposes is still in its infancy. We recently developed a computational framework, named RNA-MoIP, to reconcile RNA secondary structure and local 3D motif information available in databases. In this paper, we introduce a web service using our software for predicting RNA hybrid 2D-3D structures from sequence data only...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28518405/setting-ambitious-yet-achievable-targets-using-probabilistic-projections-meeting-demand-for-family-planning
#2
Vladimíra Kantorová, Jin Rou New, Ann Biddlecom, Leontine Alkema
In 2015, governments adopted 17 internationally agreed goals to ensure progress and well-being in the economic, social, and environmental dimensions of sustainable development. These new goals present a challenge for countries to set empirical targets that are ambitious yet achievable and that can account for different starting points and rates of progress. We used probabilistic projections of family planning indicators, based on a global data set and Bayesian hierarchical modeling, to generate illustrative targets at the country level...
May 18, 2017: Studies in Family Planning
https://www.readbyqxmd.com/read/28513206/a-general-architecture-for-robotics-systems-a-perception-based-approach-to-artificial-life
#3
Rupert Young
Departing from the conventional view of the reasons for the behavior of living systems, this research presents a radical and unique view of that behavior, as the observed side effects of a hierarchical set of simple, continuous, and dynamic negative feedback control systems, by way of an experimental model implemented on a real-world autonomous robotic rover. Rather than generating specific output from input, the systems control their perceptual inputs by varying output. The variables controlled do not exist in the environment, but are entirely internal perceptions constructed as a result of the layout and connections of the neural architecture...
May 17, 2017: Artificial Life
https://www.readbyqxmd.com/read/28510584/identification-of-novel-risk-factors-for-community-acquired-clostridium-difficile-infection-using-spatial-statistics-and-geographic-information-system-analyses
#4
Deverick J Anderson, Leoncio Flavio Rojas, Shera Watson, Lauren P Knelson, Sohayla Pruitt, Sarah S Lewis, Rebekah W Moehring, Emily E Sickbert Bennett, David J Weber, Luke F Chen, Daniel J Sexton
BACKGROUND: The rate of community-acquired Clostridium difficile infection (CA-CDI) is increasing. While receipt of antibiotics remains an important risk factor for CDI, studies related to acquisition of C. difficile outside of hospitals are lacking. As a result, risk factors for exposure to C. difficile in community settings have been inadequately studied. MAIN OBJECTIVE: To identify novel environmental risk factors for CA-CDI. METHODS: We performed a population-based retrospective cohort study of patients with CA-CDI from 1/1/2007 through 12/31/2014 in a 10-county area in central North Carolina...
2017: PloS One
https://www.readbyqxmd.com/read/28506987/development-of-the-larval-lymphatic-system-in-the-zebrafish
#5
Hyun Min Jung, Daniel Castranova, Matthew R Swift, Van N Pham, Marina Venero Galanternik, Sumio Isogai, Matthew G Butler, Timothy S Mulligan, Brant M Weinstein
The lymphatic vascular system is a hierarchically organized complex network essential for tissue fluid homeostasis, immune trafficking, and absorption of dietary fats in the human body. Despite its importance, the assembly of the lymphatic network is still not fully understood. The zebrafish is a powerful model organism that enables study of lymphatic vessel development using high-resolution imaging and sophisticated genetic and experimental manipulation. Although several studies have described early lymphatic development in the fish, lymphatic development at later stages has not been completely elucidated...
May 15, 2017: Development
https://www.readbyqxmd.com/read/28505251/false-discovery-rate-control-incorporating-phylogenetic-tree-increases-detection-power-in-microbiome-wide-multiple-testing
#6
Jian Xiao, Hongyuan Cao, Jun Chen
Motivation: Next generation sequencing technologies have enabled the study of the human microbiome through direct sequencing of microbial DNA, resulting in an enormous amount of microbiome sequencing data. One unique characteristic of microbiome data is the phylogenetic tree that relates all the bacterial species. Closely related bacterial species have a tendency to exhibit a similar relationship with the environment or disease. Thus, incorporating the phylogenetic tree information can potentially improve the detection power for microbiome-wide association studies, where hundreds or thousands of tests are conducted simultaneously to identify bacterial species associated with a phenotype of interest...
May 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28503665/probabilistic-modeling-of-bifurcations-in-single-cell-gene-expression-data-using-a-bayesian-mixture-of-factor-analyzers
#7
Kieran R Campbell, Christopher Yau
Modeling bifurcations in single-cell transcriptomics data has become an increasingly popular field of research. Several methods have been proposed to infer bifurcation structure from such data, but all rely on heuristic non-probabilistic inference. Here we propose the first generative, fully probabilistic model for such inference based on a Bayesian hierarchical mixture of factor analyzers. Our model exhibits competitive performance on large datasets despite implementing full Markov-Chain Monte Carlo sampling, and its unique hierarchical prior structure enables automatic determination of genes driving the bifurcation process...
March 15, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28502001/clustering-and-network-analysis-of-reverse-phase-protein-array-data
#8
Adam Byron
Molecular profiling of proteins and phosphoproteins using a reverse phase protein array (RPPA) platform, with a panel of target-specific antibodies, enables the parallel, quantitative proteomic analysis of many biological samples in a microarray format. Hence, RPPA analysis can generate a high volume of multidimensional data that must be effectively interrogated and interpreted. A range of computational techniques for data mining can be applied to detect and explore data structure and to form functional predictions from large datasets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28495092/response-surface-fits-and-calibration-transfer-for-the-correction-of-the-oxygen-effect-in-the-quantification-of-carbon-dioxide-via-ftir-spectroscopy
#9
Felicia Seichter, Josef Vogt, Peter Radermacher, Boris Mizaikoff
During routine Fourier-Transform Infrared Spectroscopy (FTIR) based quantification of carbon dioxide in breath, it is necessary to account for a non-linear signal response to the analyte concentration and disturbance factors arising from the gas background matrix. These factors as well as day-to-day fluctuation should be corrected via calibration. We present a novel strategy to combine the information of previous calibrations with a minimal number of actual calibration measurements to obtain a precise calibration...
June 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28492681/statistical-modelling-and-simulation-of-nanohybrid-shish-kebab-architecture-of-pe-b-peg-copolymers-and-carbon-nanotubes
#10
Tuan Le, Nina Collazos, Austin Simoneaux, Siva Murru, Dilip Depan, Ramalingam Subramaniam
Carbon nanotubes have been known to develop hierarchically ordered polymer nanocomposites by virtue of epitaxial crystallization. A unique product of CNT induced crystallization is generation of nanohybrid shish-kebab (NHSK) structure, which has gained tremendous attention owing to its unique applications. However, research faces major challenges in terms of producing tunable patterns on CNTs, which are largely governed by precise control of the crystallization parameters. Conventional methods of experimentation can mislead the effect of experimental conditions on NHSK structure...
May 11, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28491495/dorsolateral-prefrontal-cortex-contributes-to-the-impaired-behavioral-adaptation-in-alcohol-dependence
#11
Sinem Balta Beylergil, Anne Beck, Lorenz Deserno, Robert C Lorenz, Michael A Rapp, Florian Schlagenhauf, Andreas Heinz, Klaus Obermayer
Substance-dependent individuals often lack the ability to adjust decisions flexibly in response to the changes in reward contingencies. Prediction errors (PEs) are thought to mediate flexible decision-making by updating the reward values associated with available actions. In this study, we explored whether the neurobiological correlates of PEs are altered in alcohol dependence. Behavioral, and functional magnetic resonance imaging (fMRI) data were simultaneously acquired from 34 abstinent alcohol-dependent patients (ADP) and 26 healthy controls (HC) during a probabilistic reward-guided decision-making task with dynamically changing reinforcement contingencies...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28489045/discontinuity-detection-in-the-shield-metal-arc-welding-process
#12
José Alberto Naves Cocota, Gabriel Carvalho Garcia, Adilson Rodrigues da Costa, Milton Sérgio Fernandes de Lima, Filipe Augusto Santos Rocha, Gustavo Medeiros Freitas
This work proposes a new methodology for the detection of discontinuities in the weld bead applied in Shielded Metal Arc Welding (SMAW) processes. The detection system is based on two sensors-a microphone and piezoelectric-that acquire acoustic emissions generated during the welding. The feature vectors extracted from the sensor dataset are used to construct classifier models. The approaches based on Artificial Neural Network (ANN) and Support Vector Machine (SVM) classifiers are able to identify with a high accuracy the three proposed weld bead classes: desirable weld bead, shrinkage cavity and burn through discontinuities...
May 10, 2017: Sensors
https://www.readbyqxmd.com/read/28488234/microphysiological-human-brain-and-neural-systems-on-a-chip-potential-alternatives-to-small-animal-models-and-emerging-platforms-for-drug-discovery-and-personalized-medicine
#13
Alexander P Haring, Harald Sontheimer, Blake N Johnson
Translational challenges associated with reductionist modeling approaches, as well as ethical concerns and economic implications of small animal testing, drive the need for developing microphysiological neural systems for modeling human neurological diseases, disorders, and injuries. Here, we provide a comprehensive review of microphysiological brain and neural systems-on-a-chip (NSCs) for modeling higher order trajectories in the human nervous system. Societal, economic, and national security impacts of neurological diseases, disorders, and injuries are highlighted to identify critical NSC application spaces...
May 10, 2017: Stem Cell Reviews
https://www.readbyqxmd.com/read/28487968/a-pilot-study-identifying-a-potential-plasma-biomarker-for-determining-egfr-mutations-in-exons%C3%A2-19-or-21-in-lung-cancer-patients
#14
Aryo D Pamungkas, Carl A Medriano, Eunjung Sim, Sungyong Lee, Youngja H Park
The most common type of lung cancer is non‑small cell lung cancer (NSCLC), which is frequently characterized by a mutation in the epidermal growth factor receptor (EGFR). Determining the presence of an EGFR mutation in lung cancer is important, as it determines the type of treatment that a patients will receive. Therefore, the aim of the present study was to apply high‑resolution metabolomics (HRM) using liquid chromatography‑mass spectrometry to identify significant compounds in human plasma samples obtained from South Korean NSCLC patients, as potential biomarkers for providing early detection and diagnosis of minimally‑invasive NSCLC...
June 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28485089/materials-nanoarchitecturing-via-cation-mediated-protein-assembly-making-limpet-teeth-without-mineral
#15
Tina Ukmar-Godec, Luca Bertinetti, John W C Dunlop, Aljaž Godec, Michal A Grabiger, Admir Masic, Huynh Nguyen, Igor Zlotnikov, Paul Zaslansky, Damien Faivre
Teeth are designed to deliver high forces while withstanding the generated stresses. Aside from isolated mineral-free exception (e.g., marine polychaetes and squids), minerals are thought to be indispensable for tooth-hardening and durability. Here, the unmineralized teeth of the giant keyhole limpet (Megathura crenulata) are shown to attain a stiffness, which is twofold higher than any known organic biogenic structures. In these teeth, protein and chitin fibers establish a stiff compact outer shell enclosing a less compact core...
May 9, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28484629/multiple-phase-transitions-in-an-agent-based-evolutionary-model-with-neutral-fitness
#16
Dawn M King, Adam D Scott, Sonya Bahar
Null models are crucial for understanding evolutionary processes such as speciation and adaptive radiation. We analyse an agent-based null model, considering a case without selection-neutral evolution-in which organisms are defined only by phenotype. Universal dynamics has previously been demonstrated in a related model on a neutral fitness landscape, showing that this system belongs to the directed percolation (DP) universality class. The traditional null condition of neutral fitness (where fitness is defined as the number of offspring each organism produces) is extended here to include equal probability of death among organisms...
April 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28472220/the-spike-and-slab-lasso-cox-model-for-survival-prediction-and-associated-genes-detection
#17
Zaixiang Tang, Yueping Shen, Xinyan Zhang, Nengjun Yi
Motivation: Large-scale molecular profiling data have offered extraordinary opportunities to improve survival prediction of cancers and other diseases and to detect disease associated genes. However, there are considerable challenges in analyzing large-scale molecular data. Results: We propose new Bayesian hierarchical Cox proportional hazards models, called the spike-and-slab lasso Cox, for predicting survival outcomes and detecting associated genes. We also develop an efficient algorithm to fit the proposed models by incorporating EM steps (Expectation-Maximization) into the extremely fast cyclic coordinate descent algorithm...
May 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28471384/non-uniform-fusion-tree-generation-in-a-dynamic-multi-sensor-system
#18
Kyuoke Yeun, Daeyoung Kim
This paper addresses the proposal that the number of processed air tracks of a two-tier fusion process can be increased by applying a balanced fusion tree which can balance tracks across local fusion nodes. Every fusion cycle, a fusion process combines duplicate tracks from multiple radars and creates a single integrated air picture (SIAP). The two-tier fusion process divides the fusion process into local and global. The results of the local fusion process, executed at local fusion nodes, are used in the global fusion process...
May 4, 2017: Sensors
https://www.readbyqxmd.com/read/28447843/seeing-what-through-why-evidence-from-probing-the-causal-structure-of-hierarchical-motion
#19
Haokui Xu, Ning Tang, Jifan Zhou, Mowei Shen, Tao Gao
Although our world is hierarchically organized, the perception, attention, and memory of hierarchical structures remain largely unknown. The current study shows how a hierarchical motion representation enhances the inference of an object's position in a dynamic display. The motion hierarchy is formed as an acyclic tree in which each node represents a distinctive motion component. Each individual object is instantiated as a node in the tree. In a position inference task, participants were asked to infer the position of a target object, given how it moved jointly with other objects...
April 27, 2017: Journal of Experimental Psychology. General
https://www.readbyqxmd.com/read/28447811/likelihood-based-parameter-estimation-and-comparison-of-dynamical-cognitive-models
#20
Heiko H Schütt, Lars O M Rothkegel, Hans A Trukenbrod, Sebastian Reich, Felix A Wichmann, Ralf Engbert
Dynamical models of cognition play an increasingly important role in driving theoretical and experimental research in psychology. Therefore, parameter estimation, model analysis and comparison of dynamical models are of essential importance. In this article, we propose a maximum likelihood approach for model analysis in a fully dynamical framework that includes time-ordered experimental data. Our methods can be applied to dynamical models for the prediction of discrete behavior (e.g., movement onsets); in particular, we use a dynamical model of saccade generation in scene viewing as a case study for our approach...
April 27, 2017: Psychological Review
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