Read by QxMD icon Read


Cannada Andrew Lewis, Justus Aaron Calvin, Edward F Valeev
We describe the Clustered Low Rank (CLR) framework for block-sparse and block-low-rank tensor representation and computation. The CLR framework exploits the tensor structure revealed by basis clustering; computational savings arise from low-rank compression of tensor blocks and performing block arithmetic in the low-rank form whenever beneficial. The precision is rigorously controlled by 2 parameters, avoiding ad-hoc heuristics, such as domains: one controls the CLR block rank truncation and the other controls screening of small contributions in arithmetic operations on CLR tensors to propagate sparsity through expressions...
October 26, 2016: Journal of Chemical Theory and Computation
Sheng-Jou Hung, Yi-Lin Chen, Chia-Hung Chu, Chuan-Chun Lee, Wan-Li Chen, Ya-Lan Lin, Ming-Ching Lin, Chung-Liang Ho, Tsunglin Liu
BACKGROUND: T cells and B cells are essential in the adaptive immunity via expressing T cell receptors and immunoglogulins respectively for recognizing antigens. To recognize a wide variety of antigens, a highly diverse repertoire of receptors is generated via complex recombination of the receptor genes. Reasonably, frequencies of the recombination events have been shown to predict immune diseases and provide insights into the development of immunity. The field is further boosted by high-throughput sequencing and several computational tools have been released to analyze the recombined sequences...
October 26, 2016: BMC Bioinformatics
Xian Teng, Sen Pei, Flaviano Morone, Hernán A Makse
Identifying the most influential spreaders that maximize information flow is a central question in network theory. Recently, a scalable method called "Collective Influence (CI)" has been put forward through collective influence maximization. In contrast to heuristic methods evaluating nodes' significance separately, CI method inspects the collective influence of multiple spreaders. Despite that CI applies to the influence maximization problem in percolation model, it is still important to examine its efficacy in realistic information spreading...
October 26, 2016: Scientific Reports
Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé
BACKGROUND: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. METHODS: When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH...
2016: PeerJ
Justin Donhauser
The world's leading environmental advisory institutions look to ecological theory and research as an objective guide for policy and resource management decision-making. In addition to the theoretical and broadly philosophical merits of doing so, it is therefore practically significant to clear up confusions about ecology's conceptual foundations and to clarify the basic workings of inferential methods used in the science. Through discussion of key moments in the genesis of the theoretical branch of ecology, this essay elucidates a general heuristic role of teleological metaphors in ecological research and defuses certain enduring confusions about work in ecology...
October 22, 2016: Studies in History and Philosophy of Biological and Biomedical Sciences
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
Wenzhangzhi Guo, Parham Aarabi
We present a method for binary classification using neural networks (NNs) that performs training and classification on the same data using the help of a pretraining heuristic classifier. The heuristic classifier is initially used to segment data into three clusters of high-confidence positives, high-confidence negatives, and low-confidence sets. The high-confidence sets are used to train an NN, which is then used to classify the low-confidence set. Applying this method to the binary classification of hair versus nonhair patches, we obtain a 2...
October 18, 2016: IEEE Transactions on Neural Networks and Learning Systems
Jiaxiang Huang, Maoguo Gong, Lijia Ma
Molecular interactions data increase exponentially with the advance of biotechnology. This makes it possible and necessary to comparatively analyse the different data at a network level. Global network alignment is an important network comparison approach to identify conserved subnetworks and get insight into evolutionary relationship across species. Network alignment which is analogous to subgraph isomorphism is known to be an NP-hard problem. In this paper, we introduce a novel heuristic Particle-Swarm-Optimization based Network Aligner (PSONA), which optimizes a weighted global alignment model considering both protein sequence similarity and interaction conservations...
October 19, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Donald Glowinski, Fabrizio Bracco, Carlo Chiorri, Didier Grandjean
The present contribution provides readers from diverse fields of psychology with a new and comprehensive model for the understanding of the characteristics of music ensembles. The model is based on a novel heuristic approach whose key construct is resilience, intended here as the ability of a system to adapt to external perturbations and anticipate future events. The paper clarifies the specificity of music ensemble as an original social and creative activity, and how some mechanisms, at an individual (cognitive) and group (coordination) level, are enacted in a particular way that endows these groups with exceptional capacity for resilience...
2016: Frontiers in Psychology
Julian Wiemer, Paul Pauli
Fear-relevant illusory correlations (ICs) are defined as the overestimation of the relationship between a fear-relevant stimulus and aversive consequences. ICs reflect biased cognitions affecting the learning and unlearning of fear in anxiety disorders, and a deeper understanding might help to improve treatment. A model for the maintenance of ICs is proposed that highlights the importance of amplified aversiveness and salience of fear-relevant outcomes, impaired executive contingency monitoring and an availability heuristic...
October 17, 2016: Journal of Anxiety Disorders
Óscar J C Dias, Jorge E Santos, Benson Way
According to heuristic arguments, global AdS_{5}×S^{5} black holes are expected to undergo a phase transition in the microcanonical ensemble. At high energies, one expects black holes that respect the symmetries of the S^{5}; at low energies, one expects "localized" black holes that appear pointlike on the S^{5}. According to anti-de Sitter/conformal field theory correspondence, N=4 supersymmetric Yang-Mills (SYM) theory on a 3-sphere should therefore exhibit spontaneous R-symmetry breaking at strong coupling...
October 7, 2016: Physical Review Letters
Wayne D Gray, John K Lindstedt
The framework of plateaus, dips, and leaps shines light on periods when individuals may be inventing new methods of skilled performance. We begin with a review of the role performance plateaus have played in (a) experimental psychology, (b) human-computer interaction, and (c) cognitive science. We then reanalyze two classic studies of individual performance to show plateaus and dips which resulted in performance leaps. For a third study, we show how the statistical methods of Changepoint Analysis plus a few simple heuristics may direct our focus to periods of performance change for individuals...
October 20, 2016: Cognitive Science
Yasin Gocgun
We study radiation therapy scheduling problem where dynamically and stochastically arriving patients of different types are scheduled to future days. Unlike similar models in the literature, we consider cancellation of treatments. We formulate this dynamic multi-appointment patient scheduling problem as a Markov Decision Process (MDP). Since the MDP is intractable due to large state and action spaces, we employ a simulation-based approximate dynamic programming (ADP) approach to approximately solve our model...
October 20, 2016: Health Care Management Science
Julio Fernandez-Mendoza
PURPOSE OF REVIEW: It was first proposed in the late 1990s that objective markers of sleep disturbance could serve as an index of the biological severity of insomnia. In 2013, a heuristic model of two insomnia phenotypes based on objective sleep duration was proposed. Herein, we review the studies conducted in the past 3 years on the insomnia with short sleep duration phenotype and its implications for a clinical research agenda. RECENT FINDINGS: Studies have shown that insomnia with objective short sleep duration is associated with physiologic hyperarousal and cardiometabolic and neurocognitive morbidity, whereas insomnia with normal sleep duration is not...
October 18, 2016: Current Opinion in Psychiatry
Peter A Bos
Variation in the quality of parental care has a tremendous impact on a child's social-emotional development. Research investigating the predictors of this variability in human caregiving behavior has mostly focused on learning mechanisms. Evidence is currently accumulating for the complementary underlying role of steroid hormones and neuropeptides. An overview is provided of the hormones and neuropeptides relevant for human caregiving behavior. Then the developmental factors are described that stimulate variability in sensitivity to these hormones and neuropeptides, which may result in variability in the behavioral repertoire of caregiving...
October 20, 2016: Development and Psychopathology
Andriy Temko, Gordon Lightbody
It is now generally accepted that EEG is the only reliable way to accurately detect newborn seizures and, as such, prolonged EEG monitoring is increasingly being adopted in neonatal intensive care units. Long EEG recordings may last from several hours to a few days. With neurophysiologists not always available to review the EEG during unsociable hours, there is a pressing need to develop a reliable and robust automatic seizure detection method-a computer algorithm that can take the EEG signal, process it, and output information that supports clinical decision making...
October 2016: Journal of Clinical Neurophysiology: Official Publication of the American Electroencephalographic Society
Andreas Holzinger
Machine learning (ML) is the fastest growing field in computer science, and health informatics is among the greatest challenges. The goal of ML is to develop algorithms which can learn and improve over time and can be used for predictions. Most ML researchers concentrate on automatic machine learning (aML), where great advances have been made, for example, in speech recognition, recommender systems, or autonomous vehicles. Automatic approaches greatly benefit from big data with many training sets. However, in the health domain, sometimes we are confronted with a small number of data sets or rare events, where aML-approaches suffer of insufficient training samples...
June 2016: Brain Informatics
Fausto Carnevale Neto, Alan C Pilon, Denise M Selegato, Rafael T Freire, Haiwei Gu, Daniel Raftery, Norberto P Lopes, Ian Castro-Gamboa
Dereplication based on hyphenated techniques has been extensively applied in plant metabolomics, thereby avoiding re-isolation of known natural products. However, due to the complex nature of biological samples and their large concentration range, dereplication requires the use of chemometric tools to comprehensively extract information from the acquired data. In this work we developed a reliable GC-MS-based method for the identification of non-targeted plant metabolites by combining the Ratio Analysis of Mass Spectrometry deconvolution tool (RAMSY) with Automated Mass Spectral Deconvolution and Identification System software (AMDIS)...
2016: Frontiers in Molecular Biosciences
Yong Yang
Recently, research on utilitarian walking has gained momentum due to its benefits on both health and the environment. However, our overall understanding of how built and social environments affect travel mode choice (walking or not) is still limited, and most existing frameworks on travel mode choice lack dynamic processes. After a review of several mainstream theories and a number of frameworks, we propose an integrated framework. The basic constructs in the travel mode choice function are utilities, constraints, attitudes, and habits...
September 2016: Journal of Transport & Health
Carl Brunius, Lin Shi, Rikard Landberg
INTRODUCTION: Liquid chromatography-mass spectrometry (LC-MS) is a commonly used technique in untargeted metabolomics owing to broad coverage of metabolites, high sensitivity and simple sample preparation. However, data generated from multiple batches are affected by measurement errors inherent to alterations in signal intensity, drift in mass accuracy and retention times between samples both within and between batches. These measurement errors reduce repeatability and reproducibility and may thus decrease the power to detect biological responses and obscure interpretation...
2016: Metabolomics: Official Journal of the Metabolomic Society
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"