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https://www.readbyqxmd.com/read/28088527/navigation-in-the-electronic-health-record-a-review-of-the-safety-and-usability-literature
#1
REVIEW
Lisette C Roman, Jessica S Ancker, Stephen B Johnson, Yalini Senathirajah
OBJECTIVE: Inefficient navigation in electronic health records has been shown to increase users' cognitive load, which may increase potential for errors, reduce efficiency, and increase fatigue. However, navigation has received insufficient recognition and attention in the electronic health record (EHR) literature as an independent construct and contributor to overall usability. Our aims in this literature review were to (1) assess the prevalence of navigation-related topics within the EHR usability and safety research literature, (2) categorize types of navigation actions within the EHR, (3) capture relationships between these navigation actions and usability principles, and (4) collect terms and concepts related to EHR navigation...
January 11, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28088189/mars-improving-multiple-circular-sequence-alignment-using-refined-sequences
#2
Lorraine A K Ayad, Solon P Pissis
BACKGROUND: A fundamental assumption of all widely-used multiple sequence alignment techniques is that the left- and right-most positions of the input sequences are relevant to the alignment. However, the position where a sequence starts or ends can be totally arbitrary due to a number of reasons: arbitrariness in the linearisation (sequencing) of a circular molecular structure; or inconsistencies introduced into sequence databases due to different linearisation standards. These scenarios are relevant, for instance, in the process of multiple sequence alignment of mitochondrial DNA, viroid, viral or other genomes, which have a circular molecular structure...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28088147/hopping-charge-transport-in-amorphous-semiconductors-with-the-spatially-correlated-exponential-density-of-states
#3
S V Novikov
Hopping charge transport in amorphous semiconductors having spatially correlated exponential density of states has been considered. Average carrier velocity is exactly calculated for the quasi-equilibrium (nondispersive) transport regime. We suggest also a heuristic approach for the consideration of the carrier velocity for the non-equilibrium dispersive regime.
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28087895/crohn-disease-risk-prediction-best-practices-and-pitfalls-with-exome-data
#4
Manuel Giollo, David T Jones, Marco Carraro, Emanuela Leonardi, Carlo Ferrari, Silvio C E Tosatto
The Critical Assessment of Genome Interpretation (CAGI) experiment is the first attempt to evaluate the state-of-the-art in genetic data interpretation. Among the proposed challenges, Crohn disease (CD) risk prediction has become the most classic problem spanning three editions. The scientific question is very hard: can anybody assess the risk to develop CD given the exome data alone? This is one of the ultimate goals of genetic analysis, which motivated most CAGI participants to look for powerful new methods...
January 13, 2017: Human Mutation
https://www.readbyqxmd.com/read/28074861/deployment-of-check-in-nodes-in-complex-networks
#5
Zhong-Yuan Jiang, Jian-Feng Ma
In many real complex networks such as the city road networks and highway networks, vehicles often have to pass through some specially functioned nodes to receive check-in like services such as gas supplement at gas stations. Based on existing network structures, to guarantee every shortest path including at least a check-in node, the location selection of all check-in nodes is very essential and important to make vehicles to easily visit these check-in nodes, and it is still remains an open problem in complex network studies...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28073329/the-other-side-of-magic
#6
Vebjørn Ekroll, Bilge Sayim, Johan Wagemans
When magicians perform spectacles that seem to defy the laws of nature, they do so by manipulating psychological reality. Hence, the principles underlying the art of conjuring are potentially of interest to psychological science. Here, we argue that perceptual and cognitive principles governing how humans experience hidden things and reason about them play a central role in many magic tricks. Different from tricks based on many other forms of misdirection, which require considerable skill on the part of the magician, many elements of these tricks are essentially self-working because they rely on automatic perceptual and cognitive processes...
January 2017: Perspectives on Psychological Science: a Journal of the Association for Psychological Science
https://www.readbyqxmd.com/read/28072847/heuristic-strategies-for-persuader-selection-in-contagions-on-complex-networks
#7
Peng Wang, Li-Jie Zhang, Xin-Jian Xu, Gaoxi Xiao
Individual decision to accept a new idea or product is often driven by both self-adoption and others' persuasion, which has been simulated using a double threshold model [Huang et al., Scientific Reports 6, 23766 (2016)]. We extend the study to consider the case with limited persuasion. That is, a set of individuals is chosen from the population to be equipped with persuasion capabilities, who may succeed in persuading their friends to take the new entity when certain conditions are satisfied. Network node centrality is adopted to characterize each node's influence, based on which three heuristic strategies are applied to pick out persuaders...
2017: PloS One
https://www.readbyqxmd.com/read/28072555/on-constructing-ensembles-for-combinatorial-optimisation
#8
Emma Hart, Kevin Sim
Although the use of ensemble methods in machine-learning is ubiquitous due to their proven ability to outperform their constituent algorithms, ensembles of optimisation algorithms have received relatively little attention. Existing approaches lag behind machine-learning in both theory and practice, with no principled design guide-lines available. In this paper, we address fundamental questions regarding ensemble composition in optimisation using the domain of bin-packing as a example; in particular we investigate the trade-off between accuracy and diversity, and whether diversity metrics can be used as a proxy for constructing an ensemble, proposing a number of novel metrics for comparing algorithm diversity...
January 10, 2017: Evolutionary Computation
https://www.readbyqxmd.com/read/28069165/on-the-quantification-and-visualization-of-transient-periodic-instabilities-in-pulsatile-flows
#9
Muhammad Owais Khan, Christophe Chnafa, Diego Gallo, Filippo Molinari, Umberto Morbiducci, David A Steinman, Kristian Valen-Sendstad
Turbulent-like flows without cycle-to-cycle variations are more frequently being reported in studies of cardiovascular flows. The associated stimuli might be of mechanobiological relevance, but how to quantify them objectively is not obvious. Classical Reynolds decomposition, where the flow is separated into mean and fluctuating velocity components, is not applicable as the phase-average is zero. We therefore expanded on established techniques and present the idea, analogous to Reynolds decomposition, to decompose a flow with transient instabilities into low- versus high frequency components, respectively, to discriminate flow instabilities from the underlying cardiac pulsatility...
December 31, 2016: Journal of Biomechanics
https://www.readbyqxmd.com/read/28068248/clinical-implementation-of-dual-energy-ct-for-proton-treatment-planning-on-pseudo-monoenergetic-ct-scans
#10
Patrick Wohlfahrt, Christian Möhler, Volker Hietschold, Stefan Menkel, Steffen Greilich, Mechthild Krause, Michael Baumann, Wolfgang Enghardt, Christian Richter
PURPOSE: To determine whether a standardized clinical application of dual-energy computed tomography (DECT) for proton treatment planning based on pseudomonoenergetic CT scans (MonoCTs) is feasible and increases the precision of proton therapy in comparison with single-energy CT (SECT). METHODS AND MATERIALS: To define an optimized DECT protocol, CT scan settings were analyzed experimentally concerning beam hardening, image quality, and influence on the heuristic conversion of CT numbers into stopping-power ratios (SPRs) and were compared with SECT scans with identical CT dose...
February 1, 2017: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/28066917/balancing-exploration-and-exploitation-in-population-based-sampling-improves-fragment-based-de-novo-protein-structure-prediction
#11
David Simoncini, Thomas Schiex, Kam Y J Zhang
Conformational search space exploration remains a major bottleneck for protein structure prediction methods. Population-based meta-heuristics typically enable the possibility to control the search dynamics and to tune the balance between local energy minimization and search space exploration. EdaFold is a fragment-based approach that can guide search by periodically updating the probability distribution over the fragment libraries used during model assembly. We implement the EdaFold algorithm as a Rosetta protocol and provide two different probability update policies: a cluster-based variation (EdaRosec ) and an energy-based one (EdaRoseen ) We analyze the search dynamics of our new Rosetta protocols and show that EdaRosec EdaRosec is able to provide predictions with lower Cα RMSD to the native structure than EdaRoseen and Rosetta AbInitio Relax protocol...
January 9, 2017: Proteins
https://www.readbyqxmd.com/read/28060429/reconfiguring-social-value-in-health-research-through-the-lens-of-liminality
#12
Agomoni Ganguli-Mitra, Edward S Dove, Graeme T Laurie, Samuel Taylor-Alexander
Despite the growing importance of 'social value' as a central feature of research ethics, the term remains both conceptually vague and to a certain extent operationally rigid. And yet, perhaps because the rhetorical appeal of social value appears immediate and self-evident, the concept has not been put to rigorous investigation in terms of its definition, strength, function, and scope. In this article, we discuss how the anthropological concept of liminality can illuminate social value and differentiate and reconfigure its variegated approaches...
February 2017: Bioethics
https://www.readbyqxmd.com/read/28059326/augmented-design-and-analysis-of-computer-experiments-a-novel-tolerance-embedded-global-optimization-approach-applied-to-swir-hyperspectral-illumination-design
#13
Janos C Keresztes, R John Koshel, Karlien D'huys, Bart De Ketelaere, Jan Audenaert, Peter Goos, Wouter Saeys
A novel meta-heuristic approach for minimizing nonlinear constrained problems is proposed, which offers tolerance information during the search for the global optimum. The method is based on the concept of design and analysis of computer experiments combined with a novel two phase design augmentation (DACEDA), which models the entire merit space using a Gaussian process, with iteratively increased resolution around the optimum. The algorithm is introduced through a series of cases studies with increasing complexity for optimizing uniformity of a short-wave infrared (SWIR) hyperspectral imaging (HSI) illumination system (IS)...
December 26, 2016: Optics Express
https://www.readbyqxmd.com/read/28055941/a-dynamic-neighborhood-learning-based-gravitational-search-algorithm
#14
Aizhu Zhang, Genyun Sun, Jinchang Ren, Xiaodong Li, Zhenjie Wang, Xiuping Jia
Balancing exploration and exploitation according to evolutionary states is crucial to meta-heuristic search (M-HS) algorithms. Owing to its simplicity in theory and effectiveness in global optimization, gravitational search algorithm (GSA) has attracted increasing attention in recent years. However, the tradeoff between exploration and exploitation in GSA is achieved mainly by adjusting the size of an archive, named Kbest, which stores those superior agents after fitness sorting in each iteration. Since the global property of Kbest remains unchanged in the whole evolutionary process, GSA emphasizes exploitation over exploration and suffers from rapid loss of diversity and premature convergence...
December 30, 2016: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28055216/quantum-confined-and-enhanced-optical-absorption-of-colloidal-pbs-quantum-dots-at-wavelengths-with-expected-bulk-behavior
#15
Doriana Debellis, Giuseppe Gigli, Stephanie Ten Brinck, Ivan Infante, Carlo Giansante
Nowadays it is well-accepted to attribute bulk-like optical absorption properties to colloidal PbS quantum dots (QDs) at wavelengths above 400 nm. This assumption permits to describe PbS QD light absorption by using bulk optical constants and to determine QD concentration in colloidal solutions from simple spectrophotometric measurements. Here we demonstrate that PbS QDs experience the quantum confinement regime across the entire near UV-Vis-NIR spectral range, therefore also between 350 and 400 nm already proposed to be sufficiently far above the band gap to suppress quantum confinement...
January 5, 2017: Nano Letters
https://www.readbyqxmd.com/read/28054711/nature-meets-nurture-in-religious-and-spiritual-development
#16
Pehr Granqvist, Frances Nkara
We consider nurture's (including culture's) sculpting influences on the evolved psychological predispositions that are expressed in religious and spiritual (R&S) development. An integrated understanding of R&S development requires a move away from the largely one-sided (nature-or-nurture) and additive (nature + nurture) accounts provided in the extant literature. R&S development has been understood as an expression of evolved cognitive modules (nature) on the one hand, and of socialization and social learning (nurture) on the other, or in similar albeit additive terms (e...
January 5, 2017: British Journal of Developmental Psychology
https://www.readbyqxmd.com/read/28053140/efficient-bayesian-species-tree-inference-under-the-multispecies-coalescent
#17
Bruce Rannala, Ziheng Yang
We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we implement two efficient MCMC proposals: the first is based on the Subtree Pruning and Regrafting (SPR) algorithm and the second is based on a node-slider algorithm. Like the Nearest-Neighbor Interchange (NNI) algorithm we implemented previously, both new algorithms propose changes to the species tree while simultaneously altering the gene trees at multiple genetic loci to automatically avoid conflicts with the newly proposed species tree...
January 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28052046/fast-approximate-delivery-of-fluence-maps-for-imrt-and-vmat
#18
Marleen Balvert, David L Craft
In this article we provide a method to generate the trade-off between delivery time and fluence map matching quality for dynamically delivered fluence maps. At the heart of our method lies a mathematical programming model that, for a given duration of delivery, optimizes leaf trajectories and dose rates such that the desired fluence map is reproduced as well as possible. We begin with the single fluence map case and then generalize the model and the solution technique to the delivery of sequential fluence maps...
January 4, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28049820/on-demand-high-capacity-ride-sharing-via-dynamic-trip-vehicle-assignment
#19
Javier Alonso-Mora, Samitha Samaranayake, Alex Wallar, Emilio Frazzoli, Daniela Rus
Ride-sharing services are transforming urban mobility by providing timely and convenient transportation to anybody, anywhere, and anytime. These services present enormous potential for positive societal impacts with respect to pollution, energy consumption, congestion, etc. Current mathematical models, however, do not fully address the potential of ride-sharing. Recently, a large-scale study highlighted some of the benefits of car pooling but was limited to static routes with two riders per vehicle (optimally) or three (with heuristics)...
January 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28049428/pergola-fast-and-deterministic-linkage-mapping-of-polyploids
#20
Fabian Grandke, Soumya Ranganathan, Nikkie van Bers, Jorn R de Haan, Dirk Metzler
BACKGROUND: A large share of agriculturally and horticulturally important plant species are polyploid. Linkage maps are used to locate associations between genes and traits by breeders and geneticists. Linkage map creation for polyploid species is not supported by standard tools. We want to overcome this limitation and validate our results with simulation studies. RESULTS: We developed PERGOLA, a deterministic and heuristic method that addresses this problem. We show that it creates correct linkage groups, marker orders and distances for simulated and real datasets...
January 4, 2017: BMC Bioinformatics
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