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https://www.readbyqxmd.com/read/28431121/starbeast2-brings-faster-species-tree-inference-and-accurate-estimates-of-substitution-rates
#1
Huw A Ogilvie, Remco R Bouckaert, Alexei J Drummond
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28427384/imbalanced-target-prediction-with-pattern-discovery-on-clinical-data-repositories
#2
Tak-Ming Chan, Yuxi Li, Choo-Chiap Chiau, Jane Zhu, Jie Jiang, Yong Huo
BACKGROUND: Clinical data repositories (CDR) have great potential to improve outcome prediction and risk modeling. However, most clinical studies require careful study design, dedicated data collection efforts, and sophisticated modeling techniques before a hypothesis can be tested. We aim to bridge this gap, so that clinical domain users can perform first-hand prediction on existing repository data without complicated handling, and obtain insightful patterns of imbalanced targets for a formal study before it is conducted...
April 20, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28426940/prospective-assessment-of-virtual-screening-heuristics-derived-using-a-novel-fusion-score
#3
Dante A Pertusi, Gregory O'Donnell, Michelle F Homsher, Kelli Solly, Amita Patel, Shannon L Stahler, Daniel Riley, Michael F Finley, Eleftheria N Finger, Gregory C Adam, Juncai Meng, David J Bell, Paul D Zuck, Edward M Hudak, Michael J Weber, Jennifer E Nothstein, Louis Locco, Carissa Quinn, Adam Amoss, Brian Squadroni, Michelle Hartnett, Mee Ra Heo, Tara White, S Alex May, Evelyn Boots, Kenneth Roberts, Patrick Cocchiarella, Alex Wolicki, Anthony Kreamer, Peter S Kutchukian, Anne Mai Wassermann, Victor N Uebele, Meir Glick, Andrew Rusinko, J Christopher Culberson
High-throughput screening (HTS) is a widespread method in early drug discovery for identifying promising chemical matter that modulates a target or phenotype of interest. Because HTS campaigns involve screening millions of compounds, it is often desirable to initiate screening with a subset of the full collection. Subsequently, virtual screening methods prioritize likely active compounds in the remaining collection in an iterative process. With this approach, orthogonal virtual screening methods are often applied, necessitating the prioritization of hits from different approaches...
April 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28425923/connectivity-restoration-in-wireless-sensor-networks-via-space-network-coding
#4
Alfred Uwitonze, Jiaqing Huang, Yuanqing Ye, Wenqing Cheng
The problem of finding the number and optimal positions of relay nodes for restoring the network connectivity in partitioned Wireless Sensor Networks (WSNs) is Non-deterministic Polynomial-time hard (NP-hard) and thus heuristic methods are preferred to solve it. This paper proposes a novel polynomial time heuristic algorithm, namely, Relay Placement using Space Network Coding (RPSNC), to solve this problem, where Space Network Coding, also called Space Information Flow (SIF), is a new research paradigm that studies network coding in Euclidean space, in which extra relay nodes can be introduced to reduce the cost of communication...
April 20, 2017: Sensors
https://www.readbyqxmd.com/read/28424527/unified-alignment-of-protein-protein-interaction-networks
#5
Noël Malod-Dognin, Kristina Ban, Nataša Pržulj
Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423832/building-snomed-ct-post-coordinated-expressions-from-annotation-groups
#6
Jose Antonio Miñarro-Giménez, Catalina Martínez-Costa, Pablo López-García, Stefan Schulz
SNOMED CT supports post-coordination, a technique to combine clinical concepts to ontologically define more complex concepts. This technique follows the validity restrictions defined in the SNOMED CT Concept Model. Pre-coordinated expressions are compositional expressions already in SNOMED CT, whereas post-coordinated expressions extend its content. In this project we aim to evaluate the suitability of existing pre-coordinated expressions to provide the patterns for composing typical clinical information based on a defined list of sets of interrelated SNOMED CT concepts...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28422093/quantum-enhanced-inference-in-markov-logic-networks
#7
Peter Wittek, Christian Gogolin
Markov logic networks (MLNs) reconcile two opposing schools in machine learning and artificial intelligence: causal networks, which account for uncertainty extremely well, and first-order logic, which allows for formal deduction. An MLN is essentially a first-order logic template to generate Markov networks. Inference in MLNs is probabilistic and it is often performed by approximate methods such as Markov chain Monte Carlo (MCMC) Gibbs sampling. An MLN has many regular, symmetric structures that can be exploited at both first-order level and in the generated Markov network...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28415344/simple-noise-reduction-method-based-on-nonlinear-forecasting
#8
James P L Tan
Nonparametric detrending or noise reduction methods are often employed to separate trends from noisy time series when no satisfactory models exist to fit the data. However, conventional noise reduction methods depend on subjective choices of smoothing parameters. Here we present a simple multivariate noise reduction method based on available nonlinear forecasting techniques. These are in turn based on state-space reconstruction for which a strong theoretical justification exists for their use in nonparametric forecasting...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28413365/integrating-the-principles-of-evidence-based-medicine-and-evidence-based-public-health-impact-on-the-quality-of-patient-care-and-hospital-readmission-rates-in-jordan
#9
Mohammad S Alyahya, Heba H Hijazi, Hussam A Alshraideh, Mohammad Aser Alsharman, Rabah Al Abdi, Heather Lea Harvey
INTRODUCTION: Hospital readmissions impose not only an extra burden on health care systems but impact patient health outcomes. Identifying modifiable behavioural risk factors that are possible causes of potentially avoidable readmissions can lower readmission rates and healthcare costs. METHODS: Using the core principles of evidence based medicine and public health, the purpose of this study was to develop a heuristic guide that could identify what behavioural risk factors influence hospital readmissions through adopting various methods of analysis including regression models, t-tests, data mining, and logistic regression...
August 31, 2016: International Journal of Integrated Care
https://www.readbyqxmd.com/read/28410114/multilayer-optimization-of-heterogeneous-networks-using-grammatical-genetic-programming
#10
Michael Fenton, David Lynch, Stepan Kucera, Holger Claussen, Michael O'Neill
Heterogeneous cellular networks are composed of macro cells (MCs) and small cells (SCs) in which all cells occupy the same bandwidth. Provision has been made under the third generation partnership project-long term evolution framework for enhanced intercell interference coordination (eICIC) between cell tiers. Expanding on previous works, this paper instruments grammatical genetic programming to evolve control heuristics for heterogeneous networks. Three aspects of the eICIC framework are addressed including setting SC powers and selection biases, MC duty cycles, and scheduling of user equipments (UEs) at SCs...
April 6, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28410107/feature-sensitive-label-fusion-with-random-walker-for-atlas-based-image-segmentation
#11
Siqi Bao, Albert C S Chung
In this paper, a novel label fusion method is proposed for brain magnetic resonance image segmentation. This label fusion method is formulated on a graph, which embraces both label priors from atlases and anatomical priors from target image. To represent a pixel in a comprehensive way, three kinds of feature vectors are generated, including intensity, gradient and structural signature. To select candidate atlas nodes for fusion, rather than exact searching, randomized k-d tree with spatial constraint is introduced as an efficient approximation for high-dimensional feature matching...
April 6, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28409977/hamiltonian-for-the-zeros-of-the-riemann-zeta-function
#12
Carl M Bender, Dorje C Brody, Markus P Müller
A Hamiltonian operator H[over ^] is constructed with the property that if the eigenfunctions obey a suitable boundary condition, then the associated eigenvalues correspond to the nontrivial zeros of the Riemann zeta function. The classical limit of H[over ^] is 2xp, which is consistent with the Berry-Keating conjecture. While H[over ^] is not Hermitian in the conventional sense, iH[over ^] is PT symmetric with a broken PT symmetry, thus allowing for the possibility that all eigenvalues of H[over ^] are real...
March 31, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28407016/learning-from-label-proportions-in-brain-computer-interfaces-online-unsupervised-learning-with-guarantees
#13
David Hübner, Thibault Verhoeven, Konstantin Schmid, Klaus-Robert Müller, Michael Tangermann, Pieter-Jan Kindermans
OBJECTIVE: Using traditional approaches, a brain-computer interface (BCI) requires the collection of calibration data for new subjects prior to online use. Calibration time can be reduced or eliminated e.g., by subject-to-subject transfer of a pre-trained classifier or unsupervised adaptive classification methods which learn from scratch and adapt over time. While such heuristics work well in practice, none of them can provide theoretical guarantees. Our objective is to modify an event-related potential (ERP) paradigm to work in unison with the machine learning decoder, and thus to achieve a reliable unsupervised calibrationless decoding with a guarantee to recover the true class means...
2017: PloS One
https://www.readbyqxmd.com/read/28405366/processing-political-misinformation-comprehending-the-trump-phenomenon
#14
Briony Swire, Adam J Berinsky, Stephan Lewandowsky, Ullrich K H Ecker
This study investigated the cognitive processing of true and false political information. Specifically, it examined the impact of source credibility on the assessment of veracity when information comes from a polarizing source (Experiment 1), and effectiveness of explanations when they come from one's own political party or an opposition party (Experiment 2). These experiments were conducted prior to the 2016 Presidential election. Participants rated their belief in factual and incorrect statements that President Trump made on the campaign trail; facts were subsequently affirmed and misinformation retracted...
March 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28401510/a-systematic-literature-review-of-us-engineering-ethics-interventions
#15
Justin L Hess, Grant Fore
Promoting the ethical formation of engineering students through the cultivation of their discipline-specific knowledge, sensitivity, imagination, and reasoning skills has become a goal for many engineering education programs throughout the United States. However, there is neither a consensus throughout the engineering education community regarding which strategies are most effective towards which ends, nor which ends are most important. This study provides an overview of engineering ethics interventions within the U...
April 11, 2017: Science and Engineering Ethics
https://www.readbyqxmd.com/read/28398920/spitz-nevus-intermingling-with-hemangioma-angiomatoid-spitz-nevus-angiotropism-and-vascular-co-option-viewed-with-differing-availability-heuristics
#16
Thomas N Helm, Klaus F Helm
No abstract text is available yet for this article.
March 16, 2017: American Journal of Dermatopathology
https://www.readbyqxmd.com/read/28394995/video-analysis-of-factors-associated-with-response-time-to-physiologic-monitor-alarms-in-a-children-s-hospital
#17
Christopher P Bonafide, A Russell Localio, John H Holmes, Vinay M Nadkarni, Shannon Stemler, Matthew MacMurchy, Miriam Zander, Kathryn E Roberts, Richard Lin, Ron Keren
Importance: Bedside monitor alarms alert nurses to life-threatening physiologic changes among patients, but the response times of nurses are slow. Objective: To identify factors associated with physiologic monitor alarm response time. Design, Setting, and Participants: This prospective cohort study used 551 hours of video-recorded care administered by 38 nurses to 100 children in a children's hospital medical unit between July 22, 2014, and November 11, 2015...
April 10, 2017: JAMA Pediatrics
https://www.readbyqxmd.com/read/28394156/the-readiness-for-integrated-care-questionnaire-ricq-an-instrument-to-assess-readiness-to-integrate-behavioral-health-and-primary-care
#18
Victoria C Scott, Tara Kenworthy, Erin Godly-Reynolds, Gilberte Bastien, Jonathan Scaccia, Courtney McMickens, Sharon Rachel, Sayon Cooper, Glenda Wrenn, Abraham Wandersman
Integration of behavioral health and primary care services is a promising approach for reducing health disparities. The growing national emphasis on care coordination has mobilized efforts to integrate behavioral health and primary care services across the United States. These efforts align with broader health care system goals of improving health care quality, health equity, utilization efficiency, and patient outcomes. Drawing from our work on a multiyear integrated care initiative (Integrated Care Leadership Program; ICLP) and an implementation science heuristic for organizational readiness (Readiness = Motivation x General Capacity and Innovation-Specific Capacity; R = MC2), this article describes the development and implementation of a tool to assess organizational readiness for integrated care, referred to as the Readiness for Integrated Care Questionnaire (RICQ)...
April 10, 2017: American Journal of Orthopsychiatry
https://www.readbyqxmd.com/read/28390544/obesity-heuristic-reasoning-and-the-organisation-of-communicative-embarrassment-in-diagnostic-radiography
#19
P K Miller, A L Woods, C Sloane, L Booth
This paper, the second of three arising from a broader qualitative study, explores difficulties emerging around radiographer-patient communication regarding obesity in hospital-based encounters, and the situated strategies found by experienced radiographers for handling such situations. Semi-structured interviews with eight clinicians working in plain radiography (mean experience = 21.56 years) were analysed using Interpretative Phenomenological Analysis (IPA), so as to highlight the practical, nuanced and real-world experiences of these individuals regarding obesity communication...
May 2017: Radiography
https://www.readbyqxmd.com/read/28390283/chemometrics-enhanced-one-dimensional-comprehensive-two-dimensional-gas-chromatographic-analysis-for-bioactive-terpenoids-and-phthalides-in-chaihu-shugan-san-essential-oils
#20
Min He, Zhi-Yu Yang, Tian-Biao Yang, Ying Ye, Juan Nie, Yong Hu, Pan Yan
Chemometrics-enhanced one-dimensional/comprehensive two-dimensional gas chromatographic (GC/GC×GC) technologies, were used to explore the compositions of Chaihu Shugan San essential oils, that were extracted from the herbal formulae by different schemes. We have shown that chemometric resolution using gas chromatographic- mass spectrometry (GC-MS) could be used for the qualitative and quantitative analysis of the majority of Terpenoids or Phthalides from herb formulae and single herbs. A GC×GC system was further optimized to achieve the increased peak capacity and the enhanced signal of the hydro-distillation sample (CSSh)...
March 30, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
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