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Bajuna Rashid Salehe, Chris Ian Jones, Giuseppe Di Fatta, Liam James McGuffin
Advances in omics technologies have led to the discovery of genetic markers, or single nucleotide polymorphisms (SNPs), that are associated with particular diseases or complex traits. Although there have been significant improvements in the approaches used to analyse associations of SNPs with disease, further optimised and rapid techniques are needed to keep up with the rate of SNP discovery, which has exacerbated the 'missing heritability' problem. Here, we have devised a novel, integrated, heuristic-based, hybrid analytical computational pipeline, for rapidly detecting novel or key genetic variants that are associated with diseases or complex traits...
2017: PloS One
Kathryn Miller, Thomas Kim
This study investigates the role of representational competence in student responses to an assessment of hydrogen bonding. The assessment couples the use of a multiple-select item ("Choose all that apply") with an open-ended item to allow for an examination of students' cognitive processes as they relate to the assignment of hydrogen bonding within a structural representation. Response patterns from the multiple-select item implicate heuristic usage as a contributing factor to students' incorrect responses...
April 25, 2017: Biochemistry and Molecular Biology Education
Sruthy Agnisarman, Shraddhaa Narasimha, Kapil Chalil Madathil, Brandon Welch, Fnu Brinda, Aparna Ashok, James McElligott
BACKGROUND: Telemedicine is the use of technology to provide and support health care when distance separates the clinical service and the patient. Home-based telemedicine systems involve the use of such technology for medical support and care connecting the patient from the comfort of their homes with the clinician. In order for such a system to be used extensively, it is necessary to understand not only the issues faced by the patients in using them but also the clinician. OBJECTIVES: The aim of this study was to conduct a heuristic evaluation of 4 telemedicine software platforms-Doxy...
April 24, 2017: JMIR Human Factors
G V S S Praneeth Varma, Rayapati Sushma, Vandana Sharma, Abhinav Kumar, G V V Sharma
In this paper, a simple heuristic power allocation scheme is proposed for a random LED array to obtain uniform irradiance on the projection surface. This is done by considering a binomial point process (BPP) for modeling the LED location and using the quality factor as a performance metric. Numerical results are provided to validate the proposed model and demonstrate its simplicity over existing LED geometries.
April 17, 2017: Optics Express
Yaoming Zhou, Jiuh-Biing Sheu, Junwei Wang
Robustness measures a system's ability of being insensitive to disturbances. Previous studies assessed the robustness of transportation networks to a single disturbance without considering simultaneously happening multiple events. The purpose of this article is to address this problem and propose a new framework to assess the robustness of an urban transportation network. The framework consists of two layers. The upper layer is to define the robustness index based on the impact evaluation in different scenarios obtained from the lower layer, whereas the lower layer is to evaluate the performance of each hypothetical disrupted road network given by the upper layer...
April 24, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
Ivo Hedtke, Ioana Lemnian, Ivo Grosse, Matthias Muller-Hannemann
Read trimming is a fundamental first step of the analysis of next generation sequencing (NGS) data. Traditionally, it is performed heuristically, and algorithmic work in this area has been neglected. Here, we address this topic and formulate three optimization problems for block-based trimming (truncating the same low-quality positions at both ends for all reads and removing low-quality truncated reads). We find that all problems are NP-hard. Hence, we investigate the approximability of the problems. Two of them are NP-hard to approximate...
April 24, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Masumeh Gharabaghi, Shant Shahbazian
The quantum theory of atoms in molecules (QTAIM) is based on the clamped nucleus paradigm and solely working with the electronic wavefunctions, so does not include nuclear vibrations in the AIM analysis. On the other hand, the recently extended version of the QTAIM, called the multi-component QTAIM (MC-QTAIM), incorporates both electrons and quantum nuclei, i.e., those nuclei treated as quantum waves instead of clamped point charges, into the AIM analysis using non-adiabatic wavefunctions. Thus, the MC-QTAIM is the natural framework to incorporate the role of nuclear vibrations into the AIM analysis...
April 21, 2017: Journal of Chemical Physics
Vincenzo Crupi, Fabrizio Elia
No abstract text is available yet for this article.
April 21, 2017: Internal and Emergency Medicine
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
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
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
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
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
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
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
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
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
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
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...
June 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
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
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