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Xia Jie J State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P.R. China; Molecular Modeling and Drug Discovery Core for District of Columbia Developmental Center for AIDS Research (DC D-CFAR), Laboratory of Cheminfomatics and Drug Design, Department of Pharmaceutical Sciences, College of Pharmacy, Howard University, Washington, DC 20059, - - 2014
Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts. However, the intrinsic differences of benchmarking sets to the real screening chemical libraries can cause biased assessment. Herein, we summarize the history of ...
Diller Kyle I - - 2014
The VSviewer3D is simple Java tool for visual exploration of 3D virtual screening data. The VSviewer3D brings together the ability to explore numerical data, such as calculated properties and virtual screening scores, structure depiction, interactive topological and 3D similarity searching, and 3D visualization. By doing so the user is better ...
Balzer Laura B LB Division of Biostatistics, University of California, Berkeley, CA, 94110-7358, - - 2014
In randomized trials, pair-matching is an intuitive design strategy to protect study validity and to potentially increase study power. In a common design, candidate units are identified, and their baseline characteristics used to create the best n/2 matched pairs. Within the resulting pairs, the intervention is randomized, and the outcomes ...
Spotts Ryan R Ames Laboratory, Iowa State University, 2220 Hoover, Ames, IA, - - 2014
Due to historical legal challenges, there is a driving force for the development of objective methods of forensic toolmark identification. This study utilizes an algorithm to separate matching and nonmatching shear cut toolmarks created using fifty sequentially manufactured pliers. Unlike previously analyzed striated screwdriver marks, shear cut marks contain discontinuous ...
Muramatsu Daigo - - 2014
Gait recognition is a useful biometric trait for person authentication because it is usable even with low image resolution. One challenge is robustness to a view change (crossview matching); view transformation models (VTMs) have been proposed to solve this. VTMs work well if the target views are the same as ...
Myhrvold Nathan P NP Intellectual Ventures, 3150 139th Ave SE, Bellevue, WA, - - 2014
Erickson and coworkers fit a two parameter sigmoidal growth model to mass-at-age data for Psittacosaurus lujiatunensis, finding parameters a and b by least squares regression (Erickson et al. 2009a). These results were then used to describe the developmental timing and stages at which major changes in mortality rates occurred, and ...
Bush Michael M Department of Sport & Exercise Science, University of Sunderland, UK; Performance Analysis Department, Academy of Light, Sunderland AFC, - - 2014
This study aimed to investigate position-specific evolution of physical and technical performance parameters in the English Premier League (EPL). Match performance observations (n=14700) were collected using a multiple-camera computerized tracking system across seven seasons (2006-07 to 2012-13). Data were analyzed relative to five playing positions: central defenders (n=3792), full backs ...
Anwar Md Nishat MN Department of Electrical Engineering, Indian School of Mines, Dhanbad 826004, India. Electronic address: - - 2014
In this paper, a PID controller design method for the integrating processes based on frequency response matching is presented. Two approaches are proposed for the controller design. In the first approach, a double feedback loop configuration is considered where the inner loop is designed with a stabilizing gain. In the ...
Quesada-Martínez Manuel M Facultad de Informática, Campus de Espinardo, Universidad de Murcia, 30100 Murcia, Spain. Electronic address: - - 2014
The main goal of this work is to measure how lexical regularities in biomedical ontology labels can be used for the automatic creation of formal relationships between classes, and to evaluate the results of applying our approach to the Gene Ontology (GO). In recent years, we have developed a method ...
Tangkaratt Voot V Department of Computer Science, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan - - 2014
Regression aims at estimating the conditional mean of output given input. However, regression is not informative enough if the conditional density is multimodal, heteroskedastic, and asymmetric. In such a case, estimating the conditional density itself is preferable, but conditional density estimation (CDE) is challenging in high-dimensional space. A naive approach ...
Campbell Colin C Department of Physics, Pennsylvania State University, 122 Davey Laboratory, University Park, PA 16802, USA. Department of Biology, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA. - - 2014
Ruths and Ruths (Reports, 21 March 2014, p. 1373) find that existing synthetic random network models fail to generate control profiles that match those found in real network models. Here, we show that a straightforward extension to the Barabási-Albert model allows the control profile to be "tuned" across the control ...
Pang Chao C Department of Genetics, Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The - - 2014
Pooling data across biobanks is necessary to increase statistical power, reveal more subtle associations, and synergize the value of data sources. However, searching for desired data elements among the thousands of available elements and harmonizing differences in terminology, data collection, and structure, is arduous and time consuming. To speed up ...
Han Eunjung E Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA - - 2014
The distribution of allele frequencies across polymorphic sites, also known as the site frequency spectrum (SFS), is of primary interest in population genetics. It is a complete summary of sequence variation at unlinked sites and more generally, its shape reflects underlying population genetic processes. One practical challenge is that inferring ...
Nguyen Nam-Phuong NP Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL - - 2014
Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling ...
Osad'ko I S IS Institute for spectroscopy RAS, Troitsk, 142190 Moscow, - - 2014
It has been recently found [Gh. Galland, Y. Ghosh, A. Steinbrück, M. Sykora, J. A. Hollingsworth, and V. I. Klimov, Nature (London) 479, 203 (2011)] that semiconductor core/shell nanocrystals (NCs) with blinking photoluminescence (PL) can be of "A" or "B" type. NCs of A-type exhibit correlation between the intensity of ...
Wang Jim Jing-Yan JJ Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. Electronic address: - - 2014
Nonnegative Matrix Factorization (NMF) has been a popular representation method for pattern classification problems. It tries to decompose a nonnegative matrix of data samples as the product of a nonnegative basis matrix and a nonnegative coefficient matrix. The columns of the coefficient matrix can be used as new representations of ...
Li Qin - - 2014
In this paper, we propose a new spatial encoding method that integrates the random binary pattern and the improved phase-difference-matching method to acquire a dense and precise depth map. The adopted binary pattern can simplify pattern projecting devices compared with the patterns that use color. The density of speckles in ...
Jia Bin B Intelligent Fusion Technology, Inc., Germantown, MD 20876, - - 2014
In this paper, a new Rauch-Tung-Striebel type of nonlinear smoothing method is proposed based on a class of high-degree cubature integration rules. This new class of cubature Kalman smoothers generalizes the conventional third-degree cubature Kalman smoother using the combination of Genz׳s or Mysovskikh׳s high-degree spherical rule with the moment matching ...
Islam Nabiul - - 2014
Bacterial conjugation-based nanonetwork has been recently proposed as a novel molecular communication paradigm, in which the bacteria act as carriers. This is the foundational work proposing the phenomenon of collision which occurs in the form of multi-conjugation of multiple carrier bacteria at the side of receiver nanodevice. We show the ...
Marinoni Andrea A Department of Electrical, Computer and Biomedical engineering, University of Pavia, via Ferrata 1 Pavia 27100 Italy. Electronic address: - - 2014
Genotyping Next Generation Sequencing (NGS) data of a diploid genome aims to assign the zygosity of identified variants through comparison with a reference genome. Current methods typically employ probabilistic models that rely on the pileup of bases at each locus and on a-priori knowledge. We present a new algorithm, called ...
Hummer Gerhard - - 2014
We develop a systematic procedure for obtaining rate and transition matrices that optimally describe the dynamics of aggregated superstates formed by combining (clustering or lumping) microstates. These reduced dynamical models are constructed by matching the time-dependent occupancy-number correlation functions of the superstates in the full and aggregated systems. Identical results ...
Hof M H P MH Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center - University of Amsterdam, AZ, 1105, Amsterdam, - - 2014
Combining information from two data sources depends on finding records that belong to the same individual (matches). Sometimes, unique identifiers per individual are not available, and we have to rely on partially identifying variables that are registered in both data sources. A risk of relying on these variables is that ...
Jiang Xinwei - - 2014
Dimensionality reduction (DR) has been considered as one of the most significant tools for data analysis. One type of DR algorithms is based on latent variable models (LVM). LVM-based models can handle the preimage problem easily. In this paper we propose a new LVM-based DR model, named thin plate spline ...
Liu Wei W State Key Laboratory of Newtech for Chinese Mdeicine Pharmaceutical Process, Jiangsu Kanion Pharmaceutical Co. Ltd., Lianyungang, Jiangsu Province, 222001, China ; College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian Liaoning province, 116600, - - 2014
Peach kernels which contain kinds of fatty acids play an important role in the regulation of a variety of physiological and biological functions. To establish an innovative and rapid diffuse reflectance near-infrared spectroscopy (DR-NIR) analysis method along with chemometric techniques for the qualitative and quantitative determination of a peach kernel. ...
Bradley Anthony - - 2014
There is an ever increasing resource in terms of both structural information and activity data for many protein targets. In this paper we describe OOMMPPAA, a novel computational tool designed to inform compound design by combining such data. OOMMPPAA uses 3D matched molecular pairs to generate 3D ligand conformations. It ...
Li Xinyang X NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119613, Singapore. Institute for Infocomm Research, Agency for Science, Technology and Research, Singapore 138632, - - 2014
Objective. Session-to-session nonstationarity is inherent in brain-computer interfaces based on electroencephalography. The objective of this paper is to quantify the mismatch between the training model and test data caused by nonstationarity and to adapt the model towards minimizing the mismatch. Approach. We employ a tensor model to estimate the mismatch ...
Gao Yang - - 2014
To take full advantage of hyperspectral information, to avoid data redundancy and to address the curse of dimensionality concern, dimensionality reduction (DR) becomes particularly important to analyze hyperspectral data. Exploring the tensor characteristic of hyperspectral data, a DR algorithm based on class-aware tensor neighborhood graph and patch alignment is proposed ...
White K Geoffrey KG University of Otago, New Zealand. Electronic address: - - 2014
The reinforcement context model for performance in delayed matching-to- sample tasks (White and Brown, 2014) predicts the course of forgetting based on the assumption that rewards for extraneous behavior compete with rewards for accurate matching and increase as a linear function of retention-interval duration. In the differential outcomes effect, greater ...
Liu Kun - - 2014
In this paper, we develop an optimized stereo-matching method used in an active binocular three-dimensional measurement system. A traditional dense stereo-matching algorithm is time consuming due to a long search range and the high complexity of a similarity evaluation. We project a binary fringe pattern in combination with a series ...
Castro Victor M VM Partners Research Information Systems and Computing, Partners HealthCare System, One Constitution Center, Boston, MA 02129, United States. Electronic address: - - 2014
The success of many population studies is determined by proper matching of cases to controls. Some of the confounding and bias that afflict electronic health record (EHR)-based observational studies may be reduced by creating effective methods for finding adequate controls. We implemented a method to match case and control populations ...
de la Vega de León Antonio - - 2014
Matched molecular pairs (MMPs) consist of pairs of compounds that are transformed into each other by a substructure exchange. If MMPs are formed by compounds sharing the same biological activity, they encode a potency change. If the potency difference between MMP compounds is very small, the substructure exchange (chemical transformation) ...
Mazrouee Sepideh S Computer Science Department, University of California Los Angeles (UCLA), 3551 Boelter Hall, Los Angeles, CA 90095-1596, - - 2014
Understanding exact structure of an individual's haplotype plays a significant role in various fields of human genetics. Despite tremendous research effort in recent years, fast and accurate haplotype reconstruction remains as an active research topic, mainly owing to the computational challenges involved. Existing haplotype assembly algorithms focus primarily on improving ...
Ali Waqar W Department of Statistics, University of Oxford, Oxford OX1 3TG, UK and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, CA 90089-2910, - - 2014
Biological network comparison software largely relies on the concept of alignment where close matches between the nodes of two or more networks are sought. These node matches are based on sequence similarity and/or interaction patterns. However, because of the incomplete and error-prone datasets currently available, such methods have had limited ...
Adisa Akinyele Olumuyiwa AO Department of Oral Pathology, University of Ibadan and University College Hospital, Ibadan, - - 2014
Objective: This study was conducted to assess the accuracy of palatal rugae as a tool for human identification and to determine factors that may limit accuracy. This will serve as a potential basis for advising national health policy formulation on human identification as forensic rugoscopy is unexplored in sub-Saharan Africa. ...
Zhang Zhaojun Z Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina - - 2014
A general Bayesian model, Diploffect, is described for estimating the effects of founder haplotypes at quantitative trait loci (QTL) detected in multiparental genetic populations; such populations include the Collaborative Cross (CC), Heterogeneous Socks (HS), and many others for which local genetic variation is well described by an underlying, usually probabilistically ...
Wyss Richard R Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel - - 2014
The prognostic score, or disease risk score (DRS), is a summary score that is used to control for confounding in non-experimental studies. While the DRS has been shown to effectively control for measured confounders, unmeasured confounding continues to be a fundamental obstacle in non-experimental research. Both theory and simulations have ...
Cauley Stephen F SF Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA; Department of Radiology, Harvard Medical School, Boston, Massachusetts, - - 2014
MR fingerprinting (MRF) is a technique for quantitative tissue mapping using pseudorandom measurements. To estimate tissue properties such as T1 , T2 , proton density, and B0 , the rapidly acquired data are compared against a large dictionary of Bloch simulations. This matching process can be a very computationally demanding ...
Wu Zhenke Z Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, - - 2014
We address estimation of intervention effects in experimental designs in which (a) interventions are assigned at the cluster level; (b) clusters are selected to form pairs, matched on observed characteristics; and (c) intervention is assigned to one cluster at random within each pair. One goal of policy interest is to ...
DeGiorgio Michael M Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of - - 2014
While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated methods for identifying sites under balancing selection. Here we develop two composite likelihood ...
Blasco Víctor V IVI Sevilla, Sevilla, - - 2014
To correlate the detection of follicle rupture and the number of uterine contractions per minute with the outcome of IUI and to build a predictive model for the outcome of IUI including these parameters. Retrospective cohort study. Fertility clinic. We analyzed data from 610 women who underwent homologous or donor ...
Yang Sheng-wei - - 2014
Reconstructing the spectrum rapidly and accurately is the key to the research on high-fidelity reproduction. A characteristic spectrum extracting and matching method for high-fidelity printing is proposed aiming at the problem of complex conversion between spectrum and ink combination caused by multi-color. The method filters and extracts feature bands of ...
Lesperance Marielle M Carleton Laboratory for Radiotherapy Physics, Department of Physics, Carleton University, Ottawa, Ontario K1S 5B6, - - 2014
To investigate dosimetry for ocular brachytherapy for a range of eye plaque models containing(103)Pd, (125)I, or (131)Cs seeds with model-based dose calculations. Five representative plaque models are developed based on a literature review and are compared to the standardized COMS plaque, including plaques consisting of a stainless steel backing and ...
Gordon Deborah M DM Department of Biology, Stanford University, Stanford, California, United States of - - 2014
Similar patterns of interaction, such as network motifs and feedback loops, are used in many natural collective processes, probably because they have evolved independently under similar pressures. Here I consider how three environmental constraints may shape the evolution of collective behavior: the patchiness of resources, the operating costs of maintaining ...
Kim Hee-Dong HD School of Electrical Engineering, Korea University, Anam-dong 5-ga, Seongbuk-gu, Seoul 136-701, Republic of - - 2014
The improved resistive switching (RS) performance characteristics of nickel nitride (NiN) films-based crossbar array (CBA) memory resistors-such as reduction in the operating voltages, reset current and current/voltage variations; no initial forming process; and set/reset speeds-are demonstrated using nanopyramid-patterned (NPP) platinum-bottom electrodes. Compared with a conventional CBA sample with flat-bottom electrodes, ...
Takahashi Ayuko A Boston University, Biomedical Engineering, Boston, Massachusetts, United States ; - - 2014
Rationale: Extracellular matrix (ECM) remodeling and tissue rupture are factors contributing to the progression of emphysema. Lung tissue elasticity is governed by the tensile stiffness of fibers and the compressive stiffness of proteoglycans. It is not known how proteoglycan remodeling affects tissue stability and destruction in emphysema. Objectives: To characterize ...
Holzapfel Gerhard A GA Graz University of Technology, Institute of Biomechanics, Kronesgasse 5-I, 8010 Graz, Austria. Electronic address: - - 2014
Vulnerable and stable atherosclerotic plaques are heterogeneous living materials with peculiar mechanical behaviors depending on geometry, composition, loading and boundary conditions. Computational approaches have the potential to characterize the three-dimensional stress/strain distributions in patient-specific diseased arteries of different types and sclerotic morphologies and to estimate the risk of plaque rupture ...
Tang An A Department of Radiology, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada; Department of Radiology, Radio-Oncology and Nuclear Medicine, Université de Montréal, Montréal, Québec, Canada; Institute of Biomedical Engineering, Université de Montréal, Montréal, Québec, - - 2014
To identify geometric indices of abdominal aortic aneurysms (AAAs) on computed tomography that are associated with higher risk of rupture. This retrospective case-control, institutional review board-approved study involved 63 cases with ruptured or symptomatic AAA and 94 controls with asymptomatic AAA. Three-dimensional models were generated from computed tomography segmentation and ...
Akyildiz Ali C AC Department of Biomedical Engineering, Thoraxcenter, Erasmus Medical Center, Rotterdam, The - - 2014
Progression and rupture of atherosclerotic plaques in coronary and carotid arteries are the key processes underlying myocardial infarctions and strokes. Biomechanical stress analyses to compute mechanical stresses in a plaque can potentially be used to assess plaque vulnerability. The stress analyses strongly rely on accurate representation of the mechanical properties ...
Chai Chen-Ket CK Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands. Electronic address: - - 2014
Accurate material models and associated parameters of atherosclerotic plaques are crucial for reliable biomechanical plaque prediction models. These biomechanical models have the potential to increase our understanding of plaque progression and failure, possibly improving risk assessment of plaque rupture, which is the main cause of ischaemic strokes and myocardial infarction. ...
Houlié N N 1] Berkeley Seismological Laboratory - University of California [2] ETH, SEG, Zurich, CH [3] ETH, GGL, Zurich, - - 2014
We compute a series of finite-source parameter inversions of the fault rupture of the 2004 Parkfield earthquake based on 1 Hz GPS records only. We confirm that some of the co-seismic slip at shallow depth (<5 km) constrained by InSAR data processing results from early post-seismic deformation. We also show 1) that ...
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