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Webb Benjamin B University of California at San Francisco, San Francisco, - - 2014
Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a ...
Masso Majid M Laboratory for Structural Bioinformatics, School of Systems Biology, George Mason University, Manassas, VA 20110, - - 2014
The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three of the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two additional ...
Chen Jing J National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Drive, Building 50, Room 3306, Bethesda, Maryland 20892, - - 2014
The spindle assembly checkpoint arrests mitotic progression until each kinetochore secures a stable attachment to the spindle. Despite fluctuating noise, this checkpoint remains robust and remarkably sensitive to even a single unattached kinetochore among many attached kinetochores; moreover, the checkpoint is silenced only after the final kinetochore-spindle attachment. Experimental observations ...
Liu Hao H Nanjing University of Aeronautics and Astronautics, P.R. China Jinling Hospital, Department Orthopedics, Nanjing University School of Medicine, P.R. - - 2014
Separation of the femur head and acetabulum is one of main difficulties in the diseased hip joint due to deformed shapes and extreme narrowness of the joint space. To improve the segmentation accuracy is the key point of existing automatic or semi-automatic segmentation methods. In this paper, we propose a ...
Kuhapatanakul Kantaphon K Department of Mathematics, Faculty of Science, Kasetsart University, Bangkok, - - 2014
Recently Holliday and Komatsu extended the results of Ohtsuka and Nakamura on reciprocal sums of Fibonacci numbers to reciprocal sums of generalized Fibonacci numbers. The aim of this work is to give similar results for the alternating sums of reciprocals of the generalized Fibonacci numbers with indices in arithmetic progression. ...
Yan Luchun L School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Xueyuan Road 30, Haidian District, Beijing 100083, China. - - 2014
A novel odor interaction model was proposed for binary mixtures of benzene and substituted benzenes by a partial differential equation (PDE) method. Based on the measurement method (tangent-intercept method) of partial molar volume, original parameters of corresponding formulas were reasonably displaced by perceptual measures. By these substitutions, it was possible ...
Ke Shengnan S School of Software, Jiangxi Normal University, Nanchang 330022, China. - - 2014
In recent years, there has been tremendous growth in the field of indoor and outdoor positioning sensors continuously producing huge volumes of trajectory data that has been used in many fields such as location-based services or location intelligence. Trajectory data is massively increased and semantically complicated, which poses a great ...
Smith Jeremy D JD School of Sport & Exercise Science, University of Northern Colorado; - - 2014
The purpose of this study was two-fold: (1) demonstrate a technique that can be used to directly estimate the inertial properties of a below-knee prosthesis, and (2) contrast the effects of the proposed technique and that of using intact limb inertial properties on joint kinetic estimates during walking in unilateral, ...
Suh Young Soo YS Department of Electrical Engineering, University of Ulsan, Namgu 680-749, Ulsan, Korea. - - 2014
Location-dependent differences of ambient magnetic fields inside a building can be used to estimate location. In this paper, an inertial/magnetic sensor is attached to a belt position and its location is estimated using the ambient magnetic field. The walking distance is estimated using the linear relationship between the walking step ...
Guenole Nigel N IBM Smarter Workforce Institute London, UK ; Institute of Management Studies, Goldsmiths, University of London London, - - 2014
We report a Monte Carlo study examining the effects of two strategies for handling measurement non-invariance - modeling and ignoring non-invariant items - on structural regression coefficients between latent variables measured with item response theory models for categorical indicators. These strategies were examined across four levels and three types of ...
Ni Yang Y Department of Statistics, Rice University, Houston, Texas, - - 2014
Rapid development of genome-wide profiling technologies has made it possible to conduct integrative analysis on genomic data from multiple platforms. In this study, we develop a novel integrative Bayesian network approach to investigate the relationships between genetic and epigenetic alterations as well as how these mutations affect a patient's clinical ...
Ta Vinh-Thong - - 2014
Automatic segmentation methods are important tools for quantitative analysis of magnetic resonance images. Recently, patch-based label fusion approaches demonstrated state-of-the-art segmentation accuracy. In this paper, we introduce a new patch-based method using the PatchMatch algorithm to perform segmentation of anatomical structures. Based on an Optimized PAtchMatch Label fusion (OPAL) strategy, ...
Loohuis Loes Olde LO Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, United States of - - 2014
Existing techniques to reconstruct tree models of progression for accumulative processes, such as cancer, seek to estimate causation by combining correlation and a frequentist notion of temporal priority. In this paper, we define a novel theoretical framework called CAPRESE (CAncer PRogression Extraction with Single Edges) to reconstruct such models based ...
Van Leemput Koen - - 2014
In this paper we analyze the properties of the well-known segmentation fusion algorithm STAPLE, using a novel inference technique that analytically marginalizes out all model parameters. We demonstrate both theoretically and empirically that when the number of raters is large, or when consensus regions are included in the model, STAPLE ...
Moolan-Feroze Oliver - - 2014
Accurate automated segmentation of the right ventricle is difficult due in part to the large shape variation found between patients. We explore the ability of manifold learning based shape models to represent the complexity of shape variation found within an RV dataset as compared to a typical PCA based model. ...
Bender Mariana G MG Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, SC, - - 2014
In the last decades, a number of studies based on historical records revealed the diversity loss in the oceans and human-induced changes to marine ecosystems. These studies have improved our understanding of the human impacts in the oceans. They also drew attention to the shifting baseline syndrome and the importance ...
Xu Yuan Y Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian, - - 2014
Network motifs are overly represented as topological patterns that occur more often in a given network than in random networks, and take on some certain functions in practical biological applications. Existing methods of detecting network motifs have focused on computational efficiency. However, detecting network motifs also presents huge challenges in ...
Russo Danilo D Wildlife Research Unit, Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Napoli, Italy; School of Biological Sciences, University of Bristol, Bristol, United - - 2014
Competition may lead to changes in a species' environmental niche in areas of sympatry and shifts in the niche of weaker competitors to occupy areas where stronger ones are rarer. Although mainland Mediterranean (Rhinolophus euryale) and Mehely's (R. mehelyi) horseshoe bats mitigate competition by habitat partitioning, this may not be ...
Wallace David J DJ Clinical Research, Investigation and Systems Modeling of Acute Illness (CRISMA) Center, the Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA; The Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, - - 2014
Estimates of prehospital transport times are an important part of emergency care system research and planning; however, the accuracy of these estimates is unknown. The authors examined the accuracy of three estimation methods against observed transport times in a large cohort of prehospital patient transports. This was a validation study ...
- - 2014
[This corrects the article DOI: 10.1371/journal.pone.0099063.].
Kamisetty Hetunandan H Department of Biochemistry, University of - - 2014
In studying the strength and specificity of interaction between members of two protein families, key questions center on which pairs of possible partners actually interact, how well they interact, and why they interact while others do not. The advent of large-scale experimental studies of interactions between members of a target ...
Tange Julie I JI Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, - - 2013
Warfarin dosing relies on accurate measurements of international normalized ratio (INR), which is calculated from the prothrombin time (PT), International Sensitivity Index international sensitivity index (ISI) of the thromboplastin, and the geometric mean of normal PT (MNPT). However, ISI assignments of certain reagent/instrument combinations are frequently unavailable, especially when the ...
McMurphy Timothy B TB Department of Biomedical Materials Science, University of Mississippi Medical Center, Jackson, MS, - - 2013
To develop a method, which is precise, accurate, and insensitive to the angle of inclination for determining the fractal dimensional increment (D*) of a surface. Brownian interpolation was used to generate simulated ceramic fracture surfaces having known D* values of 0.1, 0.2, 0.3, and 0.4 with 10 surfaces at each ...
Liang Tai-Ran TR Department of Physics, Nankai University, Tianjin 300071, - - 2013
The Chinese spallation neutron source (CSNS) is a high-performance pulsed neutron source, having 20 neutron beamlines for neutron scattering instruments. The shielding design of these beamlines is usually needed for Monte Carlo (MC) calculation, and the use of variance reduction methods is critical to carrying out an efficient, reliable MC ...
Brehm Wolfgang W Department of Biology, Universität Konstanz, Box 647, 78457 Konstanz, - - 2014
In serial crystallography, a very incomplete partial data set is obtained from each diffraction experiment (a `snapshot'). In some space groups, an indexing ambiguity exists which requires that the indexing mode of each snapshot needs to be established with respect to a reference data set. In the absence of such ...
Debin Marion - - 2013
Assessing the accuracy of influenza epidemic periods determined by statistical models is important to improve the performance of algorithms used in real-time syndromic surveillance systems. This is a difficult problem to address in the absence of a reliable gold standard. The objective of this study is to establish an expert-based ...
Unal Yavuz Y Education Faculty, Amasya University, Amasya, - - 2014
In this paper, an innovative data pre-processing method to improve the classification performance and to determine automatically the vertebral column disorders including disk hernia (DH), spondylolisthesis (SL) and normal (NO) groups has been proposed. In the classification of vertebral column disorders' dataset with three classes, a pairwise fuzzy C-means (FCM) ...
Göhring Janett J Max F. Perutz Laboratories, Medical University of Vienna, Vienna 1030, Austria, Gregor Mendel Institute, Vienna 1030, Austria, Institute for Applied Physics, Johannes Kepler University Linz, Linz 4040, Austria and Upper Austria University of Applied Sciences, Campus Linz, Linz 4020, - - 2013
Telomeres comprise the protective caps of natural chromosome ends and function in the suppression of DNA damage signaling and cellular senescence. Therefore, techniques used to determine telomere length are important in a number of studies, ranging from those investigating telomeric structure to effects on human disease. Terminal restriction fragment (TRF) ...
Gentsch Lydia L Institute of Agricultural Sciences, ETH Zurich, Universitatsstrasse 2, 8092 Zurich, Switzerland; INRA, UR1263 Ephyse, 33140 Villenave d'Ornon, - - 2013
Field measurements of photosynthetic carbon isotope discrimination ((13) Δ) of Fagus sylvatica, conducted with branch bags and laser spectrometry, revealed a high variability of (13) Δ, both on diurnal and day-to-day timescales. We tested the prediction capability of three versions of a commonly-used model for (13) Δ [called here comprehensive ...
Xu Wenxiang W Institute of Soft Matter Mechanics, College of Mechanics and Materials, Hohai University, Nanjing 210098, China. - - 2013
The effect of microstructures of interfacial layers on transport behaviors of particulate composites has been found to be significant, thus microstructural characteristics of interfacial layers should be considered in the analysis for better prediction of transport properties of particulate composites. However, it is very difficult to determine the volume fraction ...
Hemmati Berivanlou Nima N Control and Intelligent Processing Center of Excellence, School of Electrical and Computer Engineering, College of Engineering, University of Tehran, Tehran, - - 2014
The quality of the functional near infrared spectroscopy (fNIRS) recordings is highly degraded by the presence of physiological interferences. It is crucial to efficiently separate the evoked hemodynamic responses (EHRs) from other background hemodynamic activities prior to any further processing. This paper presents a novel algorithm for physiological interferences reduction ...
Tellinghuisen Joel J Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA 37235. Electronic address: - - 2013
New methods are used to compare seven qPCR analysis methods for their performance in estimating the quantification cycle (Cq) and amplification efficiency (E) for a large test data set (94 samples for each of 4 dilutions) from a recent study. Precision and linearity are assessed using chi-square (χ2), which is ...
Greve Douglas N DN Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, - - 2013
Exploratory (i.e., voxelwise) spatial methods are commonly used in neuroimaging to identify areas that show an effect when a region-of-interest (ROI) analysis cannot be performed because no strong a priori anatomical hypothesis exists. However, noise at a single voxel is much higher than noise in a ROI making noise management ...
Eder Maximilian M Research Group CAPS-Computer Aided Plastic Surgery, Department of Plastic Surgery and Hand Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675, Munich, - - 2013
Biomechanical breast modeling using finite element (FE) analysis to predict 3-D breast deformations is of interest for various biomedical applications. Currently no consensus of reliable magnitudes of mechanical breast tissue properties exists. We therefore applied 12 material properties proposed in the literature to FE simulation models derived from prone MRI ...
Sinha Samiran S Department of Statistics, Texas A&M University, College Station, Texas 77843-3143, - - 2013
We take a semiparametric approach in fitting a linear transformation model to a right censored data when predictive variables are subject to measurement errors. We construct consistent estimating equations when repeated measurements of a surrogate of the unobserved true predictor are available. The proposed approach applies under minimal assumptions on ...
Schneider D D Clinic of Fixed and Removable Prosthodontics and Dental Material Science, Center of Dental Medicine, University of Zurich, - - 2013
The use of periodontal probes harbors the risk of measurement errors. The aim of this study was to investigate the accuracy of the digital determination of gingival recession and papilla height on virtual jaw models, given the hypothesis that they show lower intrarater and interrater variability than conventional linear measurements ...
McGinitie Teague M TM Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G2G2, - - 2013
A new method for estimating the thermodynamic parameters of ΔH(T0), ΔS(T0), and ΔCP for use in thermodynamic modeling of GC×GC separations has been developed. The method is an alternative to the traditional isothermal separations required to fit a three-parameter thermodynamic model to retention data. Herein, a non-linear optimization technique is ...
Prudhomme Christel C Centre for Ecology and Hydrology, Wallingford OX10 8BB, United - - 2013
Increasing concentrations of greenhouse gases in the atmosphere are expected to modify the global water cycle with significant consequences for terrestrial hydrology. We assess the impact of climate change on hydrological droughts in a multimodel experiment including seven global impact models (GIMs) driven by bias-corrected climate from five global climate ...
Hero Robert R University of California, Davis, - - 2013
In this paper, we present a high quality and interactive method for volume rendering curvilinear-grid datasets. This method is based on a two-stage parallel transformation of the sample position into intermediate computational space then into texture space through the use of multiple 1 and 2D deformation textures using hardware acceleration. ...
Dwyer Michael G MG Buffalo Neuroimaging Analysis Center, Department of Neurology, School of Medicine and Biomedical Science, University at Buffalo, State University of New York, Buffalo, NY, USA. Electronic address: - - 2013
SIENA and similar techniques have demonstrated the utility of performing "direct" measurements as opposed to post-hoc comparison of cross-sectional data for the measurement of whole brain (WB) atrophy over time. However, gray matter (GM) and white matter (WM) atrophy are now widely recognized as important components of neurological disease progression, ...
Murad Havi H 1Biostatistics Unit, Gertner Institute for Epidemiology and Health Policy Research, Tel-Hashomer, - - 2013
Assessing interactions in linear regression models when covariates have measurement error (ME) is complex.We previously described regression calibration (RC) methods that yield consistent estimators and standard errors for interaction coefficients of normally distributed covariates having classical ME. Here we extend normal based RC (NBRC) and linear RC (LRC) methods to ...
Grabowski T - - 2013
Regulatory agencies do not specify how to plan the sampling intervals in pharmacokinetics (PK) studies. Every interval between each sampling point forms one of the fractions of the area under the curve (AUC). The aim of this study is to propose a method of qualitative evaluation of PK studies, on ...
Hirve Siddhivinayak S Vadu Rural Health Program, KEM Hospital Research Center, Pune, India; Umeå Centre for Global Health Research, Division of Epidemiology and Global Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden. Electronic address: - - 2013
We compared prevalence estimates of self-rated health (SRH) derived indirectly using four different small area estimation methods for the Vadu (small) area from the national Study on Global AGEing (SAGE) survey with estimates derived directly from the Vadu SAGE survey. The indirect synthetic estimate for Vadu was 24% whereas the ...
Kuhlmann Levin - - 2013
Bayesian spiking neurons (BSNs) provide a probabilistic interpretation of how neurons perform inference and learning. Online learning in BSNs typically involves parameter estimation based on maximum-likelihood expectation-maximization (ML-EM) which is computationally slow and limits the potential of studying networks of BSNs. An online learning algorithm, fast learning (FL), is presented ...
Chen Baojiang - - 2013
In statistical analysis, a regression model is needed if one is interested in finding the relationship between a response variable and covariates. When the response depends on the covariate, then it may also depend on the function of this covariate. If one has no knowledge of this functional form but ...
Grosswendt B - - 2013
The track nanodosemeter developed at the National Laboratories of Legnaro (LNL), Italy allows the direct investigation of the properties of particle tracks, by measuring ionisation-cluster-size distributions caused by ionising particles within a 'nanometre-sized' target volume while passing it at a well-specified impact parameter. To supplement the measurements, a dedicated Monte ...
Caruel M - - 2013
Complex 3D beating heart models are now available, but their complexity makes calibration and validation very difficult tasks. We thus propose a systematic approach of deriving simplified reduced-dimensional models, in "0D"-typically, to represent a cardiac cavity, or several coupled cavities-and in "1D"-to model elongated structures such as muscle samples or ...
Brocchini Maurizio M D.I.C.E.A. , Università Politecnica delle Marche , Via Brecce Bianche 12, 60131 Ancona, - - 2013
This paper, which is largely the fruit of an invited talk on the topic at the latest International Conference on Coastal Engineering, describes the state of the art of modelling by means of Boussinesq-type models (BTMs). Motivations for using BTMs as well as their fundamentals are illustrated, with special attention ...
Wang Kun - - 2013
Lopinavir (LPV)/ritonavir (RTV) co-formulation (LPV/RTV) is a widely used protease inhibitor (PI)-based regimen to treat HIV-infection. As with all PIs, the trough concentration (C trough) is a primary determinant of response, but the optimum exposure remains poorly defined. The primary objective was to develop an integrated LPV population pharmacokinetic model ...
Dutra José Diogo L - - 2013
In this study, we propose three different methods for calculation of Judd-Ofelt intensity parameters of poly-europium systems. The first, named Centroid Method, proposes the calculation considering the center of the dimeric system as the half distances between the two europium centers. The second method, called Overlapped Polyhedra Method, proposes the ...
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