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Viti Carlo C Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), University of Florence, P.le delle Cascine, 24, Florence, 50144, Italy, - - 2015
Standard protocols are available in order to apply Phenotype MicroArray (PM) technology to characterize different groups of microorganisms. Nevertheless, there is the need to pay attention to several crucial steps in order to obtain high-quality and reproducible data from PM, such as the choice of the Dye mix, the type ...
Priyadarshana Madawa M Faculty of Science, Department of Statistics, Macquarie University, Sydney, NSW, 2109, Australia, - - 2015
Array comparative genomic hybridization (aCGH) is one of the techniques that can be used to detect copy number variations in DNA sequences in high resolution. It has been identified that abrupt changes in the human genome play a vital role in the progression and development of many complex diseases. In ...
Louf Rémi R Institut de Physique Théorique, CEA, CNRS-URA 2306, Gif-sur-Yvette 91191, France - - 2014
We propose a quantitative method to classify cities according to their street pattern. We use the conditional probability distribution of shape factor of blocks with a given area and define what could constitute the 'fingerprint' of a city. Using a simple hierarchical clustering method, these fingerprints can then serve as ...
Lima Eduardo A EA Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts. 02139, USA ; Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee. 37235, - - 2014
Multianalyte microphysiometry is a powerful technique for studying cellular metabolic flux in real time. Monitoring several analytes concurrently in a number of individual chambers, however, requires specific instrumentation that is not available commercially in a single, compact, benchtop form at an affordable cost. We developed a multipotentiostat system capable of ...
Park Sang Hyuk SH Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South - - 2014
We developed and validated an interinstrument comparison method for automatic hematology analyzers based on the 99th percentile coefficient of variation (CV) cutoff of daily means and validated in both patient samples and quality control (QC) materials. A total of 120 patient samples were obtained over 6 months. Data from the ...
Cappel Daniel D Schrödinger GmbH, Dynamostr. 13, 68165, Mannheim, - - 2014
3-D ligand conformations are required for most ligand-based drug design methods, such as pharmacophore modeling, shape-based screening, and 3-D QSAR model building. Many studies of conformational search methods have focused on the reproduction of crystal structures (i.e. bioactive conformations); however, for ligand-based modeling the key question is how to generate ...
Donkin Chris C School of Psychology, University of New South Wales, Sydney, NSW, Australia, - - 2014
The slots model of visual working memory, despite its simplicity, has provided an excellent account of data across a number of change detection experiments. In the current research, we provide a new test of the slots model by investigating its ability to account for the increased prevalence of errors when ...
Hu Yuh-Jyh - - 2014
BackgroundOne of the major challenges in the field of vaccine design is identifying B-cell epitopes in continuously evolving viruses. Various tools have been developed to predict linear or conformational epitopes, each relying on different physicochemical properties and adopting distinct search strategies. We propose a meta-learning approach for epitope prediction based ...
Biarnés Marc M -, Institut de la màcula i de la retina, Vilana 12, Barcelona, Barcelona, 08022, Spain - - 2014
PURPOSE. To reappraise fundus autofluorescence (FAF) patterns in patients with geographic atrophy (GA) with the aim of simplifying the existing classification and to evaluate their stability with time using a data-driven approach, latent class analysis (LCA). METHODS. One hundred seventy-one patients of the prospective, natural history study on GA (GAIN, ...
Shenker Sol S Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York 10065, - - 2014
Major applications of RNA-seq data include studies of how the transcriptome is modulated at the levels of gene expression and RNA processing, and how these events are related to cellular identity, environmental condition, and/or disease status. While many excellent tools have been developed to analyze RNA-seq data, these generally have ...
Ashkenazy Haim H Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, - - 2014
It is often assumed that it is unlikely that the same insertion or deletion (indel) event occurred at the same position in two independent evolutionary lineages, and thus, indel-based inference of phylogeny should be less subject to homoplasy compared to standard inference which is based on substitution events. Indeed, indels ...
Smith Amy F AF Oxford Centre for Collaborative Applied Mathematics, Mathematical Institute, University of Oxford, Woodstock Road, Oxford, OX2 6GG, UK; Department of Physiology, University of Arizona, Tucson, Arizona, - - 2014
Recent developments in high-resolution imaging techniques have enabled digital reconstruction of three-dimensional sections of microvascular networks down to the capillary scale. To better interpret these large data sets, our goal is to distinguish branching trees of arterioles and venules from capillaries. Two novel algorithms are presented for classifying vessels in ...
Gross Samuel M SM Department of Statistics, Stanford University, Stanford, CA 94305, USA - - 2014
We consider the scenario where one observes an outcome variable and sets of features from multiple assays, all measured on the same set of samples. One approach that has been proposed for dealing with these type of data is "sparse multiple canonical correlation analysis" (sparse mCCA). All of the current ...
Zhang Jing J Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California 90089, - - 2014
The deconvolution of isoform expression from RNA-seq remains challenging because of non-uniform read sampling and subtle differences among isoforms. We present a weighted-log-likelihood expectation maximization method on isoform quantification (WemIQ). WemIQ integrates an effective bias removal with a weighted expectation maximization (EM) algorithm to distribute reads among isoforms efficiently. The ...
Hsu Wei-Yen WY Department of Information Management, National Chung Cheng University, Chiayi County, Taiwan Advanced Institute of Manufacturing with High-Tech Innovations, National Chung Cheng University, Chiayi County, Taiwan shenswy@gmail.com - - 2014
An electroencephalogram recognition system considering phase features is proposed to enhance the performance of motor imagery classification in this study. It mainly consists of feature extraction, feature selection and classification. Surface Laplacian filter is used for background removal. Several potential features, including phase features, are then extracted to enhance the ...
Hermundstad Ann M AM Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, United - - 2014
Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime - when sampling limitations constrain performance - efficient coding implies ...
Newby Danielle - - 2014
The biopharmaceutical classification system (BCS) is now well established and utilised for the development and biowaivers of immediate oral dosage forms. The prediction of BCS class can be carried out using multi-label classification. Unlike single label classification, multi-label classification methods predict more than one class labels at the same time. ...
Chen L L Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G - - 2014
Accuracy of predicting genomic breeding values for carcass merit traits including hot carcass weight, longissimus muscle area (REA), carcass average backfat thickness (AFAT), lean meat yield (LMY) and carcass marbling score (CMAR) was evaluated based on 543 Angus and 400 Charolais steers genotyped on the Illumina BovineSNP50 Beadchip. For the ...
Prades Nebot Jose - - 2014
Angular Intra Prediction (AIP) is a coding tool that has been incorporated into the video coding standards H.264/AVC and HEVC. In this paper, we study how the efficiency of AIP depends on its prediction parameters. To carry out this study, we first theoretically analyze the variance of the error incurred ...
Tjärnberg Andreas A Stockholm Bioinformatics Centre, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden. - - 2014
Statistical regularisation methods such as LASSO and related L1 regularised regression methods are commonly used to construct models of gene regulatory networks. Although they can theoretically infer the correct network structure, they have been shown in practice to make errors, i.e. leave out existing links and include non-existing links. We ...
Moscetti R R Department of Science and Technology for Agriculture, Forest, Nature and Energy, Tuscia University, Via S. Camillo de Lellis snc, 01100, Viterbo, - - 2014
This study investigates the possibility of using Near-Infrared spectroscopy for the authentication of the 'Nocciola Romana' hazelnut (Corylus avellana L. cvs. 'Tonda Gentile Romana' and 'Nocchione') as a protected designation of origin (PDO) hazelnut from Central Italy. Algorithms for the selection of the optimal pretreatments were tested in combination with ...
Tousseyn Simon S Laboratory for Epilepsy Research, UZ Leuven & KU Leuven, Leuven, Belgium; Medical Imaging Research Center, UZ Leuven & KU Leuven, Leuven, - - 2014
A prerequisite for the implementation of interictal electroencephalography-correlated functional magnetic resonance imaging (EEG-fMRI) in the presurgical work-up for epilepsy surgery is straightforward processing. We propose a new semi-automatic method as alternative for the challenging and time-consuming visual spike identification. Our method starts from a patient-specific spike-template, built by averaging spikes ...
Ju Zhenlin Z Department of Bioinformatics and Computational Biology, Department of Systems Biology, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, - - 2014
High-throughput reverse-phase protein array (RPPA) technology allows for the parallel measurement of protein expression levels in ~1000 samples. However, the many steps required in the complex protocol (sample lysate preparation, slide printing, hybridization, washing, and amplified detection) may create substantial variability in data quality. We are not aware of any ...
Stango Antonietta - - 2014
Research on pattern recognition for myoelectric control has usually focused on a small number of EMG channels, because of better clinical acceptability and low computational load with respect to multi-channel EMG. However, recently, high density (HD) EMG technology has substantially improved, also in practical usability, and can thus be applied ...
Lombaert Eric E Inra, UMR 1355 ISA, 06903, Sophia-Antipolis, France; Université de Nice Sophia Antipolis, UMR ISA, 06903, Sophia-Antipolis, France; CNRS, UMR 7254 ISA, 06903, Sophia-Antipolis, - - 2014
Inferences about introduction histories of invasive species remain challenging because of the stochastic demographic processes involved. Approximate Bayesian computation (ABC) can help to overcome these problems, but such method requires a prior understanding of population structure over the study area, necessitating the use of alternative methods and an intense sampling ...
Kenttä Tuomas T Medical Research Center Oulu, University of Oulu and University Hospital of Oulu, Oulu, - - 2014
Early repolarization (ER) is defined as an elevation of the QRS-ST junction in at least two inferior or lateral leads of the standard 12-lead electrocardiogram (ECG). Our purpose was to create an algorithm for the automated detection and classification of ER. A total of 6,047 electrocardiograms were manually graded for ...
Hess Brian J BJ Dr. Hess is a consultant, Hess Consulting, St-Nicolas, Québec, Canada. Dr. Lipner is senior vice president of evaluation, research and development, American Board of Internal Medicine, Philadelphia, Pennsylvania. Dr. Thompson is professor of cognitive psychology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada. Dr. Holmboe is senior vice president of milestone development and evaluation, Accreditation Council for Graduate Medical Education, Chicago, Illinois. Dr. Graber is senior research fellow, RTI International, Research Triangle Park, North Carolina, and professor emeritus, at SUNY Stony Brook University School of Medicine, Stony Brook, New - - 2014
Experienced clinicians derive many diagnoses intuitively, because most new problems they see closely resemble problems they've seen before. The majority of these diagnoses, but not all, will be correct. This study determined whether further reflection regarding initial diagnoses improves diagnostic accuracy during a high-stakes board exam, a model for studying ...
Speiser Jaime Lynn JL Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, - - 2014
Classification of objects into pre-defined groups based on known information is a fundamental problem in the field of statistics. Although approaches for solving this problem exist, finding an accurate classification method can be challenging in an orphan disease setting, where data are minimal and often not normally distributed. The purpose ...
Heller Ruth R Department of Statistics and Operations Research and - - 2014
We propose a formal method to declare that findings from a primary study have been replicated in a follow-up study. Our proposal is appropriate for primary studies that involve large-scale searches for rare true positives (i.e., needles in a haystack). Our proposal assigns an r value to each finding; this ...
Kunz Michael M Global Research and Clinical Development Statistics, Bayer Pharma AG, Berlin, - - 2014
In this paper, three analysis procedures for repeated correlated binary data with no a priori ordering of the measurements are described and subsequently investigated. Examples for correlated binary data could be the binary assessments of subjects obtained by several raters in the framework of a clinical trial. This topic is ...
Allhoff Manuel M IZKF Computational Biology Research Group, RWTH Aachen University Medical School, Germany Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Germany Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Germany Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, - - 2014
Detection of changes in DNA-protein interactions from ChIP-seq data is a crucial step in unraveling the regulatory networks behind biological processes. The simplest variation of this problem is the differential peak calling problem. Here one has to find genomic regions with ChIP-seq signal changes between two cellular conditions in the ...
Fakhraei Shobeir S Medical Image Analysis Laboratory, Department of Radiology, Henry Ford Health System, Detroit, MI 48202, USA ; Department of Computer Science, University of Maryland, College Park, MD 20740, - - 2014
Feature rankings are often used for supervised dimension reduction especially when discriminating power of each feature is of interest, dimensionality of dataset is extremely high, or computational power is limited to perform more complicated methods. In practice, it is recommended to start dimension reduction via simple methods such as feature ...
Wulsin Drausin F DF Department of Bioengineering, University of Pennsylvania, Philadelphia, - - 2014
Patients with epilepsy can manifest short, sub-clinical epileptic "bursts" in addition to full-blown clinical seizures. We believe the relationship between these two classes of events-something not previously studied quantitatively-could yield important insights into the nature and intrinsic dynamics of seizures. A goal of our work is to parse these complex ...
Okayasu Hiromasa H Research, Policy and Product Development, Global Polio Eradication Department, World Health Organization, Geneva, - - 2014
To assess the quality of supplementary immunization activities (SIAs), the Global Polio Eradication Initiative (GPEI) has used cluster lot quality assurance sampling (C-LQAS) methods since 2009. However, since the inception of C-LQAS, questions have been raised about the optimal balance between operational feasibility and precision of classification of lots to ...
Pang Yanwei - - 2014
In vision and learning, low computational complexity and high generalization are two important goals for video object detection. Low computational complexity here means not only fast speed but also less energy consumption. The sliding window object detection method with linear support vector machines (SVMs) is a general object detection framework. ...
Soltani Azadeh - - 2014
A new confabulation-inspired association rule mining (CARM) algorithm is proposed using an interestingness measure inspired by cogency. Cogency is only computed based on pairwise item conditional probability, so the proposed algorithm mines association rules by only one pass through the file. The proposed algorithm is also more efficient for dealing ...
Nagaraj Sunil Belur - - 2014
Atomic decomposition (AD) can be used to efficiently decompose an arbitrary signal. In this paper, we present a method to detect neonatal electroencephalogram (EEG) seizure based on AD via orthogonal matching pursuit using a novel, application-specific, dictionary. The dictionary consists of pseudoperiodic Duffing oscillator atoms which are designed to be ...
Budhram Gavin G Department of Emergency Medicine, Tufts University School of Medicine, Baystate Medical Center, Springfield, Massachusetts USA (G.B., L.L.); and Department of Emergency Medicine, University of Vermont, Burlington, Vermont USA (D.M., A.S.). - - 2014
Several recent studies have investigated methods to confirm endotracheal tube (ETT) placement with sonography, using diaphragmatic movement, lung sliding, and transtracheal visualization of the ETT. To our knowledge, no studies have directly compared these 3 methods. This study aimed to directly compare the test characteristics of these 3 methods to ...
Vivekanand Aruna - - 2014
Posterior capsule opacification (PCO) is a common complication in patients who have undergone cataract surgery, occurring in up to 50% of patients by two to three years after the operation. Assessment of PCO has been mainly subjective, making it difficult to understand its progression over time or assess the effectiveness ...
Farronato Giampietro G From the Department of Orthodontics, Fondazione IRCCS Cà Granda-Ospedale Maggiore Policlinico, University of Milan, Milan, - - 2014
The precision of presurgical orthodontic diagnostic protocol plays a key role for the success of orthognathic surgery.Recently, the introduction of cone beam computed tomography and the development of digital technologies led to the possibility to create new virtual protocols of diagnostic protocol.The purposes of this study were to describe the ...
Budianto B - - 2014
This paper presents a novel marker encoded fringe projection profilometry (FPP) scheme for efficient 3-dimensional (3D) model acquisition. Traditional FPP schemes can introduce large errors to the reconstructed 3D model when the target object has an abruptly changing height profile. For the proposed scheme, markers are encoded in the projected ...
NÄ›mec Tomáš T Institute of Thermomechanics ASCR, Dolejškova 5, 18200, Praha 8, Czech Republic, - - 2014
A scaling law for bubble nucleation data is developed based on the classical nucleation theory and a scaled surface tension correlation. The scaled approach is applied to a set of bubble nucleation data for lower alkanes available in the literature. The results are found to agree well also with the ...
Matic Vladimir V KU Leuven, Department of Electrical Engineering (ESAT) STADIUS Centre for Dynamical Systems, Signal Processing and Data Analytics, Leuven, Belgium. iMinds Medical IT Department, Leuven, - - 2014
Objective. To develop an automated algorithm to quantify background EEG abnormalities in full-term neonates with hypoxic ischemic encephalopathy. Approach. The algorithm classifies 1 h of continuous neonatal EEG (cEEG) into a mild, moderate or severe background abnormality grade. These classes are well established in the literature and a clinical neurophysiologist ...
Everds Nancy E NE Amgen Inc, Seattle, Washington, USA - - 2014
During the conduct of in vivo toxicology studies, in-life, clinical pathology, and anatomic pathology parameters are collected and interpreted. These sets of parameters are evaluated in an integrative manner to determine the overall toxicity of a test article. For clinical pathology parameters, the inherent variability and physiologic factors affecting each ...
Maretty Lasse - - 2014
RNA-seq allows for simultaneous transcript discovery and quantification, but reconstructing complete transcripts from such data remains difficult. Here, we introduce the Bayesembler, a novel probabilistic method for transcriptome assembly built on a Bayesian model of the RNA sequencing process. Under this model, samples from the posterior distribution over transcripts and ...
Malmivaara Antti A Centre for Health and Social Economics, National Institute for Health and Welfare , Helsinki , - - 2014
The GRADE method (Grading of Recommendations, Assessment, Development, and Evaluation) provides a tool for rating the quality of evidence for systematic reviews and clinical guidelines. This article aims to analyse conceptually how well grounded the GRADE method is, and to suggest improvements. The eight criteria for rating the quality of ...
Xiao Yingchao - - 2014
Gaussian processes (GPs) provide predicted outputs with a full conditional statistical description, which can be used to establish confidence intervals and to set hyperparameters. This characteristic provides GPs with competitive or better performance in various applications. However, the specificity of one-class classification (OCC) makes GPs unable to select suitable hyperparameters ...
Salvatelli Valentina V Physics Department and INFN, Università di Roma "La Sapienza", Ple Aldo Moro 2, 00185 Rome, - - 2014
We show that a general late-time interaction between cold dark matter and vacuum energy is favored by current cosmological data sets. We characterize the strength of the coupling by a dimensionless parameter q_{V} that is free to take different values in four redshift bins from the primordial epoch up to ...
Anthony Karen K From The Dubowitz Neuromuscular Centre (K.A., V.A.-G., S.T., L.F., N.J., C.A.S., J.E.M., F.M.), UCL, Institute of Child Health, London, UK; The Center for Gene Therapy (L.E.T., A.V., Y.K., K.M.F.), The Research Institute at Nationwide Children's Hospital, Columbus, OH; Institut de Myologie (G.B., M.B., T.V.), UPMC UM76, INSERM U 794, CNRS UMR 7215, Paris, France; Institute of Genetic Medicine (R.B., M.H., S.L., V.S.), Newcastle University, UK; and Prosensa Therapeutics (A.L., G.C.), Leiden, the Netherlands. V.A.-G. is currently affiliated with the Neuromuscular Disorders Group, BioCruces Health Research Institute, Barakaldo, - - 2014
We formed a multi-institution collaboration in order to compare dystrophin quantification methods, reach a consensus on the most reliable method, and report its biological significance in the context of clinical trials. Five laboratories with expertise in dystrophin quantification performed a data-driven comparative analysis of a single reference set of normal ...
Yi Hui H Virginia - - 2014
The data from genome-wide association studies (GWAS) in humans are still predominantly analyzed using single marker association methods. As an alternative to Single Marker Analysis (SMA), all or subsets of markers can be tested simultaneously. This approach requires a form of Penalized Regression (PR) as the number of SNPs is ...
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