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Scientific Reports | 27578529 | PMC5006166 | 10.1038/srep32404 | Large-Scale Discovery of Disease-Disease and Disease-Gene Associations | Data-driven phenotype analyses on Electronic Health Record (EHR) data have recently drawn benefits across many areas of clinical practice, uncovering new links in the medical sciences that can potentially affect the well-being of millions of patients. In this paper, EHR data is used to discover novel relationships betw... | Background and related workIn the treatment of ailments, the focus of medical practitioners can be roughly divided between two complementary approaches: 1) treating the symptoms of already sick patients (reactive medicine); and 2) understanding disease etiology in order to prevent manifestation and further spread of th... | [
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{
"pmid": "21587298",
"title": "Using electronic health records to drive discovery in disease genomics.",
"abstract": "If genomic studies are to be a clinically relevant and timely reflection of the relationship between genetics and health status--whether for common or rare variants--cost-effective ways... |
Frontiers in Psychology | 27721800 | PMC5033969 | 10.3389/fpsyg.2016.01429 | Referential Choice: Predictability and Its Limits | We report a study of referential choice in discourse production, understood as the choice between various types of referential devices, such as pronouns and full noun phrases. Our goal is to predict referential choice, and to explore to what extent such prediction is possible. Our approach to referential choice include... | Related WorkAs was discussed in Section “Discussion: Referential Choice Is Not Always Categorical”, referential variation and non-categoricity is clearly gaining attention in the modern linguistic, computational, and psycholinguistic literature. Referential variation may be due to the interlocutors’ perspective taking ... | [
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"pmid": "18449327",
"title": "The effect of additional characters on choice of referring expression: Everyone counts.",
"abstract": "Two story-telling experiments examine the process of choosing between pronouns and proper names in speaking. Such choices are traditionally attributed to speakers strivi... |
Journal of Cheminformatics | 28316646 | PMC5034616 | 10.1186/s13321-016-0164-0 | An ensemble model of QSAR tools for regulatory risk assessment | Quantitative structure activity relationships (QSARs) are theoretical models that relate a quantitative measure of chemical structure to a physical property or a biological effect. QSAR predictions can be used for chemical risk assessment for protection of human and environmental health, which makes them interesting to... | Related workThere are studies that investigate methods for combining predictions from multiple QSAR tools to gain better predictive performance for various toxic endpoints: (1) Several QSAR models were developed and compared using different clustering algorithms (multiple linear regression, radial basis function neural... | [
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"pmid": "17643090",
"title": "The application of discovery toxicology and pathology towards the design of safer pharmaceutical lead candidates.",
"abstract": "Toxicity is a leading cause of attrition at all stages of the drug development process. The majority of safety-related attrition occurs preclin... |
JMIR Medical Education | 27731840 | PMC5041364 | 10.2196/mededu.4789 | A Conceptual Analytics Model for an Outcome-Driven Quality Management Framework as Part of Professional Healthcare Education | BackgroundPreparing the future health care professional workforce in a changing world is a significant undertaking. Educators and other decision makers look to evidence-based knowledge to improve quality of education. Analytics, the use of data to generate insights and support decisions, have been applied successfully ... | Related WorkEducational Informatics is a multidisciplinary research area that uses Information and Communication Technology (ICT) in education. It has many sub-disciplines, a number of which focus on learning or teaching (eg, simulation), and others that focus on administration of educational programs (eg, curriculum m... | [
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{
"pmid": "20054502",
"title": "Recommendations of the International Medical Informatics Association (IMIA) on Education in Biomedical and Health Informatics. First Revision.",
"abstract": "Objective: The International Medical Informatics Association (IMIA) agreed on revising the existing international ... |
Scientific Reports | 27686748 | PMC5043229 | 10.1038/srep34181 | Accuracy Improvement for Predicting Parkinson’s Disease Progression | Parkinson’s disease (PD) is a member of a larger group of neuromotor diseases marked by the progressive death of dopamineproducing cells in the brain. Providing computational tools for Parkinson disease using a set of data that contains medical information is very desirable for alleviating the symptoms that can help th... | Related WorkFor effective diagnosis of Parkinson’s Disease (PD), different types of classification methods were examined by Das30. The computation of the performance score of the classifiers was based on various evaluation methods. According to the results of application scores, they found that Neural Networks (NNs) cl... | [
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"title": "Predicting Parkinson's disease - why, when, and how?",
"abstract": "Parkinson's disease (PD) is a progressive disorder with a presymptomatic interval; that is, there is a period during which the pathologic process has begun, but motor signs required for the clinical diagn... |
Scientific Reports | 27694950 | PMC5046183 | 10.1038/srep33985 | Multi-Pass Adaptive Voting for Nuclei Detection in Histopathological Images | Nuclei detection is often a critical initial step in the development of computer aided diagnosis and prognosis schemes in the context of digital pathology images. While over the last few years, a number of nuclei detection methods have been proposed, most of these approaches make idealistic assumptions about the staini... | Previous Related Work and Novel ContributionsTable 1 enumerates some recent techniques for nuclei detection. Most approaches typically tend to use image derived cues, such as color/intensity2528293031, edges192124323334, texture35, self learned features1336, and symmetry22242737.The color and texture-based methods requ... | [
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"pmid": "26186772",
"title": "Feature Importance in Nonlinear Embeddings (FINE): Applications in Digital Pathology.",
"abstract": "Quantitative histomorphometry (QH) refers to the process of computationally modeling disease appearance on digital pathology images by extracting hundreds of image feature... |
Scientific Reports | 27703256 | PMC5050509 | 10.1038/srep34759 | Feature Subset Selection for Cancer Classification Using Weight Local Modularity | Microarray is recently becoming an important tool for profiling the global gene expression patterns of tissues. Gene selection is a popular technology for cancer classification that aims to identify a small number of informative genes from thousands of genes that may contribute to the occurrence of cancers to obtain a ... | Related WorkOwing to the importance of gene selection in the analysis of the microarray dataset and the diagnosis of cancer, various techniques for gene selection problems have been proposed.Because of the high dimensionality of most microarray analyses, fast and efficient gene selection techniques such as univariate f... | [
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{
"pmid": "23124059",
"title": "Selection of interdependent genes via dynamic relevance analysis for cancer diagnosis.",
"abstract": "Microarray analysis is widely accepted for human cancer diagnosis and classification. However the high dimensionality of microarray data poses a great challenge to classi... |
Frontiers in Neuroscience | 27774048 | PMC5054006 | 10.3389/fnins.2016.00454 | Design and Evaluation of Fusion Approach for Combining Brain and Gaze Inputs for Target Selection | Gaze-based interfaces and Brain-Computer Interfaces (BCIs) allow for hands-free human–computer interaction. In this paper, we investigate the combination of gaze and BCIs. We propose a novel selection technique for 2D target acquisition based on input fusion. This new approach combines the probabilistic models for each... | 2. Related workThis section presents the most relevant studies related to the scope of this paper. We focus on target selection tasks, in particular on existing gaze- and SSVEP-based methods for target selection.2.1. Target selectionAccording to Foley et al. (1984), any interaction task can be decomposed into a small s... | [
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"pmid": "23486216",
"title": "Enhanced perception of user intention by combining EEG and gaze-tracking for brain-computer interfaces (BCIs).",
"abstract": "Speller UI systems tend to be less accurate because of individual variation and the noise of EEG signals. Therefore, we propose a new method to co... |
JMIR Medical Informatics | 27658571 | PMC5054236 | 10.2196/medinform.5353 | Characterizing the (Perceived) Newsworthiness of Health Science Articles: A Data-Driven Approach | BackgroundHealth science findings are primarily disseminated through manuscript publications. Information subsidies are used to communicate newsworthy findings to journalists in an effort to earn mass media coverage and further disseminate health science research to mass audiences. Journal editors and news journalists ... | Motivation and Related WorkThe news media are powerful conduits by which to disseminate important information to the public [8]. There is a chasm between the constant demand for up-to-date information and shrinking budgets and staff at newspapers around the globe. Information subsidies such as press releases are often ... | [
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"pmid": "15249264",
"title": "Health attitudes, health cognitions, and health behaviors among Internet health information seekers: population-based survey.",
"abstract": "BACKGROUND\nUsing a functional theory of media use, this paper examines the process of health-information seeking in different doma... |
BioData Mining | 27777627 | PMC5057496 | 10.1186/s13040-016-0110-8 | FEDRR: fast, exhaustive detection of redundant hierarchical relations for quality improvement of large biomedical ontologies | BackgroundRedundant hierarchical relations refer to such patterns as two paths from one concept to another, one with length one (direct) and the other with length greater than one (indirect). Each redundant relation represents a possibly unintended defect that needs to be corrected in the ontology quality assurance pro... | Related workThere has been related work on exploring redundant relations in biomedical ontologies or terminologies [24–28]. Bodenreider [24] investigated the redundancy of hierarchical relations across biomedical terminologies in the UMLS. Different from Bodenreider’s work, FEDRR focuses on developing a fast and scalab... | [
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{
"pmid": "17095826",
"title": "SNOMED-CT: The advanced terminology and coding system for eHealth.",
"abstract": "A clinical terminology is essential for Electronic Health records. It represents clinical information input into clinical IT systems by clinicians in a machine-readable manner. Use of a Clin... |
BMC Medical Informatics and Decision Making | 27756371 | PMC5070096 | 10.1186/s12911-016-0371-7 | Predicting influenza with dynamical methods | BackgroundPrediction of influenza weeks in advance can be a useful tool in the management of cases and in the early recognition of pandemic influenza seasons.MethodsThis study explores the prediction of influenza-like-illness incidence using both epidemiological and climate data. It uses Lorenz’s well-known Method of A... | Related workA survey of influenza forecasting methods [3] yielded 35 publications organized into categories based on the epidemiological application – population-based, medical facility-based, and forecasting regionally or globally. Within these categories, the forecasting methods varied along with the types of data us... | [
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{
"pmid": "27127415",
"title": "Prediction of Peaks of Seasonal Influenza in Military Health-Care Data.",
"abstract": "Influenza is a highly contagious disease that causes seasonal epidemics with significant morbidity and mortality. The ability to predict influenza peak several weeks in advance would al... |
BioData Mining | 27785153 | PMC5073928 | 10.1186/s13040-016-0113-5 | Developing a modular architecture for creation of rule-based clinical diagnostic criteria | BackgroundWith recent advances in computerized patient records system, there is an urgent need for producing computable and standards-based clinical diagnostic criteria. Notably, constructing rule-based clinical diagnosis criteria has become one of the goals in the International Classification of Diseases (ICD)-11 revi... | Related workPrevious studies have been conducted in integrating and formally expressing diagnostic rules from different perspectives. These rules are usually extracted from free-text-based clinical guidelines or diagnostic criteria, and integrated into computerized decision support systems to improve clinical performan... | [
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"pmid": "23523876",
"title": "An ontology-driven, diagnostic modeling system.",
"abstract": "OBJECTIVES\nTo present a system that uses knowledge stored in a medical ontology to automate the development of diagnostic decision support systems. To illustrate its function through an example focused on the... |
Frontiers in Neuroscience | 27833526 | PMC5081358 | 10.3389/fnins.2016.00479 | Sound Source Localization through 8 MEMS Microphones Array Using a Sand-Scorpion-Inspired Spiking Neural Network | Sand-scorpions and many other arachnids perceive their environment by using their feet to sense ground waves. They are able to determine amplitudes the size of an atom and locate the acoustic stimuli with an accuracy of within 13° based on their neuronal anatomy. We present here a prototype sound source localization sy... | Related workPrior work for bioinspired acoustic surveillance units (ASU; from flies), such as that of Cauwenberghs et al. used spatial and temporal derivatives of the field over a sensor array of MEMS microphones, power series expansion, and Independent Component Analysis (ICA) for localizing and separating mixtures of... | [
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{
"pmid": "19115011",
"title": "Brian: a simulator for spiking neural networks in python.",
"abstract": "\"Brian\" is a new simulator for spiking neural networks, written in Python (http://brian. di.ens.fr). It is an intuitive and highly flexible tool for rapidly developing new models, especially networ... |
Frontiers in Neuroinformatics | 27867355 | PMC5095137 | 10.3389/fninf.2016.00048 | Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience | Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat... | 2. Background and related workThe scientific community utilizes a broad range of data formats. Basic formats explicitly specify how data is laid out and formatted in binary or text data files (e.g., CSV, BOF, etc). While such basic formats are common, they generally suffer from a lack of portability, scalability and a ... | [
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"title": "NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail.",
"abstract": "Biologically detailed single neuron and network models are important for understanding how ion channels, synapses and anatomical connectiv... |
JMIR Public Health and Surveillance | 27765731 | PMC5095368 | 10.2196/publichealth.5901 | Evaluating Google, Twitter, and Wikipedia as Tools for Influenza Surveillance Using Bayesian Change Point Analysis: A Comparative Analysis | BackgroundTraditional influenza surveillance relies on influenza-like illness (ILI) syndrome that is reported by health care providers. It primarily captures individuals who seek medical care and misses those who do not. Recently, Web-based data sources have been studied for application to public health surveillance, a... | Related WorkAs the number of Internet users has increased [11], researchers have identified the use of Google, Twitter, and Wikipedia as novel surveillance approaches to complement traditional methods. Google Flu Trends, which monitors Google users’ searches for information related to influenza, has shown correlation w... | [
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{
"pmid": "25835538",
"title": "Estimating influenza attack rates in the United States using a participatory cohort.",
"abstract": "We considered how participatory syndromic surveillance data can be used to estimate influenza attack rates during the 2012-2013 and 2013-2014 seasons in the United States. ... |
Frontiers in Neuroscience | 27877107 | PMC5099523 | 10.3389/fnins.2016.00508 | Training Deep Spiking Neural Networks Using Backpropagation | Deep spiking neural networks (SNNs) hold the potential for improving the latency and energy efficiency of deep neural networks through data-driven event-based computation. However, training such networks is difficult due to the non-differentiable nature of spike events. In this paper, we introduce a novel technique, wh... | 1.1. Related workGradient descent methods for SNNs have not been deeply investigated because both spike trains and the underlying membrane potentials are not differentiable at the time of spikes. The most successful approaches to date have used indirect methods, such as training a network in the continuous rate domain ... | [
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"pmid": "25910252",
"title": "Turn Down That Noise: Synaptic Encoding of Afferent SNR in a Single Spiking Neuron.",
"abstract": "We have added a simplified neuromorphic model of Spike Time Dependent Plasticity (STDP) to the previously described Synapto-dendritic Kernel Adapting Neuron (SKAN), a hardwa... |
PLoS Computational Biology | 27835647 | PMC5105998 | 10.1371/journal.pcbi.1005113 | Network Receptive Field Modeling Reveals Extensive Integration and Multi-feature Selectivity in Auditory Cortical Neurons | Cortical sensory neurons are commonly characterized using the receptive field, the linear dependence of their response on the stimulus. In primary auditory cortex neurons can be characterized by their spectrotemporal receptive fields, the spectral and temporal features of a sound that linearly drive a neuron. However, ... | Related workA number of methods have been used previously to examine the spectrotemporal sensitivity of auditory cortical neurons. Previous studies have attempted to extend the application of the LN model to auditory cortical data, mostly using maximum-likelihood methods. Indeed, several studies have used approaches th... | [
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"pmid": "3973762",
"title": "Spatiotemporal energy models for the perception of motion.",
"abstract": "A motion sequence may be represented as a single pattern in x-y-t space; a velocity of motion corresponds to a three-dimensional orientation in this space. Motion sinformation can be extracted by a s... |
Frontiers in Psychology | 27899905 | PMC5110545 | 10.3389/fpsyg.2016.01793 | Effects of Individual Differences in Working Memory on Plan Presentational Choices | This paper addresses research questions that are central to the area of visualization interfaces for decision support: (RQ1) whether individual user differences in working memory should be considered when choosing how to present visualizations; (RQ2) how to present the visualization to support effective decision making... | 2. Related workThis section discusses related work addressing how visual presentational choices have been applied and evaluated in the past.2.1. RQ1: whether individual user differences in working memory should be consideredAnecdotal evidence about individual differences has motivated research on presenting the same in... | [
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"pmid": "26357185",
"title": "An Empirical Study on Using Visual Embellishments in Visualization.",
"abstract": "In written and spoken communications, figures of speech (e.g., metaphors and synecdoche) are often used as an aid to help convey abstract or less tangible concepts. However, the benefits of... |
BMC Medical Research Methodology | 27875988 | PMC5118882 | 10.1186/s12874-016-0259-3 | Common data elements for secondary use of electronic health record data for clinical trial execution and serious adverse event reporting | BackgroundData capture is one of the most expensive phases during the conduct of a clinical trial and the increasing use of electronic health records (EHR) offers significant savings to clinical research. To facilitate these secondary uses of routinely collected patient data, it is beneficial to know what data elements... | Related workIn the EHR4CR project, data inventories for ‘protocol feasibility’ [24] and ‘patient identification and recruitment’ [23] have been performed by Doods et al. There, 75 data elements were identified for feasibility assessment and 150 data elements for patient identification and recruitment. Despite the diffe... | [
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{
"pmid": "20798168",
"title": "A progress report on electronic health records in U.S. hospitals.",
"abstract": "Given the substantial federal financial incentives soon to be available to providers who make \"meaningful use\" of electronic health records, tracking the progress of this health care techno... |
Scientific Reports | 27876847 | PMC5120294 | 10.1038/srep37470 | A simplified computational memory model from information processing | This paper is intended to propose a computational model for memory from the view of information processing. The model, called simplified memory information retrieval network (SMIRN), is a bi-modular hierarchical functional memory network by abstracting memory function and simulating memory information processing. At fi... | Related WorkIn traditional memory studies memory has been accepted as network10, and visual modeling has been used from psychological to neural, physiological, anatomical, computational etc.12345678910 around neuron, cortex, physical signal, chemical signal and information processing910111213; various memory networks w... | [
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"title": "Dynamic searching in the brain.",
"abstract": "Cognitive functions rely on the extensive use of information stored in the brain, and the searching for the relevant information for solving some problem is a very complex task. Human cognition largely uses biological search ... |
Scientific Reports | 27905523 | PMC5131304 | 10.1038/srep38185 | Test of quantum thermalization in the two-dimensional transverse-field Ising model | We study the quantum relaxation of the two-dimensional transverse-field Ising model after global quenches with a real-time variational Monte Carlo method and address the question whether this non-integrable, two-dimensional system thermalizes or not. We consider both interaction quenches in the paramagnetic phase and f... | Related workRecently an exact theorem on generalized thermalization in D-dimensional quantum systems in the thermodynamic limit has been formulated55. The theorem states that generalized thermalization can be observed if the state of the system is algebraically sizably clustering. It also holds for exponentially sizabl... | [
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{
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"title": "Effect of suddenly turning on interactions in the Luttinger model.",
"abstract": "The evolution of correlations in the exactly solvable Luttinger model (a model of interacting fermions in one dimension) after a suddenly switched-on interaction is analytically studied. Whe... |
BioData Mining | 27980679 | PMC5139023 | 10.1186/s13040-016-0116-2 | MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification | BackgroundContinuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DN... | Related workThe above problem contains several complex aspects. The main one is that searching for many subsequences with desirable properties is much more difficult than searching for a single optimal one. Additionally, the dimensions of the problem to be solved are typically very large (i.e., DNA sequences with thous... | [
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{
"pmid": "270744",
"title": "Phylogenetic structure of the prokaryotic domain: the primary kingdoms.",
"abstract": "A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising a... |
Scientific Reports | 27929098 | PMC5144062 | 10.1038/srep38433 | EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm | We present EP-DNN, a protocol for predicting enhancers based on chromatin features, in different cell types. Specifically, we use a deep neural network (DNN)-based architecture to extract enhancer signatures in a representative human embryonic stem cell type (H1) and a differentiated lung cell type (IMR90). We train EP... | Related WorkSeveral computational methods that use histone modification signatures to identify enhancer regions have been developed. Won et al. proposed the use of Hidden Markov Models (HMMs) to predict enhancers using three primary histone modifications30. Firpi et al. focused on the importance of recognizing the hist... | [
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{
"pmid": "20025863",
"title": "Enhancers: the abundance and function of regulatory sequences beyond promoters.",
"abstract": "Transcriptional control in mammals and Drosophila is often mediated by regulatory sequences located far from gene promoters. Different classes of such elements - particularly en... |
Frontiers in Psychology | 28018271 | PMC5149550 | 10.3389/fpsyg.2016.01936 | Comparing a Perceptual and an Automated Vision-Based Method for Lie Detection in Younger Children | The present study investigates how easily it can be detected whether a child is being truthful or not in a game situation, and it explores the cue validity of bodily movements for such type of classification. To achieve this, we introduce an innovative methodology – the combination of perception studies (in which eye-t... | Related WorkChildren’s Lying BehaviorPrevious research suggests that children between 3 and 7 years old are quite good manipulators of their non-verbal behavior when lying, which makes the discrimination between truth-tellers and lie-tellers very difficult to accomplish (Lewis et al., 1989; Talwar and Lee, 2002a; Talwa... | [
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{
"pmid": "16859438",
"title": "Accuracy of deception judgments.",
"abstract": "We analyze the accuracy of deception judgments, synthesizing research results from 206 documents and 24,483 judges. In relevant studies, people attempt to discriminate lies from truths in real time with no special aids or tr... |
JMIR Medical Informatics | 27903489 | PMC5156821 | 10.2196/medinform.6373 | Finding Important Terms for Patients in Their Electronic Health Records: A Learning-to-Rank Approach Using Expert Annotations | BackgroundMany health organizations allow patients to access their own electronic health record (EHR) notes through online patient portals as a way to enhance patient-centered care. However, EHR notes are typically long and contain abundant medical jargon that can be difficult for patients to understand. In addition, m... | Related WorksNatural Language Processing Systems Facilitating Concept-Level Electronic Health Record ComprehensionThere has been active research on linking medical terms to lay terms [11,30,31], consumer-oriented definitions [12] and educational materials [32], and showing improved comprehension with such interventions... | [
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{
"pmid": "24359554",
"title": "The Medicare Electronic Health Record Incentive Program: provider performance on core and menu measures.",
"abstract": "OBJECTIVE\nTo measure performance by eligible health care providers on CMS's meaningful use measures.\n\n\nDATA SOURCE\nMedicare Electronic Health Recor... |
Frontiers in Neuroscience | 28066170 | PMC5177654 | 10.3389/fnins.2016.00587 | An Improved Unscented Kalman Filter Based Decoder for Cortical Brain-Machine Interfaces | Brain-machine interfaces (BMIs) seek to connect brains with machines or computers directly, for application in areas such as prosthesis control. For this application, the accuracy of the decoding of movement intentions is crucial. We aim to improve accuracy by designing a better encoding model of primary motor cortical... | Related workReviews of research in decoding for BMIs can be found elsewhere (Homer M. L. et al., 2013; Andersen et al., 2014; Baranauskas, 2014; Bensmaia and Miller, 2014; Kao et al., 2014; Li, 2014). Here we discuss the decoders compared in the present study.The improved unscented Kalman filter decoder proposed in thi... | [
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{
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"title": "State-based decoding of hand and finger kinematics using neuronal ensemble and LFP activity during dexterous reach-to-grasp movements.",
"abstract": "The performance of brain-machine interfaces (BMIs) that continuously control upper limb neuroprostheses may benefit from d... |
BMC Medical Informatics and Decision Making | 28049465 | PMC5209873 | 10.1186/s12911-016-0389-x | Secure and scalable deduplication of horizontally partitioned health data for privacy-preserving distributed statistical computation | BackgroundTechniques have been developed to compute statistics on distributed datasets without revealing private information except the statistical results. However, duplicate records in a distributed dataset may lead to incorrect statistical results. Therefore, to increase the accuracy of the statistical analysis of a... | Related workSeveral PPRL protocols have been developed based on either deterministic or probabilistic matching of a set of identifiers. Interested readers are referred to [22, 23] for an extensive review of the PPRL protocols. The protocols can be broadly classified as protocols with or without a third party. In this s... | [
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{
"pmid": "24169275",
"title": "Health data use, stewardship, and governance: ongoing gaps and challenges: a report from AMIA's 2012 Health Policy Meeting.",
"abstract": "Large amounts of personal health data are being collected and made available through existing and emerging technological media and to... |
Frontiers in Neurorobotics | 28194106 | PMC5276858 | 10.3389/fnbot.2017.00003 | ReaCog, a Minimal Cognitive Controller Based on Recruitment of Reactive Systems | It has often been stated that for a neuronal system to become a cognitive one, it has to be large enough. In contrast, we argue that a basic property of a cognitive system, namely the ability to plan ahead, can already be fulfilled by small neuronal systems. As a proof of concept, we propose an artificial neural networ... | Related workIn this section, we will compare reaCog as a system with related recent approaches in order to point out differences. While there are many approaches toward cognitive systems and many proposals concerning cognitive architectures, we will concentrate on models that, like reaCog, consider a whole systems appr... | [
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{
"pmid": "20964882",
"title": "Neural reuse: a fundamental organizational principle of the brain.",
"abstract": "An emerging class of theories concerning the functional structure of the brain takes the reuse of neural circuitry for various cognitive purposes to be a central organizational principle. Ac... |
Scientific Reports | 28165495 | PMC5292966 | 10.1038/srep41831 | Multi-Instance Metric Transfer Learning for Genome-Wide Protein Function Prediction | Multi-Instance (MI) learning has been proven to be effective for the genome-wide protein function prediction problems where each training example is associated with multiple instances. Many studies in this literature attempted to find an appropriate Multi-Instance Learning (MIL) method for genome-wide protein function ... | Related WorksPrevious studies related to our work can be classified into three categories: traditional MIL, metric learning based MIL and transfer learning based MIL.Traditional MILMulti-Instance Multi-Label k-Nearest Neighbor (MIMLkNN)25 try to utilize the popular k-nearest neighbor techniques into MIL. Motivated by t... | [
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{
"pmid": "10573421",
"title": "A combined algorithm for genome-wide prediction of protein function.",
"abstract": "The availability of over 20 fully sequenced genomes has driven the development of new methods to find protein function and interactions. Here we group proteins by correlated evolution, cor... |
BMC Psychology | 28196507 | PMC5307765 | 10.1186/s40359-017-0173-4 | VREX: an open-source toolbox for creating 3D virtual reality experiments | BackgroundWe present VREX, a free open-source Unity toolbox for virtual reality research in the fields of experimental psychology and neuroscience.ResultsDifferent study protocols about perception, attention, cognition and memory can be constructed using the toolbox. VREX provides a procedural generation of (interconne... | Why VREX: Related workThere are a wide variety of Unity add-ons assisting the generation of interactive virtual worlds, such as Playmaker [10], Adventure Creator [11] and ProBuilder [12] to name a few. Yet these toolboxes are very general-purpose. There also exists some software applications similar to VREX in terms of... | [
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{
"pmid": "16480691",
"title": "Cognitive Ethology and exploring attention in real-world scenes.",
"abstract": "We sought to understand what types of information people use when they infer the attentional states of others. In our study, two groups of participants viewed pictures of social interactions. ... |
Frontiers in Neuroinformatics | 28261082 | PMC5311048 | 10.3389/fninf.2017.00009 | Automated Detection of Stereotypical Motor Movements in Autism Spectrum Disorder Using Recurrence Quantification Analysis | A number of recent studies using accelerometer features as input to machine learning classifiers show promising results for automatically detecting stereotypical motor movements (SMM) in individuals with Autism Spectrum Disorder (ASD). However, replicating these results across different types of accelerometers and thei... | 2. Related workExisting approaches to automated monitoring of SMM are based either on webcams or accelerometers. In a series of publications (Gonçalves et al., 2012a,b,c) a group from the University of Minho created methods based on the Kinect webcam sensor from Microsoft. Although, their approach shows promising resul... | [
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] | [
{
"pmid": "15149482",
"title": "The lifetime distribution of health care costs.",
"abstract": "OBJECTIVE\nTo estimate the magnitude and age distribution of lifetime health care expenditures.\n\n\nDATA SOURCES\nClaims data on 3.75 million Blue Cross Blue Shield of Michigan members, and data from the Medi... |
JMIR Medical Informatics | 28153818 | PMC5314102 | 10.2196/medinform.6918 | Ontology-Driven Search and Triage: Design of a Web-Based Visual Interface for MEDLINE | BackgroundDiverse users need to search health and medical literature to satisfy open-ended goals such as making evidence-based decisions and updating their knowledge. However, doing so is challenging due to at least two major difficulties: (1) articulating information needs using accurate vocabulary and (2) dealing wit... | Related WorkSome researchers have recognized the value of using ontologies to better support search activities (eg, [13,45]). The central focus of this research is term extraction and mapping, which is done using text mining and natural language processing techniques. In this body of work, ontologies are used to improv... | [
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{
"pmid": "18280516",
"title": "How to perform a literature search.",
"abstract": "PURPOSE\nEvidence based clinical practice seeks to integrate the current best evidence from clinical research with physician clinical expertise and patient individual preferences. We outline a stepwise approach to an effe... |
Royal Society Open Science | 28280588 | PMC5319354 | 10.1098/rsos.160896 | Understanding human queuing behaviour at exits: an empirical study | The choice of the exit to egress from a facility plays a fundamental role in pedestrian modelling and simulation. Yet, empirical evidence for backing up simulation is scarce. In this contribution, we present three new groups of experiments that we conducted in different geometries. We varied parameters such as the widt... | 2.Related worksData gathering for the exit choice of pedestrians is performed in real-world [1–4], as well as in virtual environments [5–7]. Participants might behave differently in the virtual environments where the perception is different. However, we observe in both cases that pedestrians are able to dynamically opt... | [
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] | [
{
"pmid": "11028994",
"title": "Simulating dynamical features of escape panic.",
"abstract": "One of the most disastrous forms of collective human behaviour is the kind of crowd stampede induced by panic, often leading to fatalities as people are crushed or trampled. Sometimes this behaviour is triggere... |
Scientific Reports | 28230161 | PMC5322330 | 10.1038/srep43167 | Robust High-dimensional Bioinformatics Data Streams Mining by ODR-ioVFDT | Outlier detection in bioinformatics data streaming mining has received significant attention by research communities in recent years. The problems of how to distinguish noise from an exception and deciding whether to discard it or to devise an extra decision path for accommodating it are causing dilemma. In this paper,... | Related WorkThere are many ways to categorize outlier detection approaches. To illustrate by the class objective, one-class classification outlier detection approach proposed by Tax17. The artificial outlier is generated by normal instances that are trained by a one-class classifier. Then the combination of one-class a... | [
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{
"pmid": "25134094",
"title": "Incremental Support Vector Learning for Ordinal Regression.",
"abstract": "Support vector ordinal regression (SVOR) is a popular method to tackle ordinal regression problems. However, until now there were no effective algorithms proposed to address incremental SVOR learni... |
Frontiers in Psychology | 28293202 | PMC5329031 | 10.3389/fpsyg.2017.00260 | Automating Individualized Formative Feedback in Large Classes Based on a Directed Concept Graph | Student learning outcomes within courses form the basis for course completion and time-to-graduation statistics, which are of great importance in education, particularly higher education. Budget pressures have led to large classes in which student-to-instructor interaction is very limited. Most of the current efforts t... | Related works/state of the artAn overview of four categories of approaches to analytical activities that are currently being used on data from educational settings is provided by Piety et al. (2014). Their work provides a conceptual framework for considering these different approaches and provides an overview of the st... | [] | [] |
PLoS Computational Biology | 28282375 | PMC5345757 | 10.1371/journal.pcbi.1005248 | A human judgment approach to epidemiological forecasting | Infectious diseases impose considerable burden on society, despite significant advances in technology and medicine over the past century. Advanced warning can be helpful in mitigating and preparing for an impending or ongoing epidemic. Historically, such a capability has lagged for many reasons, including in particular... | Related workAs exemplified by the fields of meteorology and econometrics, statistical and computational models are frequently used to understand, describe, and forecast the evolution of complex dynamical systems [12, 13]. The situation in epidemiological forecasting is no different; data-driven forecasting frameworks h... | [
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{
"pmid": "16731270",
"title": "Global and regional burden of disease and risk factors, 2001: systematic analysis of population health data.",
"abstract": "BACKGROUND\nOur aim was to calculate the global burden of disease and risk factors for 2001, to examine regional trends from 1990 to 2001, and to pr... |
JMIR mHealth and uHealth | 28246070 | PMC5350460 | 10.2196/mhealth.6395 | Accuracy and Adoption of Wearable Technology Used by Active Citizens: A Marathon Event Field Study | BackgroundToday, runners use wearable technology such as global positioning system (GPS)–enabled sport watches to track and optimize their training activities, for example, when participating in a road race event. For this purpose, an increasing amount of low-priced, consumer-oriented wearable devices are available. Ho... | Related WorkAccording to Düking et al [4], wearables “are lightweight, sensor-based devices that are worn close to or on the surface of the skin, where they detect, analyze, and transmit information concerning several internal and external variables to an external device (...),” (p. 2). In particular, GPS-enabled devic... | [
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{
"pmid": "25592201",
"title": "Waste the waist: a pilot randomised controlled trial of a primary care based intervention to support lifestyle change in people with high cardiovascular risk.",
"abstract": "BACKGROUND\nIn the UK, thousands of people with high cardiovascular risk are being identified by a... |
International Journal of Biomedical Imaging | 28367213 | PMC5358478 | 10.1155/2017/9749108 | Image Analysis for MRI Based Brain Tumor Detection and Feature Extraction Using Biologically Inspired BWT and SVM | The segmentation, detection, and extraction of infected tumor area from magnetic resonance (MR) images are a primary concern but a tedious and time taking task performed by radiologists or clinical experts, and their accuracy depends on their experience only. So, the use of computer aided technology becomes very necess... | 2. Related WorksMedical image segmentation for detection of brain tumor from the magnetic resonance (MR) images or from other medical imaging modalities is a very important process for deciding right therapy at the right time. Many techniques have been proposed for classification of brain tumors in MR images, most nota... | [
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{
"pmid": "23790354",
"title": "State of the art survey on MRI brain tumor segmentation.",
"abstract": "Brain tumor segmentation consists of separating the different tumor tissues (solid or active tumor, edema, and necrosis) from normal brain tissues: gray matter (GM), white matter (WM), and cerebrospin... |
Frontiers in Neurorobotics | 28381998 | PMC5360715 | 10.3389/fnbot.2017.00013 | Real-Time Biologically Inspired Action Recognition from Key Poses Using a Neuromorphic Architecture | Intelligent agents, such as robots, have to serve a multitude of autonomous functions. Examples are, e.g., collision avoidance, navigation and route planning, active sensing of its environment, or the interaction and non-verbal communication with people in the extended reach space. Here, we focus on the recognition of ... | 2. Related workThe proposed key pose based action recognition approach is motivated and inspired by recent evidences about the learning mechanisms and representations involved in the processing of articulated motion sequences, as well as hardware and software developments from various fields of visual sciences. For ins... | [
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{
"pmid": "2358548",
"title": "Pathways for motion analysis: cortical connections of the medial superior temporal and fundus of the superior temporal visual areas in the macaque.",
"abstract": "To identify the cortical connections of the medial superior temporal (MST) and fundus of the superior temporal... |
Transactions of the Association for Computational Linguistics | 28344978 | PMC5361062 | null | Large-scale Analysis of Counseling Conversations: An Application of Natural Language Processing to Mental Health | Mental illness is one of the most pressing public health issues of our time. While counseling and psychotherapy can be effective treatments, our knowledge about how to conduct successful counseling conversations has been limited due to lack of large-scale data with labeled outcomes of the conversations. In this paper, ... | 2 Related WorkOur work relates to two lines of research:Therapeutic Discourse Analysis & PsycholinguisticsThe field of conversation analysis was born in the 1960s out of a suicide prevention center (Sacks and Jefferson, 1995; Van Dijk, 1997). Since then conversation analysis has been applied to various clinical setting... | [] | [] |
Frontiers in Neuroinformatics | 28381997 | PMC5361107 | 10.3389/fninf.2017.00021 | Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System | OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed com... | 1.3. Related work1.3.1. Generic workflow enginesLike OpenMOLE, other initiatives made the choice not to target a specific community. Kepler (Altintas et al., 2004) was one of the first general-purpose scientific workflow systems, recognizing the need for transparent and simplified access to high performance computing p... | [
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{
"pmid": "24600388",
"title": "Machine learning for neuroimaging with scikit-learn.",
"abstract": "Statistical machine learning methods are increasingly used for neuroimaging data analysis. Their main virtue is their ability to model high-dimensional datasets, e.g., multivariate analysis of activation ... |
BMC Medical Informatics and Decision Making | 28330491 | PMC5363029 | 10.1186/s12911-017-0424-6 | Orchestrating differential data access for translational research: a pilot implementation | BackgroundTranslational researchers need robust IT solutions to access a range of data types, varying from public data sets to pseudonymised patient information with restricted access, provided on a case by case basis. The reason for this complication is that managing access policies to sensitive human data must consid... | Related workMany different approaches and systems are used for tackling the aims and issues we have addressed in the pilot. Biological material repositories similar to BioSD exist, varying in scope [82, 83], geographical reference area [84] and scale [85, 86]. BioSD is mainly a European reference resource for public bi... | [
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{
"pmid": "24008998",
"title": "Some experiences and opportunities for big data in translational research.",
"abstract": "Health care has become increasingly information intensive. The advent of genomic data, integrated into patient care, significantly accelerates the complexity and amount of clinical d... |
JMIR mHealth and uHealth | 28279948 | PMC5364324 | 10.2196/mhealth.6552 | Remote Monitoring of Hypertension Diseases in Pregnancy: A Pilot Study | BackgroundAlthough remote monitoring (RM) has proven its added value in various health care domains, little is known about the remote follow-up of pregnant women diagnosed with a gestational hypertensive disorders (GHD).ObjectiveThe aim of this study was to evaluate the added value of a remote follow-up program for pre... | Related WorkRM has already shown benefits in Cardiology and Pneumology [7,8]. In the prenatal care, RM has also shown an added value to improve maternal and neonatal outcomes. Various studies reported a reduction in unscheduled patient visits, low neonatal birth weight, and admissions to neonatal intensive care (NIC) f... | [
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{
"pmid": "26104418",
"title": "Diagnosis, evaluation, and management of the hypertensive disorders of pregnancy.",
"abstract": "OBJECTIVE\nThis guideline summarizes the quality of the evidence to date and provides a reasonable approach to the diagnosis, evaluation and treatment of the hypertensive diso... |
Scientific Reports | 28361913 | PMC5374503 | 10.1038/srep45639 | Multi-scale radiomic analysis of sub-cortical regions in MRI related to autism, gender and age | We propose using multi-scale image textures to investigate links between neuroanatomical regions and clinical variables in MRI. Texture features are derived at multiple scales of resolution based on the Laplacian-of-Gaussian (LoG) filter. Three quantifier functions (Average, Standard Deviation and Entropy) are used to ... | Related WorkOur review of relevant work focuses on studies using imaging techniques to identify brain regions/characteristics related to autism, gender and age.Starting with work related to ASD, various studies using MR imaging have shown that young children with autism had a significantly larger brain volume compared ... | [
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{
"pmid": "10714055",
"title": "Subgroups of children with autism by cluster analysis: a longitudinal examination.",
"abstract": "OBJECTIVES\nA hierarchical cluster analysis was conducted using a sample of 138 school-age children with autism. The objective was to examine (1) the characteristics of resul... |
International Journal of Biomedical Imaging | 28408921 | PMC5376475 | 10.1155/2017/1985796 | Phase Segmentation Methods for an Automatic Surgical Workflow Analysis | In this paper, we present robust methods for automatically segmenting phases in a specified surgical workflow by using latent Dirichlet allocation (LDA) and hidden Markov model (HMM) approaches. More specifically, our goal is to output an appropriate phase label for each given time point of a surgical workflow in an op... | 2. Related WorkNumerous methods have been developed for identifying intraoperative activities, segment common phases in a surgical workflow, and combine all gained knowledge into a model of the given workflows [4–7]. In segmentation work over surgical phases, various types of data were used, such as manual annotations ... | [
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{
"pmid": "20526819",
"title": "Analysis of surgical intervention populations using generic surgical process models.",
"abstract": "PURPOSE\nAccording to differences in patient characteristics, surgical performance, or used surgical technological resources, surgical interventions have high variability. ... |
JMIR Medical Informatics | 28347973 | PMC5387113 | 10.2196/medinform.6693 | A Software Framework for Remote Patient Monitoring by Using Multi-Agent Systems Support | BackgroundAlthough there have been significant advances in network, hardware, and software technologies, the health care environment has not taken advantage of these developments to solve many of its inherent problems. Research activities in these 3 areas make it possible to apply advanced technologies to address many ... | Related WorkOur proposal takes a similar approach to that in [19]. This paper shows the implementation of a distributed information infrastructure that uses the intelligent agent paradigm for: (1) automatically notifying the patient’s medical team regarding the abnormalities in his or her health status; (2) offering me... | [
"24452256",
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] | [
{
"pmid": "24452256",
"title": "A mobile multi-agent information system for ubiquitous fetal monitoring.",
"abstract": "Electronic fetal monitoring (EFM) systems integrate many previously separate clinical activities related to fetal monitoring. Promoting the use of ubiquitous fetal monitoring services ... |
Journal of Cheminformatics | 29086119 | PMC5395521 | 10.1186/s13321-017-0209-z | SimBoost: a read-across approach for predicting drug–target binding affinities using gradient boosting machines | Computational prediction of the interaction between drugs and targets is a standing challenge in the field of drug discovery. A number of rather accurate predictions were reported for various binary drug–target benchmark datasets. However, a notable drawback of a binary representation of interaction data is that missin... | Related workTraditional methods for drug target interaction prediction typically focus on one particular target of interest. These approaches can again be divided into two types which are target-based approaches [12–14] and ligand-based approaches [15–18]. In target-based approaches the molecular docking of a candidate... | [
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{
"pmid": "23933754",
"title": "Similarity-based machine learning methods for predicting drug-target interactions: a brief review.",
"abstract": "Computationally predicting drug-target interactions is useful to select possible drug (or target) candidates for further biochemical verification. We focus on... |
BMC Medical Informatics and Decision Making | 28427384 | PMC5399417 | 10.1186/s12911-017-0443-3 | Imbalanced target prediction with pattern discovery on clinical data repositories | BackgroundClinical 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 cli... | Problem definition and related worksIn this section, we define the problem we address and review the key related works. Data mining has been extensively applied in healthcare domain, which is believed to be able to uncover new biomedical and healthcare knowledge for clinical and administrative decision making as well a... | [
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{
"pmid": "9812073",
"title": "Implementation of a computerized cardiovascular information system in a private hospital setting.",
"abstract": "BACKGROUND\nThe use of clinical databases improves quality of care, reduces operating costs, helps secure managed care contracts, and assists in clinical resear... |
BioData Mining | 28465724 | PMC5408444 | 10.1186/s13040-017-0133-9 | Feature analysis for classification of trace fluorescent labeled protein crystallization images | BackgroundLarge number of features are extracted from protein crystallization trial images to improve the accuracy of classifiers for predicting the presence of crystals or phases of the crystallization process. The excessive number of features and computationally intensive image processing methods to extract these fea... | Related workIn general, protein crystallization trial image analysis work is compared with respect to the accuracy of classification. The accuracy depends on the number of categories, features, and the ability of classifiers to model the data. Moreover, the hardware resources, training time and real-time analysis of ne... | [
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{
"pmid": "24419610",
"title": "Introduction to protein crystallization.",
"abstract": "Protein crystallization was discovered by chance about 150 years ago and was developed in the late 19th century as a powerful purification tool and as a demonstration of chemical purity. The crystallization of protei... |
Frontiers in Computational Neuroscience | 28522969 | PMC5415673 | 10.3389/fncom.2017.00024 | Equilibrium Propagation: Bridging the Gap between Energy-Based Models and Backpropagation | We introduce Equilibrium Propagation, a learning framework for energy-based models. It involves only one kind of neural computation, performed in both the first phase (when the prediction is made) and the second phase of training (after the target or prediction error is revealed). Although this algorithm computes the g... | 4. Related workIn Section 2.3, we have discussed the relationship between Equilibrium Propagation and Backpropagation. In the weakly clamped phase, the change of the influence parameter β creates a perturbation at the output layer which propagates backwards in the hidden layers. The error derivatives and the gradient o... | [
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{
"pmid": "27870614",
"title": "Active Inference: A Process Theory.",
"abstract": "This article describes a process theory based on active inference and belief propagation. Starting from the premise that all neuronal processing (and action selection) can be explained by maximizing Bayesian model evidenc... |
Journal of Cheminformatics | 29086162 | PMC5425364 | 10.1186/s13321-017-0213-3 | Scaffold Hunter: a comprehensive visual analytics framework for drug discovery | The era of big data is influencing the way how rational drug discovery and the development of bioactive molecules is performed and versatile tools are needed to assist in molecular design workflows. Scaffold Hunter is a flexible visual analytics framework for the analysis of chemical compound data and combines techniqu... | Related workSeveral other software tools exist that address the challenges regarding the organization and analysis of chemical and biological data. Early tools such as Spotfire [8] were not originally developed to analyze these kinds of data, but are often applied to compound datasets. Simultaneously, workflow environm... | [
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{
"pmid": "27779378",
"title": "What Can We Learn from Bioactivity Data? Chemoinformatics Tools and Applications in Chemical Biology Research.",
"abstract": "The ever increasing bioactivity data that are produced nowadays allow exhaustive data mining and knowledge discovery approaches that change chemic... |
Frontiers in Psychology | 28588533 | PMC5439009 | 10.3389/fpsyg.2017.00824 | A Probabilistic Model of Meter Perception: Simulating Enculturation | Enculturation is known to shape the perception of meter in music but this is not explicitly accounted for by current cognitive models of meter perception. We hypothesize that the induction of meter is a result of predictive coding: interpreting onsets in a rhythm relative to a periodic meter facilitates prediction of f... | 1.2. Related workOur approach in some respects resembles other recent probabilistic models, in particular a generative model presented by Temperley (2007). Temperley (2007, ch. 2) models meter perception as probabilistic inference on a generative model whose parameters are estimated using a training corpus. Meter is re... | [
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{
"pmid": "23663408",
"title": "Whatever next? Predictive brains, situated agents, and the future of cognitive science.",
"abstract": "Brains, it has recently been argued, are essentially prediction machines. They are bundles of cells that support perception and action by constantly attempting to match ... |
JMIR Medical Informatics | 28487265 | PMC5442348 | 10.2196/medinform.7235 | Effective Information Extraction Framework for Heterogeneous Clinical Reports Using Online Machine Learning and Controlled Vocabularies | BackgroundExtracting structured data from narrated medical reports is challenged by the complexity of heterogeneous structures and vocabularies and often requires significant manual effort. Traditional machine-based approaches lack the capability to take user feedbacks for improving the extraction algorithm in real tim... | Related WorkA number of research efforts have been made in different fields of medical information extraction. Successful systems include caTIES [5], MedEx [6], MedLEE [7], cTAKES [8], MetaMap [9], HITEx [10], and so on. These methods either take a rule-based approach, a traditional machine learning–based approach, or ... | [
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{
"pmid": "20442142",
"title": "caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research.",
"abstract": "The authors report on the development of the Cancer Tissue Information Extraction System (caTIES)--an application t... |
Materials | null | PMC5449064 | 10.3390/ma5122465 | A Novel Fractional Order Model for the Dynamic Hysteresis of Piezoelectrically Actuated Fast Tool Servo | The main contribution of this paper is the development of a linearized model for describing the dynamic hysteresis behaviors of piezoelectrically actuated fast tool servo (FTS). A linearized hysteresis force model is proposed and mathematically described by a fractional order differential equation. Combining the dynami... | 2. A Brief Review of Related WorkMrad and Hu and Hu et al. extended the classical Preisach model to describe the rate-dependent behaviors of hysteresis by use of an explicit weighting function with respect to the average change rate of the input signal [21,22,23]. To capacitate the Preisach model to represent the dynam... | [
"20815625"
] | [
{
"pmid": "20815625",
"title": "High-speed tracking control of piezoelectric actuators using an ellipse-based hysteresis model.",
"abstract": "In this paper, an ellipse-based mathematic model is developed to characterize the rate-dependent hysteresis in piezoelectric actuators. Based on the proposed mod... |
Frontiers in Neuroscience | 28701911 | PMC5487436 | 10.3389/fnins.2017.00350 | An Event-Driven Classifier for Spiking Neural Networks Fed with Synthetic or Dynamic Vision Sensor Data | This paper introduces a novel methodology for training an event-driven classifier within a Spiking Neural Network (SNN) System capable of yielding good classification results when using both synthetic input data and real data captured from Dynamic Vision Sensor (DVS) chips. The proposed supervised method uses the spiki... | 3.7. Summary of results and comparison with related workTable 3 and Figure 7 summarize the results of this work for all data sets. More specifically, Figure 7A shows how the classification accuracy of an SNN improves as a function of the percentage of input events. This seems to be consistent with all data sets, both s... | [
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{
"pmid": "22386501",
"title": "Extraction of temporally correlated features from dynamic vision sensors with spike-timing-dependent plasticity.",
"abstract": "A biologically inspired approach to learning temporally correlated patterns from a spiking silicon retina is presented. Spikes are generated fro... |
JMIR Public Health and Surveillance | 28630032 | PMC5495967 | 10.2196/publichealth.7157 | What Are People Tweeting About Zika? An Exploratory Study Concerning Its Symptoms, Treatment, Transmission, and Prevention | BackgroundIn order to harness what people are tweeting about Zika, there needs to be a computational framework that leverages machine learning techniques to recognize relevant Zika tweets and, further, categorize these into disease-specific categories to address specific societal concerns related to the prevention, tra... | Related WorksA study by Oyeyemi et al [10] concerning misinformation about Ebola on Twitter found that 44.0% (248/564) of the tweets about Ebola were retweeted at least once, with 38.3% (95/248) of those tweets being scientifically accurate, whereas 58.9% (146/248) were inaccurate. Furthermore, most of the tweets conta... | [
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{
"pmid": "26965962",
"title": "Zika virus infection-the next wave after dengue?",
"abstract": "Zika virus was initially discovered in east Africa about 70 years ago and remained a neglected arboviral disease in Africa and Southeast Asia. The virus first came into the limelight in 2007 when it caused an... |
BMC Medical Informatics and Decision Making | 28673289 | PMC5496182 | 10.1186/s12911-017-0498-1 | Semantic relatedness and similarity of biomedical terms: examining the effects of recency, size, and section of biomedical publications on the performance of word2vec | BackgroundUnderstanding semantic relatedness and similarity between biomedical terms has a great impact on a variety of applications such as biomedical information retrieval, information extraction, and recommender systems. The objective of this study is to examine word2vec’s ability in deriving semantic relatedness an... | Related workIn this section, we first briefly introduce word2vec and then survey the related work that used word2vec on biomedical publications. These studies primarily focused on the effects of architectures and parameter settings on experimental results. A few empirical studies were identified on how to configure the... | [
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{
"pmid": "16875881",
"title": "Measures of semantic similarity and relatedness in the biomedical domain.",
"abstract": "Measures of semantic similarity between concepts are widely used in Natural Language Processing. In this article, we show how six existing domain-independent measures can be adapted t... |
JMIR Public Health and Surveillance | 28642212 | PMC5500778 | 10.2196/publichealth.6577 | Filtering Entities to Optimize Identification of Adverse Drug Reaction From Social Media: How Can the Number of Words Between Entities in the Messages Help? | BackgroundWith the increasing popularity of Web 2.0 applications, social media has made it possible for individuals to post messages on adverse drug reactions. In such online conversations, patients discuss their symptoms, medical history, and diseases. These disorders may correspond to adverse drug reactions (ADRs) or... | Related WorkThe current technological challenges include the difficulty for text mining algorithms to interpret patient lay vocabulary [23].After the review of multiple approaches, Sarker et al [9] concluded that following data collection, filtering was a real challenge. Filtering methods are likely to aid in the ADR d... | [
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{
"pmid": "7791255",
"title": "Incidence of adverse drug events and potential adverse drug events. Implications for prevention. ADE Prevention Study Group.",
"abstract": "OBJECTIVES\nTo assess incidence and preventability of adverse drug events (ADEs) and potential ADEs. To analyze preventable events to... |
BMC Medical Informatics and Decision Making | 28699564 | PMC5506580 | 10.1186/s12911-017-0464-y | Detecting clinically relevant new information in clinical notes across specialties and settings | BackgroundAutomated methods for identifying clinically relevant new versus redundant information in electronic health record (EHR) clinical notes is useful for clinicians and researchers involved in patient care and clinical research, respectively. We evaluated methods to automatically identify clinically relevant new ... | Related workA number of approaches have previously been reported around quantifying redundancy in clinical notes. For example, Weir et al., manually reviewed 1,891 notes in the Salt Lake City Veterans Affairs (VA) health care system and found that approximately 20% of notes contained copied text [11]. With respect to a... | [
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{
"pmid": "23304398",
"title": "A qualitative analysis of EHR clinical document synthesis by clinicians.",
"abstract": "Clinicians utilize electronic health record (EHR) systems during time-constrained patient encounters where large amounts of clinical text must be synthesized at the point of care. Qual... |
Frontiers in Neuroscience | 28769745 | PMC5513987 | 10.3389/fnins.2017.00406 | Sums of Spike Waveform Features for Motor Decoding | Traditionally, the key step before decoding motor intentions from cortical recordings is spike sorting, the process of identifying which neuron was responsible for an action potential. Recently, researchers have started investigating approaches to decoding which omit the spike sorting step, by directly using informatio... | Related workBesides the work of Ventura and Todorova (2015), on which this work is based, there has been other work using waveform features for decoding. Chen et al. (2012) and Kloosterman et al. (2014) used spike waveform features to decode from hippocampal recordings. Their approach is based on the spatial-temporal P... | [
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{
"pmid": "24739786",
"title": "Restoring sensorimotor function through intracortical interfaces: progress and looming challenges.",
"abstract": "The loss of a limb or paralysis resulting from spinal cord injury has devastating consequences on quality of life. One approach to restoring lost sensory and ... |
Scientific Reports | 28720794 | PMC5515977 | 10.1038/s41598-017-05988-5 | Percolation-theoretic bounds on the cache size of nodes in mobile opportunistic networks | The node buffer size has a large influence on the performance of Mobile Opportunistic Networks (MONs). This is mainly because each node should temporarily cache packets to deal with the intermittently connected links. In this paper, we study fundamental bounds on node buffer size below which the network system can not ... | Related WorksMONs is a natural evolution from traditional mobile ad hoc networks. In MONs, the links are intermittently connected due to node mobility and power on/off, mobile nodes communicate with each other opportunistically and route packets in a store-carry-and-forward style. In the past several years, much effort... | [] | [] |
Scientific Reports | 28729710 | PMC5519723 | 10.1038/s41598-017-05778-z | Learning a Health Knowledge Graph from Electronic Medical Records | Demand for clinical decision support systems in medicine and self-diagnostic symptom checkers has substantially increased in recent years. Existing platforms rely on knowledge bases manually compiled through a labor-intensive process or automatically derived using simple pairwise statistics. This study explored an auto... | Related workIn recent work, Finlayson et al. quantify the relatedness of 1 million concepts by computing their co-occurrence in free-text notes in the EMR, releasing a “graph of medicine”22. Sondhi et al. measure the distance between mentions of two concepts within a clinical note for determination of edge-strength in ... | [
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{
"pmid": "17098763",
"title": "Googling for a diagnosis--use of Google as a diagnostic aid: internet based study.",
"abstract": "OBJECTIVE\nTo determine how often searching with Google (the most popular search engine on the world wide web) leads doctors to the correct diagnosis.\n\n\nDESIGN\nInternet b... |
GigaScience | 28327936 | PMC5530313 | 10.1093/gigascience/giw013 | GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software | Abstract
Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphica... | Related workSoftware containers and DockerA software container packages an application with everything it needs to run, including supporting libraries and system resources. Containers differ from traditional virtual machines (VMs) in that the resources of the operating system (OS), and not the hardware, are virtualized... | [
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{
"pmid": "26913191",
"title": "BioShaDock: a community driven bioinformatics shared Docker-based tools registry.",
"abstract": "Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of ... |
Journal of the Association for Information Science and Technology | 28758138 | PMC5530597 | 10.1002/asi.23063 | Author Name Disambiguation for PubMed | Log analysis shows that PubMed users frequently use author names in queries for retrieving scientific literature. However, author name ambiguity may lead to irrelevant retrieval results. To improve the PubMed user experience with author name queries, we designed an author name disambiguation system consisting of simila... | Related WorkDue to the limitations of manual authorship management, numerous recent name disambiguation studies focus on automatic techniques for large-scale literature systems. To process large-scale data efficiently, it is necessary to define the scope (block) of author name disambiguation appropriately to minimize t... | [
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{
"pmid": "17971238",
"title": "PubMed related articles: a probabilistic topic-based model for content similarity.",
"abstract": "BACKGROUND\nWe present a probabilistic topic-based model for content similarity called pmra that underlies the related article search feature in PubMed. Whether or not a docu... |
Nutrients | 28653995 | PMC5537777 | 10.3390/nu9070657 | NutriNet: A Deep Learning Food and Drink Image Recognition System for Dietary Assessment | Automatic food image recognition systems are alleviating the process of food-intake estimation and dietary assessment. However, due to the nature of food images, their recognition is a particularly challenging task, which is why traditional approaches in the field have achieved a low classification accuracy. Deep neura... | 1.1. Related WorkWhile there have not been any dedicated drink image recognition systems, there have been multiple approaches to food image recognition in the past, and we will briefly mention the most important ones here. In 2009, an extensive food image and video dataset was built to encourage further research in the... | [
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{
"pmid": "26017442",
"title": "Deep learning.",
"abstract": "Deep learning allows computational models that are composed of multiple processing layers to learn representations of data with multiple levels of abstraction. These methods have dramatically improved the state-of-the-art in speech recognitio... |
Frontiers in Psychology | 28824478 | PMC5541010 | 10.3389/fpsyg.2017.01255 | Toward Studying Music Cognition with Information Retrieval Techniques: Lessons Learned from the OpenMIIR Initiative | As an emerging sub-field of music information retrieval (MIR), music imagery information retrieval (MIIR) aims to retrieve information from brain activity recorded during music cognition–such as listening to or imagining music pieces. This is a highly inter-disciplinary endeavor that requires expertise in MIR as well a... | 3. Related workRetrieval based on brain wave recordings is still a very young and largely unexplored domain. EEG signals have been used to recognize emotions induced by music perception (Lin et al., 2009; Cabredo et al., 2012) and to distinguish perceived rhythmic stimuli (Stober et al., 2014). It has been shown that o... | [
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{
"pmid": "23787338",
"title": "Representation learning: a review and new perspectives.",
"abstract": "The success of machine learning algorithms generally depends on data representation, and we hypothesize that this is because different representations can entangle and hide more or less the different e... |
BMC Medical Informatics and Decision Making | 28789686 | PMC5549299 | 10.1186/s12911-017-0512-7 | Developing a cardiovascular disease risk factor annotated corpus of Chinese electronic medical records | BackgroundCardiovascular disease (CVD) has become the leading cause of death in China, and most of the cases can be prevented by controlling risk factors. The goal of this study was to build a corpus of CVD risk factor annotations based on Chinese electronic medical records (CEMRs). This corpus is intended to be used t... | Related works based on CEMRsWang et al. [16] focused on recognizing and normalizing the names of symptoms in traditional Chinese medicine EMRs. To perform judgements, this system used a set of manually annotated clinical symptom names. Jiang et al. [14] proposed a complete annotation scheme for building a corpus of wor... | [
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{
"pmid": "24070769",
"title": "Supervised methods for symptom name recognition in free-text clinical records of traditional Chinese medicine: an empirical study.",
"abstract": "Clinical records of traditional Chinese medicine (TCM) are documented by TCM doctors during their routine diagnostic work. The... |
Frontiers in Genetics | 28848600 | PMC5552671 | 10.3389/fgene.2017.00104 | A Novel Efficient Graph Model for the Multiple Longest Common Subsequences (MLCS) Problem | Searching for the Multiple Longest Common Subsequences (MLCS) of multiple sequences is a classical NP-hard problem, which has been used in many applications. One of the most effective exact approaches for the MLCS problem is based on dominant point graph, which is a kind of directed acyclic graph (DAG). However, the ti... | 2.1. Preliminaries and related workFirst of all, let Σ denote the alphabet of the sequences, i.e., a finite set of symbols. For example, the alphabet of the DNA sequences is Σ = {A, C, G, T}.Definition 1. Let Σ denote the alphabet and s = c1c2…cn be a sequence of length n with each symbol ci ∈ Σ, for i = 1, 2, ⋯ , n. T... | [
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{
"pmid": "28187279",
"title": "Next-Generation Sequencing of Circulating Tumor DNA for Early Cancer Detection.",
"abstract": "Curative therapies are most successful when cancer is diagnosed and treated at an early stage. We advocate that technological advances in next-generation sequencing of circulati... |
JMIR Medical Informatics | 28760726 | PMC5556254 | 10.2196/medinform.7140 | Triaging Patient Complaints: Monte Carlo Cross-Validation of Six Machine Learning Classifiers | BackgroundUnsolicited patient complaints can be a useful service recovery tool for health care organizations. Some patient complaints contain information that may necessitate further action on the part of the health care organization and/or the health care professional. Current approaches depend on the manual processin... | Related WorkThe bulk of the textual artifacts in health care can be found in two main sources: clinical and nonclinical. Clinical textual artifacts are largely entries in the medical chart, comments on the case, or physician notes. Medical chart notes tend to be consciously made and well structured, whereas case commen... | [
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{
"pmid": "21226384",
"title": "Best practices for basic and advanced skills in health care service recovery: a case study of a re-admitted patient.",
"abstract": "BACKGROUND\nService recovery refers to an organizations entire process for facilitating resolution of dissatisfactions, whether or not visib... |
JMIR mHealth and uHealth | 28778851 | PMC5562934 | 10.2196/mhealth.7521 | Feature-Free Activity Classification of Inertial Sensor Data With Machine Vision Techniques: Method, Development, and Evaluation | BackgroundInertial sensors are one of the most commonly used sources of data for human activity recognition (HAR) and exercise detection (ED) tasks. The time series produced by these sensors are generally analyzed through numerical methods. Machine learning techniques such as random forests or support vector machines a... | Related WorkThe three main topics in this section are as follows: (1) a brief overview of the current human activity recognition (HAR) and exercise detection (ED) literature, (2) an account of some of the newer advances in the field that are using neural networks for certain parts of the feature discovery and reduction... | [
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{
"pmid": "27782290",
"title": "Technology in Rehabilitation: Evaluating the Single Leg Squat Exercise with Wearable Inertial Measurement Units.",
"abstract": "BACKGROUND\nThe single leg squat (SLS) is a common lower limb rehabilitation exercise. It is also frequently used as an evaluative exercise to s... |
Frontiers in Neurorobotics | 28883790 | PMC5573722 | 10.3389/fnbot.2017.00043 | Impedance Control for Robotic Rehabilitation: A Robust Markovian Approach | The human-robot interaction has played an important role in rehabilitation robotics and impedance control has been used in the regulation of interaction forces between the robot actuator and human limbs. Series elastic actuators (SEAs) have been an efficient solution in the design of this kind of robotic application. S... | 5.1. Related workThe impedance control configuration used is based on Hogan (1985) and it is aimed at the regulation of the dynamical behavior in the interaction port by variables that do not depend on the environment. The actuator together with the controller are modeled as an impedance, Zr, with velocity inputs (angu... | [
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{
"pmid": "12048669",
"title": "Risks of falls in subjects with multiple sclerosis.",
"abstract": "OBJECTIVES\nTo quantify fall risk among patients with multiple sclerosis (MS) and to report the importance of variables associated with falls.\n\n\nDESIGN\nRetrospective case-control study design with a 2-... |
Frontiers in Neurorobotics | 28900394 | PMC5581837 | 10.3389/fnbot.2017.00046 | Navigation and Self-Semantic Location of Drones in Indoor Environments by Combining the Visual Bug Algorithm and Entropy-Based Vision | We introduce a hybrid algorithm for the self-semantic location and autonomous navigation of robots using entropy-based vision and visual topological maps. In visual topological maps the visual landmarks are considered as leave points for guiding the robot to reach a target point (robot homing) in indoor environments. T... | Related workOur proposal involves the use of visual graphs, in which each node stores images associated to landmarks, and the arcs represent the paths that the UAV must follow to reach the next node. Therefore, these graphs can be used to generate the best path for an UAV to reach a specific destination, as it has been... | [
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{
"pmid": "28481277",
"title": "Obstacle Detection and Avoidance System Based on Monocular Camera and Size Expansion Algorithm for UAVs.",
"abstract": "One of the most challenging problems in the domain of autonomous aerial vehicles is the designing of a robust real-time obstacle detection and avoidance... |
Research Synthesis Methods | 28677322 | PMC5589498 | 10.1002/jrsm.1252 | An exploration of crowdsourcing citation screening for systematic reviews | Systematic reviews are increasingly used to inform health care decisions, but are expensive to produce. We explore the use of crowdsourcing (distributing tasks to untrained workers via the web) to reduce the cost of screening citations. We used Amazon Mechanical Turk as our platform and 4 previously conducted systemati... | 2.1Related workOver the past decade, crowdsourcing has become an established methodology across a diverse set of domains.6 Indeed, researchers have demonstrated the promise of harnessing the “wisdom of the crowd” with respect to everything from conducting user studies7 to aiding disaster relief.8, 9
Perhaps most releva... | [
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{
"pmid": "25588314",
"title": "Using text mining for study identification in systematic reviews: a systematic review of current approaches.",
"abstract": "BACKGROUND\nThe large and growing number of published studies, and their increasing rate of publication, makes the task of identifying relevant stud... |
Scientific Reports | 28924196 | PMC5603591 | 10.1038/s41598-017-12141-9 | Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection | As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dim... | Related WorkA wide range of approaches for projection alignment are employed in electron tomography14. The most common approach is to use cross-correlation between projections acquired at adjacent rotation angles15–18, or correlation of vertical variations in the mass of the sample19. However, two features in 3D space ... | [
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"pmid": "22852697",
"title": "An instrument for 3D x-ray nano-imaging.",
"abstract": "We present an instrument dedicated to 3D scanning x-ray microscopy, allowing a sample to be precisely scanned through a beam while the angle of x-ray incidence can be changed. The position of the sample is controlled... |
Toxics | 29051407 | PMC5606636 | 10.3390/toxics4010001 | Farmers’ Exposure to Pesticides: Toxicity Types and Ways of Prevention | Synthetic pesticides are extensively used in agriculture to control harmful pests and prevent crop yield losses or product damage. Because of high biological activity and, in certain cases, long persistence in the environment, pesticides may cause undesirable effects to human health and to the environment. Farmers are ... | 5. Pesticide-Related Work TasksPesticide use is typically associated with three basic stages: (i) mixing and loading the pesticide product, (ii) application of the spray solution, and (iii) clean-up of the spraying equipment. Mixing and loading are the tasks associated with the greatest intensity of pesticide exposure,... | [
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{
"pmid": "25096494",
"title": "Global trends of research on emerging contaminants in the environment and humans: a literature assimilation.",
"abstract": "Available literature data on five typical groups of emerging contaminants (EMCs), i.e., chlorinated paraffins (CPs), dechlorane plus and related com... |
Scientific Reports | 28959011 | PMC5620056 | 10.1038/s41598-017-12569-z | Discriminative Scale Learning (DiScrn): Applications to Prostate Cancer Detection from MRI and Needle Biopsies | There has been recent substantial interest in extracting sub-visual features from medical images for improved disease characterization compared to what might be achievable via visual inspection alone. Features such as Haralick and Gabor can provide a multi-scale representation of the original image by extracting measur... | Related Work and Brief Overview of DiScrnScale selection has been a key research issue in the computer vision community since the 1990s15. Early investigations in scale selection were based on identifying scale-invariant locations of interest10,13,16,17.Although the idea of locating high interest points is interesting,... | [
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"pmid": "20570758",
"title": "A boosted Bayesian multiresolution classifier for prostate cancer detection from digitized needle biopsies.",
"abstract": "Diagnosis of prostate cancer (CaP) currently involves examining tissue samples for CaP presence and extent via a microscope, a time-consuming and sub... |
Frontiers in Plant Science | 29033961 | PMC5625571 | 10.3389/fpls.2017.01680 | Fast High Resolution Volume Carving for 3D Plant Shoot Reconstruction | Volume carving is a well established method for visual hull reconstruction and has been successfully applied in plant phenotyping, especially for 3d reconstruction of small plants and seeds. When imaging larger plants at still relatively high spatial resolution (≤1 mm), well known implementations become slow or have pr... | 1.1. Related workMeasuring plant geometry from single view-point 2D images often suffers from insufficient information, especially when plant organs occlude each other (self-occlusion). In order to achieve more detailed information and recover the plants 3D geometric structure volume carving is a well established metho... | [
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"pmid": "27853175",
"title": "Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping.",
"abstract": "High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth an... |
Frontiers in Neuroscience | 29056897 | PMC5635061 | 10.3389/fnins.2017.00550 | Kernel-Based Relevance Analysis with Enhanced Interpretability for Detection of Brain Activity Patterns | We introduce Enhanced Kernel-based Relevance Analysis (EKRA) that aims to support the automatic identification of brain activity patterns using electroencephalographic recordings. EKRA is a data-driven strategy that incorporates two kernel functions to take advantage of the available joint information, associating neur... | 1.1. Related workThere are two alternative approaches to addressing the problem of a large amount of EEG data (Naeem et al., 2009): (i) Channel selection that intends to choose a subset of electrodes contributing the most to the desired performance. Besides of avoiding redundancy of non-focal/unnecessary channels, this... | [
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{
"pmid": "28120883",
"title": "Kernel-based Joint Feature Selection and Max-Margin Classification for Early Diagnosis of Parkinson's Disease.",
"abstract": "Feature selection methods usually select the most compact and relevant set of features based on their contribution to a linear regression model. T... |
Scientific Reports | 29042602 | PMC5645324 | 10.1038/s41598-017-13640-5 | The optimal window size for analysing longitudinal networks | The time interval between two snapshots is referred to as the window size. A given longitudinal network can be analysed from various actor-level perspectives, such as exploring how actors change their degree centrality values or participation statistics over time. Determining the optimal window size for the analysis of... | Related workThe temporal sampling of a longitudinal network is often performed opportunistically20 depending on a wide range of factors. Timmons and Preacher12 identified some of these factors, including types of social networks, competing objectives, processes and measurements, planned time horizons of the respective ... | [
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{
"pmid": "24179229",
"title": "Structural and functional brain networks: from connections to cognition.",
"abstract": "How rich functionality emerges from the invariant structural architecture of the brain remains a major mystery in neuroscience. Recent applications of network theory and theoretical ne... |
Scientific Reports | 29079836 | PMC5660213 | 10.1038/s41598-017-13923-x | Small Molecule Accurate Recognition Technology (SMART) to Enhance Natural Products Research | Various algorithms comparing 2D NMR spectra have been explored for their ability to dereplicate natural products as well as determine molecular structures. However, spectroscopic artefacts, solvent effects, and the interactive effect of functional group(s) on chemical shifts combine to hinder their effectiveness. Here,... | Related workAgain, the aforementioned grid-cell approaches28 are similar to ours in that the shifted grid positions can be thought of as corresponding to the first layer of convolutions, which have small receptive fields (like grid cells), and they are shifted across the input space like shifted grids. Also, our approa... | [
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{
"pmid": "26852623",
"title": "Natural Products as Sources of New Drugs from 1981 to 2014.",
"abstract": "This contribution is a completely updated and expanded version of the four prior analogous reviews that were published in this journal in 1997, 2003, 2007, and 2012. In the case of all approved the... |
Scientific Reports | 29093451 | PMC5665979 | 10.1038/s41598-017-12884-5 | Sleep Benefits Memory for Semantic Category Structure While Preserving Exemplar-Specific Information | Semantic memory encompasses knowledge about both the properties that typify concepts (e.g. robins, like all birds, have wings) as well as the properties that individuate conceptually related items (e.g. robins, in particular, have red breasts). We investigate the impact of sleep on new semantic learning using a propert... | Other related workThere have been a few prior studies finding effects of sleep on semantic memory45,51, but they have focused on integrating new information with existing semantic memory networks, not learning an entirely novel domain, as in our study. One study that did look at novel conceptual learning found retentio... | [
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"pmid": "16797219",
"title": "Theory-based Bayesian models of inductive learning and reasoning.",
"abstract": "Inductive inference allows humans to make powerful generalizations from sparse data when learning about word meanings, unobserved properties, causal relationships, and many other aspects of t... |
Scientific Reports | 29097661 | PMC5668259 | 10.1038/s41598-017-14411-y | GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison | Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D contact approaches study 3D structures directly and are alignment-based. Instead, 3D s... | Motivation and related workProteins perform important cellular functions. While understanding protein function is clearly important, doing so experimentally is expensive and time-consuming1,2. Because of this, the functions of many proteins remain unknown2,3. Consequently, computational prediction of protein function h... | [
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{
"pmid": "18037900",
"title": "Predicting protein function from sequence and structure.",
"abstract": "While the number of sequenced genomes continues to grow, experimentally verified functional annotation of whole genomes remains patchy. Structural genomics projects are yielding many protein structure... |
JMIR Medical Informatics | 29089288 | PMC5686421 | 10.2196/medinform.8531 | Ranking Medical Terms to Support Expansion of Lay Language Resources for Patient Comprehension of Electronic Health Record Notes: Adapted Distant Supervision Approach | BackgroundMedical terms are a major obstacle for patients to comprehend their electronic health record (EHR) notes. Clinical natural language processing (NLP) systems that link EHR terms to lay terms or definitions allow patients to easily access helpful information when reading through their EHR notes, and have shown ... | Related WorkNatural Language Processing to Facilitate Creation of Lexical EntriesPrevious studies have used both unsupervised and supervised learning methods to prioritize terms for inclusion in biomedical and health knowledge resources [32-35]. Term recognition methods, which are widely used unsupervised methods for t... | [
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{
"pmid": "24359554",
"title": "The Medicare Electronic Health Record Incentive Program: provider performance on core and menu measures.",
"abstract": "OBJECTIVE\nTo measure performance by eligible health care providers on CMS's meaningful use measures.\n\n\nDATA SOURCE\nMedicare Electronic Health Recor... |
GigaScience | 29048555 | PMC5691353 | 10.1093/gigascience/gix099 | An architecture for genomics analysis in a clinical setting using Galaxy and Docker | AbstractNext-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analys... | Related worksWorkflow management systemsThe development of high-throughput methods in molecular biology has considerably increased the volume of molecular data produced daily by biologists. Many analytical scripts and software have been developed to assist biologists and clinicians in their tasks. Commercial and open-s... | [
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{
"pmid": "15118073",
"title": "Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib.",
"abstract": "BACKGROUND\nMost patients with non-small-cell lung cancer have no response to the tyrosine kinase inhibitor gefitinib, which t... |
PLoS Computational Biology | 29131816 | PMC5703574 | 10.1371/journal.pcbi.1005857 | Automated visualization of rule-based models | Frameworks such as BioNetGen, Kappa and Simmune use “reaction rules” to specify biochemical interactions compactly, where each rule specifies a mechanism such as binding or phosphorylation and its structural requirements. Current rule-based models of signaling pathways have tens to hundreds of rules, and these numbers ... | Related workIn addition to the approaches discussed in Introduction (Fig 1A–1D) and Methods (Fig 2C), we show examples of other currently available tools (Fig 11) and how they compare with compact rule visualizations and atom-rule graphs.10.1371/journal.pcbi.1005857.g011Fig 11Other visualization approaches applied to t... | [
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{
"pmid": "15217809",
"title": "BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.",
"abstract": "BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system, and that accounts com... |
International Journal for Equity in Health | 29183335 | PMC5706427 | 10.1186/s12939-017-0702-z | Evaluating medical convenience in ethnic minority areas of Southwest China via road network vulnerability: a case study for Dehong autonomous prefecture | BackgroundSouthwest China is home to more than 30 ethnic minority groups. Since most of these populations reside in mountainous areas, convenient access to medical services is an important metric of how well their livelihoods are being protected.MethodsThis paper proposes a medical convenience index (MCI) and computati... | Related workCurrent studies by Chinese and international scholars on medical and healthcare services for residents mostly focus on accessibility to hospitals, or uniform distribution of medical and healthcare facilities [5]. When analyzing medical accessibility, the minimum travel time/distance is commonly used because... | [
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{
"pmid": "26286033",
"title": "Spatial inequity in access to healthcare facilities at a county level in a developing country: a case study of Deqing County, Zhejiang, China.",
"abstract": "BACKGROUND\nThe inequities in healthcare services between regions, urban and rural, age groups and diverse income ... |
Frontiers in Neurorobotics | 29311888 | PMC5742219 | 10.3389/fnbot.2017.00066 | Cross-Situational Learning with Bayesian Generative Models for Multimodal Category and Word Learning in Robots | In this paper, we propose a Bayesian generative model that can form multiple categories based on each sensory-channel and can associate words with any of the four sensory-channels (action, position, object, and color). This paper focuses on cross-situational learning using the co-occurrence between words and informatio... | 2Related Work2.1Lexical Acquisition by RobotStudies of language acquisition also constitute a constructive approach to the human developmental process (Cangelosi and Schlesinger, 2015), the language grounding (Steels and Hild, 2012), and the symbol emergence (Taniguchi et al., 2016c). One approach to studying language ... | [
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{
"pmid": "19596549",
"title": "Cross-situational learning of object-word mapping using Neural Modeling Fields.",
"abstract": "The issue of how children learn the meaning of words is fundamental to developmental psychology. The recent attempts to develop or evolve efficient communication protocols among... |
Frontiers in Neurorobotics | 29311889 | PMC5742615 | 10.3389/fnbot.2017.00067 | Segmenting Continuous Motions with Hidden Semi-markov Models and Gaussian Processes | Humans divide perceived continuous information into segments to facilitate recognition. For example, humans can segment speech waves into recognizable morphemes. Analogously, continuous motions are segmented into recognizable unit actions. People can divide continuous information into segments without using explicit se... | 2. Related workVarious studies have focused on learning motion primitives from manually segmented motions (Gräve and Behnke, 2012; Manschitz et al., 2015). Manschitz et al. proposed a method to generate sequential skills by using motion primitives that are learned in a supervised manner. Gräve et al. proposed segmentin... | [] | [] |
PLoS Computational Biology | 29240763 | PMC5746283 | 10.1371/journal.pcbi.1005904 | Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems | Adaptive collective systems are common in biology and beyond. Typically, such systems require a task allocation algorithm: a mechanism or rule-set by which individuals select particular roles. Here we study the performance of such task allocation mechanisms measured in terms of the time for individuals to allocate to t... | Related workThe process of task allocation and its typical outcome, division of labor, have received a lot of attention in the social insect literature. Empirical studies typically focus on determining the individual traits or experiences that shape, or at least correlate with, individual task specialization: e.g. when... | [
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"pmid": "10221902",
"title": "Notch signaling: cell fate control and signal integration in development.",
"abstract": "Notch signaling defines an evolutionarily ancient cell interaction mechanism, which plays a fundamental role in metazoan development. Signals exchanged between neighboring cells throu... |
Royal Society Open Science | 29308229 | PMC5748960 | 10.1098/rsos.170853 | Quantifying team cooperation through intrinsic multi-scale measures: respiratory and cardiac synchronization in choir singers and surgical teams | A highly localized data-association measure, termed intrinsic synchrosqueezing transform (ISC), is proposed for the analysis of coupled nonlinear and non-stationary multivariate signals. This is achieved based on a combination of noise-assisted multivariate empirical mode decomposition and short-time Fourier transform-... | 2.Related workIn addition to our recently proposed data association measures, IPS and ICoh, there also exist several other synchrony measures. Cross-correlation is a simple measure of linear synchronization between two signals, and hence it cannot effectively deal with the nonlinear coupling behaviour, thus resulting i... | [
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"pmid": "23847555",
"title": "Music structure determines heart rate variability of singers.",
"abstract": "Choir singing is known to promote wellbeing. One reason for this may be that singing demands a slower than normal respiration, which may in turn affect heart activity. Coupling of heart rate vari... |
Royal Society Open Science | 29308250 | PMC5750017 | 10.1098/rsos.171200 | A brittle star-like robot capable of immediately adapting to unexpected physical damage | A major challenge in robotic design is enabling robots to immediately adapt to unexpected physical damage. However, conventional robots require considerable time (more than several tens of seconds) for adaptation because the process entails high computational costs. To overcome this problem, we focus on a brittle star—... | 2.Related works on brittle stars2.1.Anatomical studiesBrittle stars have a circular body disc and typically five radiating arms (figure 1a). Each arm consists of a series of segments, each containing a roughly discoidal vertebral ossicle. Adjacent ossicles are linked by four muscle blocks, which enables the arm to bend... | [
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{
"pmid": "17110570",
"title": "Resilient machines through continuous self-modeling.",
"abstract": "Animals sustain the ability to operate after injury by creating qualitatively different compensatory behaviors. Although such robustness would be desirable in engineered systems, most machines fail in the... |
Scientific Reports | 29343692 | PMC5772550 | 10.1038/s41598-018-19194-4 | Symmetric Decomposition of Asymmetric Games | We introduce new theoretical insights into two-population asymmetric games allowing for an elegant symmetric decomposition into two single population symmetric games. Specifically, we show how an asymmetric bimatrix game (A,B) can be decomposed into its symmetric counterparts by envisioning and investigating the payoff... | Related WorkThe most straightforward and classical approach to asymmetric games is to treat agents as evolving separately: one population per player, where each agent in a population interacts by playing against agent(s) from the other population(s), i.e. co-evolution21. This assumes that players of these games are alw... | [
"23519283",
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"16843499",
"7412323",
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] | [
{
"pmid": "23519283",
"title": "Evolution of collective action in adaptive social structures.",
"abstract": "Many problems in nature can be conveniently framed as a problem of evolution of collective cooperative behaviour, often modelled resorting to the tools of evolutionary game theory in well-mixed p... |
Plant Methods | 29375647 | PMC5773030 | 10.1186/s13007-018-0273-z | The use of plant models in deep learning: an application to leaf counting in rosette plants | Deep learning presents many opportunities for image-based plant phenotyping. Here we consider the capability of deep convolutional neural networks to perform the leaf counting task. Deep learning techniques typically require large and diverse datasets to learn generalizable models without providing a priori an engineer... | Related workThe use of synthetic or simulation data has been explored in several visual learning contexts, including pose estimation [29] as well as viewpoint estimation [30]. In the plant phenotyping literature, models have been used as testing data to validate image-based root system descriptions [23], as well as to ... | [
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{
"pmid": "22074787",
"title": "Phenomics--technologies to relieve the phenotyping bottleneck.",
"abstract": "Global agriculture is facing major challenges to ensure global food security, such as the need to breed high-yielding crops adapted to future climates and the identification of dedicated feedsto... |
Scientific Reports | 29374175 | PMC5786031 | 10.1038/s41598-018-19440-9 | Three-dimensional reconstruction and NURBS-based structured meshing of coronary arteries from the conventional X-ray angiography projection images | Despite its two-dimensional nature, X-ray angiography (XRA) has served as the gold standard imaging technique in the interventional cardiology for over five decades. Accordingly, demands for tools that could increase efficiency of the XRA procedure for the quantitative analysis of coronary arteries (CA) are constantly ... | Related workThe majority of the available methods for reconstructing CA from XRA are semi-automatic and consist of these five steps: (1) pairing of frames acquired from different views; (2) vessel segmentation, decomposition and tracking in the XRA dynamic runs; (3) calibration of the parameters defining the device ori... | [
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{
"pmid": "19573711",
"title": "Coronary angiography: the need for improvement and the barriers to adoption of new technology.",
"abstract": "Traditional coronary angiography presents a variety of limitations related to image acquisition, content, interpretation, and patient safety. These limitations we... |
Scientific Reports | 29391406 | PMC5794926 | 10.1038/s41598-018-20037-5 | Advanced Steel Microstructural Classification by Deep Learning Methods | The inner structure of a material is called microstructure. It stores the genesis of a material and determines all its physical and chemical properties. While microstructural characterization is widely spread and well known, the microstructural classification is mostly done manually by human experts, which gives rise t... | Related WorksBased on the instrument used for imaging, we can categorize the related works into Light Optical Microscopy (LOM) and Scanning Electron Microscopy (SEM) imaging. High-resolution SEM imaging is very expensive compared with LOM imaging in terms of time and operating costs. However, low-resolution LOM imaging... | [] | [] |
Frontiers in Neuroscience | 29467600 | PMC5808221 | 10.3389/fnins.2017.00754 | White Matter Tract Segmentation as Multiple Linear Assignment Problems | Diffusion magnetic resonance imaging (dMRI) allows to reconstruct the main pathways of axons within the white matter of the brain as a set of polylines, called streamlines. The set of streamlines of the whole brain is called the tractogram. Organizing tractograms into anatomically meaningful structures, called tracts, ... | 2. Related works2.1. Supervised tract segmentationHere we review the literature on supervised tractogram segmentation and on the linear assignment problem. In order to organize the body of work in this field, we articulate the discussion on supervised tract segmentation along these five topics: alignment, embedding spa... | [
"24157921",
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{
"pmid": "24157921",
"title": "Automated longitudinal intra-subject analysis (ALISA) for diffusion MRI tractography.",
"abstract": "Fiber tractography (FT), which aims to reconstruct the three-dimensional trajectories of white matter (WM) fibers non-invasively, is one of the most popular approaches for... |
Scientific Reports | 29467401 | PMC5821733 | 10.1038/s41598-018-21715-0 | dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data | The elucidation of gene regulatory networks is one of the major challenges of systems biology. Measurements about genes that are exploited by network inference methods are typically available either in the form of steady-state expression vectors or time series expression data. In our previous work, we proposed the GENI... | Related worksLike dynGENIE3, many network inference approaches for time series data are based on an ODE model of the type (7) 8,21. These methods mainly differ in the terms present in the right-hand side of the ODE (such as decay rates or the influence of external perturbations), the mathematical form of the models fj,... | [
"22805708",
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"23203884",
"24243845",
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] | [
{
"pmid": "22805708",
"title": "Studying and modelling dynamic biological processes using time-series gene expression data.",
"abstract": "Biological processes are often dynamic, thus researchers must monitor their activity at multiple time points. The most abundant source of information regarding such ... |
Frontiers in Neurorobotics | 29515386 | PMC5825909 | 10.3389/fnbot.2018.00004 | Low-Latency Line Tracking Using Event-Based Dynamic Vision Sensors | In order to safely navigate and orient in their local surroundings autonomous systems need to rapidly extract and persistently track visual features from the environment. While there are many algorithms tackling those tasks for traditional frame-based cameras, these have to deal with the fact that conventional cameras ... | 1.3Related WorkThere is a variety of algorithms to extract lines from frames, most notably the Hough transform (Duda and Hart, 1972; Matas et al., 2000). In Grompone von Gioi et al. (2012), a line segment detector (called LSD) is proposed that works stably without parameter tuning (see also Section 3 for comparisons). ... | [
"28704206",
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] | [
{
"pmid": "28704206",
"title": "An autonomous robot inspired by insect neurophysiology pursues moving features in natural environments.",
"abstract": "OBJECTIVE\nMany computer vision and robotic applications require the implementation of robust and efficient target-tracking algorithms on a moving platfo... |
PLoS Computational Biology | 29447153 | PMC5831643 | 10.1371/journal.pcbi.1005935 | A model of risk and mental state shifts during social interaction | Cooperation and competition between human players in repeated microeconomic games offer a window onto social phenomena such as the establishment, breakdown and repair of trust. However, although a suitable starting point for the quantitative analysis of such games exists, namely the Interactive Partially Observable Mar... | Earlier and related workTrust games of various kinds have been used in behavioural economics and psychology research (see [34]). In particular, the MRT we used was based on variants in several earlier studies (see examples in [17, 35, 36]).The current MRT was first modeled using regression models (see [16]) of various ... | [
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] | [
{
"pmid": "18255038",
"title": "Self responses along cingulate cortex reveal quantitative neural phenotype for high-functioning autism.",
"abstract": "Attributing behavioral outcomes correctly to oneself or to other agents is essential for all productive social exchange. We approach this issue in high-f... |
Frontiers in Genetics | 29559993 | PMC5845696 | 10.3389/fgene.2018.00039 | Griffin: A Tool for Symbolic Inference of Synchronous Boolean Molecular Networks | Boolean networks are important models of biochemical systems, located at the high end of the abstraction spectrum. A number of Boolean gene networks have been inferred following essentially the same method. Such a method first considers experimental data for a typically underdetermined “regulation” graph. Next, Boolean... | 3.2. Related workAs a first comparison between our work and related articles, it is important to point out a difference in the type of input data. In this work, Griffin input is composed of (partial) information about the network topology (R-graphs) along with other data representing biological constraints. R-graphs co... | [
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{
"pmid": "12782112",
"title": "The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster.",
"abstract": "Expression of the Drosophila segment polarity genes is initiated by a pre-pattern of pair-rule gene products and maintained... |
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