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Computational model

Brooke N Wolford, Cristen J Willer, Ida Surakka
The combination of Electronic Health Records (EHRs) with genetic data has ushered in the next wave of complex disease genetics. Population-based biobanks and other large cohorts provide sufficient sample sizes to identify novel genetic associations across the hundreds to thousands of phenotypes gleaned from EHRs. In this review we summarize the current state of these EHR-linked biobanks, explore ongoing methods development in the field, and highlight recent discoveries of genetic associations. We enumerate the many existing biobanks with EHRs linked to genetic data, many of which are available to researchers via application and contain sample sizes > 50,000...
March 14, 2018: Human Molecular Genetics
Arjun Sethi, Valerie Voon, Hugo D Critchley, Mara Cercignani, Neil A Harrison
Computational models of reinforcement learning have helped dissect discrete components of reward-related function and characterize neurocognitive deficits in psychiatric illnesses. Stimulus novelty biases decision-making, even when unrelated to choice outcome, acting as if possessing intrinsic reward value to guide decisions toward uncertain options. Heightened novelty seeking is characteristic of attention deficit hyperactivity disorder, yet how this influences reward-related decision-making is computationally encoded, or is altered by stimulant medication, is currently uncertain...
March 13, 2018: Brain: a Journal of Neurology
Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Zhang Yanju, Tatsuya Akutsu, Kuo-Chen Chou, Richard A Strugnell, Jiangning Song, Trevor Lithgow
Motivation: Many Gram-negative bacteria use type VI secretion systems (T6SS) to export effector proteins into adjacent target cells. These secreted effectors (T6SEs) play vital roles in the competitive survival in bacterial populations, as well as pathogenesis of bacteria. Although various computational analyses have been previously applied to identify effectors secreted by certain bacterial species, there is no universal method available to accurately predict T6SS effector proteins from the growing tide of bacterial genome sequence data...
March 14, 2018: Bioinformatics
Fabien Cignetti, Marianne Vaugoyeau, Aurelie Fontan, Marianne Jover, Marie-Odile Livet, Catherine Hugonenq, Frédérique Audic, Brigitte Chabrol, Christine Assaiante
BACKGROUND AND AIM: Feedforward and online controls are two facets of predictive motor control from internal models, which is suspected to be impaired in learning disorders. We examined whether the feedforward component is affected in children (8-12 years) with developmental dyslexia (DD) and/or with developmental coordination disorder (DCD) compared to typically developing (TD) children. METHODS: Children underwent a bimanual unloading paradigm during which a load supported to one arm, the postural arm, was either unexpectedly unloaded by a computer or voluntary unloaded by the subject with the other arm...
March 13, 2018: Research in Developmental Disabilities
Melissa Tomkins, Adi Kliot, Athanasius Fm Marée, Saskia A Hogenhout
Members of the Candidatus genus Phytoplasma are small bacterial pathogens that hijack their plant hosts via the secretion of virulence proteins (effectors) leading to a fascinating array of plant phenotypes, such as witch's brooms (stem proliferations) and phyllody (retrograde development of flowers into vegetative tissues). Phytoplasma depend on insect vectors for transmission, and interestingly, these insect vectors were found to be (in)directly attracted to plants with these phenotypes. Therefore, phytoplasma effectors appear to reprogram plant development and defence to lure insect vectors, similarly to social engineering malware, which employs tricks to lure people to infected computers and webpages...
March 13, 2018: Current Opinion in Plant Biology
Alberto Perez, Florian Sittel, Gerhard Stock, Ken A Dill
The molecular actions of proteins occur along reaction coordinates. Current computer methods have limited ability to explore them. We describe a fast protocol called MELD-path that: (1) efficiently samples relevant conformational states via MELD, an accelerator of Molecular Dynamics (MD), (2) seeds multiple short MD trajectories from MELD states, then (3) constructs Markov State Models (MSM) that give the routes and kinetics. We tested the method against extensive (multi μs) MD simulations of the right-handed- to left-handed-helix transition of a 9-mer peptide of AIB, the symmetry of which allows us to establish convergence...
March 16, 2018: Journal of Chemical Theory and Computation
Harsha T Garimella, Reuben H Kraft, Andrzej J Przekwas
Subject-specific computer models (male and female) of the human head were used to investigate the possible axonal deformation resulting from the primary phase blast-induced skull flexures. The corresponding axonal tractography was explicitly incorporated into these finite element models using a recently developed technique based on the embedded finite element method. These models were subjected to extensive verification against experimental studies which examined their pressure and displacement response under a wide range of loading conditions...
2018: PloS One
Charrise M Ramkissoon, Pau Herrero, Jorge Bondia, Josep Vehi
The artificial pancreas (AP) system is designed to regulate blood glucose in subjects with type 1 diabetes using a continuous glucose monitor informed controller that adjusts insulin infusion via an insulin pump. However, current AP developments are mainly hybrid closed-loop systems that include feed-forward actions triggered by the announcement of meals or exercise. The first step to fully closing the loop in the AP requires removing meal announcement, which is currently the most effective way to alleviate postprandial hyperglycemia due to the delay in insulin action...
March 16, 2018: Sensors
Lucia Romero, Jordi Cano, Julio Gomis-Tena, Beatriz Trenor, Ferran Sanz, Manuel Pastor, Javier Saiz
Drug-induced proarrhythmicity is a major concern for regulators and pharmaceutical companies. For novel drug candidates, the standard assessment involves the evaluation of the potassium hERG channels block and the in vivo prolongation of the QT interval. However, this method is known to be too restrictive and to stop the development of potentially valuable therapeutic drugs. The aim of this work is to create an in silico tool for early detection of drug-induced proarrhythmic risk. The system is based on simulations of how different compounds affect the action potential duration (APD) of isolated endocardial, midmyocardial, and epicardial cells as well as the QT prolongation in a virtual tissue...
March 16, 2018: Journal of Chemical Information and Modeling
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Raphaël Le Bouc, Mathias Pessiglione
Motivation can be defined as the function that orients and activates the behavior. Motivation deficits such as apathy are pervasive in both neurological and psychiatric diseases, and are currently assessed with clinical scales that do not give any mechanistic insight. Here, we present another approach that consists in phenotyping the behaviour of patients in motivation tests, using computational models. These formal models impose a precise and operational definition of motivation that is embedded in decision theory...
March 2018: Médecine Sciences: M/S
Nicola Schieda, Robert S Lim, Satheesh Krishna, Matthew D F McInnes, Trevor A Flood, Rebecca E Thornhill
OBJECTIVE: The objective of our study was to evaluate tumor attenuation and texture on unenhanced CT for potential differentiation of low-grade from high-grade chromophobe renal cell carcinoma (RCC). MATERIALS AND METHODS: A retrospective study of 37 consecutive patients with chromophobe RCC (high-grade, n = 13; low-grade, n = 24) who underwent preoperative unenhanced CT between 2011 and 2016 was performed. Two radiologists (readers 1 and 2) blinded to the histologic grade of the tumor and outcome of the patients subjectively evaluated tumor homogeneity (3-point scale: completely homogeneous, mildly heterogeneous, or mostly heterogeneous)...
March 16, 2018: AJR. American Journal of Roentgenology
David Vernez, Sandrine Fraize-Frontier, Raymond Vincent, Stéphane Binet, Christophe Rousselle
OBJECTIVES: Assessment factors (AFs) are commonly used for deriving reference concentrations for chemicals. These factors take into account variabilities as well as uncertainties in the dataset, such as inter-species and intra-species variabilities or exposure duration extrapolation or extrapolation from the lowest-observed-adverse-effect level (LOAEL) to the noobserved- adverse-effect level (NOAEL). In a deterministic approach, the value of an AF is the result of a debate among experts and, often a conservative value is used as a default choice...
March 15, 2018: International Journal of Occupational Medicine and Environmental Health
Senda Sammoud, Alan Michael Nevill, Yassine Negra, Raja Bouguezzi, Helmi Chaabene, Younés Hachana
This study aimed to estimate the optimal body size, limb segment length, and girth or breadth ratios of 100-m breaststroke performance in youth swimmers. In total, 59 swimmers [male: n = 39, age = 11.5 (1.3) y; female: n = 20, age = 12.0 (1.0) y] participated in this study. To identify size/shape characteristics associated with 100-m breaststroke swimming performance, we computed a multiplicative allometric log-linear regression model, which was refined using backward elimination. Results showed that the 100-m breaststroke performance revealed a significant negative association with fat mass and a significant positive association with the segment length ratio (arm ratio = hand length/forearm length) and limb girth ratio (girth ratio = forearm girth/wrist girth)...
March 16, 2018: Pediatric Exercise Science
Andre Roelke, Nicole Franke, Chris Biemann, Ralph Radach, Arthur M Jacobs, Markus J Hofmann
The theoretical "difficulty in separating association strength from [semantic] feature overlap" has resulted in inconsistent findings of either the presence or absence of "pure" associative priming in recent literature (Hutchison, 2003, Psychonomic Bulletin & Review, 10(4), p. 787). The present study used co-occurrence statistics of words in sentences to provide a full factorial manipulation of direct association (strong/no) and the number of common associates (many/no) of the prime and target words...
March 15, 2018: Psychonomic Bulletin & Review
Jyoti Singh Kirar, R K Agrawal
This paper presents a novel algorithm (CVSTSCSP) for determining discriminative features from an optimal combination of temporal, spectral and spatial information for motor imagery brain computer interfaces. The proposed method involves four phases. In the first phase, EEG signal is segmented into overlapping time segments and bandpass filtered through frequency filter bank of variable size subbands. In the next phase, features are extracted from the segmented and filtered data using stationary common spatial pattern technique (SCSP) that can handle the non- stationarity and artifacts of EEG signal...
March 16, 2018: Journal of Medical Systems
Jose M Sanchez Bornot, KongFatt Wong-Lin, Alwani Liyana Ahmad, Girijesh Prasad
The brain's functional connectivity (FC) estimated at sensor level from electromagnetic (EEG/MEG) signals can provide quick and useful information towards understanding cognition and brain disorders. Volume conduction (VC) is a fundamental issue in FC analysis due to the effects of instantaneous correlations. FC methods based on the imaginary part of the coherence (iCOH) of any two signals are readily robust to VC effects, but neglecting the real part of the coherence leads to negligible FC when the processes are truly connected but with zero or π-phase (modulus 2π) interaction...
March 15, 2018: Brain Topography
Claudia Di Napoli, Florian Pappenberger, Hannah L Cloke
In this work, the potential of the Universal Thermal Climate Index (UTCI) as a heat-related health risk indicator in Europe is demonstrated. The UTCI is a bioclimate index that uses a multi-node human heat balance model to represent the heat stress induced by meteorological conditions to the human body. Using 38 years of meteorological reanalysis data, UTCI maps were computed to assess the thermal bioclimate of Europe for the summer season. Patterns of heat stress conditions and non-thermal stress regions are identified across Europe...
March 15, 2018: International Journal of Biometeorology
Alberto Pilotto, Raffaella Boi, Jean Petermans
Recently, the interest of industry, government agencies and healthcare professionals in technology for aging people has increased. The challenge is whether technology may play a role in enhancing independence and quality of life and in reducing individual and societal costs of caring. Information and communication technologies, i.e. tools aimed at communicating and informing, assistive technologies designed to maintain older peoples' independence and increasing safety, and human-computer interaction technologies for supporting older people with motility and cognitive impairments as humanoid robots, exoskeletons, rehabilitation robots, service robots and companion-type are interdisciplinary topics both in research and in clinical practice...
March 13, 2018: Age and Ageing
Beatriz Galatas, Helena Martí-Soler, Lidia Nhamussua, Pau Cisteró, Pedro Aide, Francisco Saute, Clara Menéndez, N Regina Rabinovich, Pedro L Alonso, Quique Bassat, Alfredo Mayor
Background: Afebrile Plasmodium falciparum infections usually remain undetected and untreated in the community and could potentially contribute to sustaining local malaria transmission in areas aiming for malaria elimination. Methods: Thirty-two men with afebrile P. falciparum infections detected with rapid diagnostic test (RDTs) were followed for 28 days. Kaplan-Meier estimates were computed to estimate probability of parasite positivity and of reducing parasitaemia by half of its initial level by day 28...
March 13, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
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