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Structure prediction

Chao Ning, Dan Wang, Huimin Kang, Raphael Mrode, Lei Zhou, Shizhong Xu, Jian-Feng Liu
Motivation: Epistasis provides a feasible way for probing potential genetic mechanism of complex traits. However, time-consuming computation challenges successful detection of interaction in practice, especially when linear mixed model (LMM) is used to control type I error in the presence of population structure and cryptic relatedness. Results: A rapid epistatic mixed-model association analysis (REMMA) method was developed to overcome computational limitation. This method first estimates individuals' epistatic effects by an extended genomic best linear unbiased prediction (EG-BLUP) model with additive and epistatic kinship matrix, then pairwise interaction effects are obtained by linear retransformations of individuals' epistatic effects...
January 12, 2018: Bioinformatics
Viviane S Straatmann, Ylva B Almquist, Aldair J Oliveira, Mikael Rostila, Claudia S Lopes
We investigated the stability and the directionality of being body bullied and a set of four variables- 1) Body Mass Index (BMI), 2) moderate and vigorous physical activity (MVPA), 3) television time (TV) and 4) video game/computer time (VG)-, termed in the present study as 'health-related state and behaviours (HRSB)'-across adolescence. The Adolescent Nutritional Assessment Longitudinal Study (ELANA) is a cohort study conducted among middle school students from two public and four private schools in Rio de Janeiro-Brazil...
2018: PloS One
Aleksandra Piotrowska, Anna Syguda, Bogdan Wyrwas, Lukasz Chrzanowski, Till Luckenbach, Hermann J Heipieper
Ionic liquids consisting of a combination of herbicidal anions with a quaternary ammonium cation act as efficient herbicides, which are under consideration to be used in the agriculture. In the present study, we used embryos of the zebrafish (Danio rerio) as a model to assess the toxic potential of ammonium-based ionic liquids for aquatic organisms. As we assumed interference of the partially hydrophobic ionic liquid cation with lipids, we investigated the adaptation response in the lipid composition of the zebrafish embryos, triggered by the ionic compound...
2018: PloS One
Svetlana Rezinciuc, Jose Vladimir Sandoval-Sierra, Yolanda Ruiz-León, Pieter van West, Javier Diéguez-Uribeondo
The secondary cysts of the fish pathogen oomycete Saprolegnia parasitica possess bundles of long hooked hairs that are characteristic to this economically important pathogenic species. Few studies have been carried out on elucidating their specific role in the S. parasitica life cycle and the role they may have in the infection process. We show here their function by employing several strategies that focus on descriptive, developmental and predictive approaches. The strength of attachment of the secondary cysts of this pathogen was compared to other closely related species where bundles of long hooked hairs are absent...
2018: PloS One
Selma Díaz-Mazariegos, Nallely Cabrera, Ruy Perez-Montfort
Proteins with great sequence similarity usually have similar structure, function and other physicochemical properties. But in many cases, one or more of the physicochemical or functional characteristics differ, sometimes very considerably, among these homologous proteins. To better understand how critical amino acids determine quantitative properties of function in proteins, the responsible residues must be located and identified. This can be difficult to achieve, particularly in cases where multiple amino acids are involved...
2018: PloS One
Rene M Boiteau, David W Hoyt, Carrie D Nicora, Hannah A Kinmonth-Schultz, Joy K Ward, Kerem Bingol
We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS²), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter out the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture, and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana...
January 17, 2018: Metabolites
Alexandre Karkas, Nicolas Menjot de Champfleur, Alain Uziel, Michel Mondain, Jean-Luc Puel, Frédéric Venail
HYPOTHESIS: Evaluate the benefit of preoperative surgical planning using computed tomography (CT) for atraumatic cochlear implantation. BACKGROUND: The surgical technique has a direct impact on hearing and structure preservation. Much interest has been given to depth of electrode insertion. We focused on electrode diameter depending on exposure of round window membrane (RWM) as calculated on preoperative CT. METHODS: Measurements were calculated radiologically and anatomically on 10 temporal bones...
January 16, 2018: Otology & Neurotology
R Smith, Tz Kokalova, C Wheldon, J E Bishop, M Freer, N Curtis, D J Parker
Excited states in certain atomic nuclei possess an unusual structure, where the dominant degrees of freedom are those of α clusters rather than individual nucleons. It has been proposed that the diffuse 3α system of the ^{12}C Hoyle state may behave like a Bose-Einstein condensate, where the α clusters maintain their bosonic identities. By measuring the decay of the Hoyle state into three α particles, we obtained an upper limit for the rare direct 3α decay branch of 0.047%. This value is now at a level comparable with theoretical predictions and could be a sensitive probe of the structure of this state...
September 29, 2017: Physical Review Letters
Michael Sinhuber, Gregory P Bewley, Eberhard Bodenschatz
Using the unique capabilities of the Variable Density Turbulence Tunnel at the Max Planck Institute for Dynamics and Self-Organization, Göttingen, we report experimental measurements in classical grid turbulence that uncover oscillations of the velocity structure functions in the inertial range. This was made possible by measuring extremely long time series of up to 10^{10} samples of the turbulent fluctuating velocity, which corresponds to O(10^{7}) integral length scales. The measurements were conducted in a well-controlled environment at a wide range of high Reynolds numbers from R_{λ}=110 up to R_{λ}=1600, using both traditional hot-wire probes as well as the nanoscale thermal anemometry probe developed at Princeton University...
September 29, 2017: Physical Review Letters
Hao Yang, Jiabin Yu, Stuart S P Parkin, Claudia Felser, Chao-Xing Liu, Binghai Yan
We predict the existence of triple point fermions in the band structure of several half-Heusler topological insulators by ab initio calculations and the Kane model. We find that many half-Heusler compounds exhibit multiple triple points along four independent C_{3} axes, through which the doubly degenerate conduction bands and the nondegenerate valence band cross each other linearly nearby the Fermi energy. When projected from the bulk to the (111) surface, most of these triple points are located far away from the surface Γ[over ¯] point, as distinct from previously reported triple point fermion candidates...
September 29, 2017: Physical Review Letters
Yasmine Meroz, Brendan J Meade
Earthquakes at seismogenic plate boundaries are a response to the differential motions of tectonic blocks embedded within a geometrically complex network of branching and coalescing faults. Elastic strain is accumulated at a slow strain rate on the order of 10^{-15}  s^{-1}, and released intermittently at intervals >100  yr, in the form of rapid (seconds to minutes) coseismic ruptures. The development of macroscopic models of quasistatic planar tectonic dynamics at these plate boundaries has remained challenging due to uncertainty with regard to the spatial and kinematic complexity of fault system behaviors...
September 29, 2017: Physical Review Letters
Amicie de Pierrefeu, Thomas Fovet, Fouad Hadj-Selem, Tommy Löfstedt, Philippe Ciuciu, Stephanie Lefebvre, Pierre Thomas, Renaud Lopes, Renaud Jardri, Edouard Duchesnay
Despite significant progress in the field, the detection of fMRI signal changes during hallucinatory events remains difficult and time-consuming. This article first proposes a machine-learning algorithm to automatically identify resting-state fMRI periods that precede hallucinations versus periods that do not. When applied to whole-brain fMRI data, state-of-the-art classification methods, such as support vector machines (SVM), yield dense solutions that are difficult to interpret. We proposed to extend the existing sparse classification methods by taking the spatial structure of brain images into account with structured sparsity using the total variation penalty...
January 16, 2018: Human Brain Mapping
Chundi Yu, Zeping Shao, Jinhui Zhang, Bing Liu, Lingjie Kong, Yan Zhang, Shuo Wang
Creatinine was found to not only act as a precursor of 2-amino-1-methyl-6-phenylimidazo [4,5-b]pyridine (PhIP) formation but also inhibit PhIP formation in a creatinine/phenylalanine model system. The dual mechanistic effects of creatinine on PhIP formation were then investigated in a model system. Adducts of creatinine-PhIP were detected by quadrupole-time-of-flight mass spectrometry and were found to be a likely explanation for the substantial decrease in the yield of PhIP when excess creatinine was supplied...
January 17, 2018: Journal of Food Science
Parivash Ashrafi, Yi Sun, Neil Davey, Roderick G Adams, Simon C Wilkinson, Gary Patrick Moss
OBJECTIVES: The aim of this study was to investigate how to improve predictions from Gaussian Process models by optimising the model hyperparameters. METHODS: Optimisation methods, including Grid Search, Conjugate Gradient, Random Search, Evolutionary Algorithm and Hyper-prior, were evaluated and applied to previously published data. Data sets were also altered in a structured manner to reduce their size, which retained the range, or 'chemical space' of the key descriptors to assess the effect of the data range on model quality...
January 17, 2018: Journal of Pharmacy and Pharmacology
Kathleen Crapanzano, Dixie Fisher, Rebecca Hammarlund, Eric P Hsieh, Win May
BACKGROUND: Physician biases toward mental conditions such as depression have been shown to adversely affect medical outcomes. OBJECTIVE: To explore the relationship between residents' explicit bias toward depressed patients and their clinical skills on a cardiac case during an objective structured clinical exam (OSCE). DESIGN: Prospective parallel randomized controlled study. PARTICIPANTS: One hundred eighty-five internal medicine residents from three residency programs in two states...
January 16, 2018: Journal of General Internal Medicine
Stefano Della Longa, Alessandro Arcovito
Antagonists of the nociceptin receptor (NOP) are raising interest for their possible clinical use as antidepressant drugs. Recently, the structure of NOP in complex with some piperidine-based antagonists has been revealed by X-ray crystallography. In this study, a multi-flexible docking (MF-docking) procedure, i.e. docking to multiple receptor conformations extracted by preliminary molecular dynamics trajectories, together with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have been carried out to provide the binding mode of two novel NOP antagonists, one of them selective (BTRX-246040, formerly named LY-2940094) and one non selective (AT-076), i...
January 16, 2018: Journal of Computer-aided Molecular Design
Ryo Kunimoto, Jürgen Bajorath
Drug-target networks have aided in many target prediction studies aiming at drug repurposing or the analysis of side effects. Conventional drug-target networks are bipartite. They contain two different types of nodes representing drugs and targets, respectively, and edges indicating pairwise drug-target interactions. In this work, we introduce a tripartite network consisting of drugs, other bioactive compounds, and targets from different sources. On the basis of analog relationships captured in the network and so-called neighbor targets of drugs, new drug targets can be inferred...
January 16, 2018: Journal of Computer-aided Molecular Design
Samina Kausar, Andre O Falcao
BACKGROUND: In-silico quantitative structure-activity relationship (QSAR) models based tools are widely used to screen huge databases of compounds in order to determine the biological properties of chemical molecules based on their chemical structure. With the passage of time, the exponentially growing amount of synthesized and known chemicals data demands computationally efficient automated QSAR modeling tools, available to researchers that may lack extensive knowledge of machine learning modeling...
January 16, 2018: Journal of Cheminformatics
Michael W Hart, Daryn A Stover, Vanessa Guerra, Sahar V Mozaffari, Carole Ober, Carina F Mugal, Ingemar Kaj
Coevolution of genes that encode interacting proteins expressed on the surfaces of sperm and eggs can lead to variation in reproductive compatibility between mates and reproductive isolation between members of different species. Previous studies in mice and other mammals have focused in particular on evidence for positive or diversifying selection that shapes the evolution of genes that encode sperm-binding proteins expressed in the egg coat or zona pellucida (ZP). By fitting phylogenetic models of codon evolution to data from the 1000 Genomes Project, we identified candidate sites evolving under diversifying selection in the human genes ZP3 and ZP2...
2018: PeerJ
Ying Li, Elaine Lai-Han Leung, Hudan Pan, Xiaojun Yao, Qingchun Huang, Min Wu, Ting Xu, Yuwei Wang, Jun Cai, Runze Li, Wei Liu, Liang Liu
Rheumatoid arthritis (RA) is a highly prevalent chronic autoimmune disease. However, genetic and environmental factors involved in RA pathogenesis are still remained largely unknown. To identify the genetic causal variants underlying pathogenesis and disease progression of RA patients, we undertook the first comprehensive whole-exome sequencing (WES) study in a total of 124 subjects including 58 RA cases and 66 healthy controls in Han Chinese population. We identified 378 novel genes that were enriched with deleterious variants in RA patients using a gene burden test...
December 19, 2017: Oncotarget
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