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Piotr Klukowski, Michal Augoff, Maciej Zieba, Maciej Drwal, Adam Gonczarek, Michal J Walczak
Motivation: Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy...
March 14, 2018: Bioinformatics
Gwyn Bevan, Alice Evans, Sabina Nuti
This paper explores what motivates improved health care performance. Previously, many have thought that performance would either improve via choice and competition or by relying on trust and altruism. But neither assumption is supported by available evidence. So instead we explore a third approach of reciprocal altruism with sanctions for unacceptably poor performance and rewards for high performance. These rewards and sanctions, however, are not monetary, but in the form of reputational effects through public reporting of benchmarking of performance...
March 16, 2018: Health Economics, Policy, and Law
Simon Badger, Christian Brønnum-Hansen, Heribertus Bayu Hartanto, Tiziano Peraro
We compute the leading-color contributions to five-gluon scattering at two loops in massless QCD. The integrands of all independent helicity amplitudes are evaluated using d-dimensional generalized unitarity cuts and finite field reconstruction techniques. Numerical evaluation of the integral basis is performed with sector decomposition methods to obtain the first benchmark results for all helicity configurations of a 2→3 scattering process in QCD.
March 2, 2018: Physical Review Letters
Peggy Stolt-Bergner, Christian Benda, Tim Bergbrede, Hüseyin Besir, Patrick H N Celie, Cindy Chang, David Drechsel, Ariane Fischer, Arie Geerlof, Barbara Giabbai, Joop van den Heuvel, Georg Huber, Wolfgang Knecht, Anita Lehner, Regis Lemaitre, Kristina Nordén, Gwynn Pardee, Ines Racke, Kim Remans, Astrid Sander, Judith Scholz, Magda Stadnik, Paola Storici, Daniel Weinbruch, Isabel Zaror, Linda H L Lua, Sabine Suppmann
Baculovirus-insect cell expression system has become one of the most widely used eukaryotic expression systems for heterologous protein production in many laboratories. The availability of robust insect cell lines, serum-free media, a range of vectors and commercially-packaged kits have supported the demand for maximizing the exploitation of the baculovirus-insect cell expression system. Naturally, this resulted in varied strategies adopted by different laboratories to optimize protein production. Most laboratories have preference in using either the E...
March 12, 2018: Journal of Structural Biology
M A Alsalem, A A Zaidan, B B Zaidan, M Hashim, H T Madhloom, N D Azeez, S Alsyisuf
CONTEXT: Acute leukaemia diagnosis is a field requiring automated solutions, tools and methods and the ability to facilitate early detection and even prediction. Many studies have focused on the automatic detection and classification of acute leukaemia and their subtypes to promote enable highly accurate diagnosis. OBJECTIVE: This study aimed to review and analyse literature related to the detection and classification of acute leukaemia. The factors that were considered to improve understanding on the field's various contextual aspects in published studies and characteristics were motivation, open challenges that confronted researchers and recommendations presented to researchers to enhance this vital research area...
May 2018: Computer Methods and Programs in Biomedicine
Shuai Zhang, Burkhard Militzer, Lorin X Benedict, François Soubiran, Philip A Sterne, Kevin P Driver
Carbon-hydrogen plasmas and hydrocarbon materials are of broad interest to laser shock experimentalists, high energy density physicists, and astrophysicists. Accurate equations of state (EOSs) of hydrocarbons are valuable for various studies from inertial confinement fusion to planetary science. By combining path integral Monte Carlo (PIMC) results at high temperatures and density functional theory molecular dynamics results at lower temperatures, we compute the EOSs for hydrocarbons from simulations performed at 1473 separate (ρ, T)-points distributed over a range of compositions...
March 14, 2018: Journal of Chemical Physics
Roel Tempelaar, David R Reichman
Fewest-switches surface hopping (FSSH) is perhaps the most widely used mixed quantum-classical approach for the modeling of non-adiabatic processes, but its original formulation is restricted to (adiabatic) population terms of the quantum density matrix, leaving its implementations with an inconsistency in the treatment of populations and coherences. In this article, we propose a generalization of FSSH that treats both coherence and population terms on equal footing and which formally reduces to the conventional FSSH algorithm for the case of populations...
March 14, 2018: Journal of Chemical Physics
Joseph R Cendagorta, Zlatko Bačić, Mark E Tuckerman
We introduce a scheme for approximating quantum time correlation functions numerically within the Feynman path integral formulation. Starting with the symmetrized version of the correlation function expressed as a discretized path integral, we introduce a change of integration variables often used in the derivation of trajectory-based semiclassical methods. In particular, we transform to sum and difference variables between forward and backward complex-time propagation paths. Once the transformation is performed, the potential energy is expanded in powers of the difference variables, which allows us to perform the integrals over these variables analytically...
March 14, 2018: Journal of Chemical Physics
Alexei A Kananenka, Xiang Sun, Alexander Schubert, Barry D Dunietz, Eitan Geva
We present a comprehensive comparison of the following mixed quantum-classical methods for calculating electronic transition rates: (1) nonequilibrium Fermi's golden rule, (2) mixed quantum-classical Liouville method, (3) mean-field (Ehrenfest) mixed quantum-classical method, and (4) fewest switches surface-hopping method (in diabatic and adiabatic representations). The comparison is performed on the Garg-Onuchic-Ambegaokar benchmark charge-transfer model, over a broad range of temperatures and electronic coupling strengths, with different nonequilibrium initial states, in the normal and inverted regimes...
March 14, 2018: Journal of Chemical Physics
Kevin P Bishop, Pierre-Nicholas Roy
Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details...
March 14, 2018: Journal of Chemical Physics
Han Liu, Xianchao Zhang, Xiaotong Zhang
Possible world has shown to be effective for handling various types of data uncertainty in uncertain data management. However, few uncertain data clustering and classification algorithms are proposed based on possible world. Moreover, existing possible world based algorithms suffer from the following issues: (1) they deal with each possible world independently and ignore the consistency principle across different possible worlds; (2) they require the extra post-processing procedure to obtain the final result, which causes that the effectiveness highly relies on the post-processing method and the efficiency is also not very good...
February 27, 2018: Neural Networks: the Official Journal of the International Neural Network Society
Samiul M Ansari, David S Palmer
Recently, Güssregen et al. used solute-solvent distribution functions calculated by the 3D Reference Interaction Site Model (3DRISM) in a 3D-QSAR approach to model activity data for a set of serine protease inhibitors; this approach was referred to as Comparative Analysis of 3D RISM MAps (CARMa). [J. Chem. Inf. MODEL: , 2017, 57, 1652-1666] Here we extend this idea by introducing probe atoms into the 3DRISM solvent model in order to directly capture other molecular interactions in addition to those related to hydration/dehydration...
March 15, 2018: Journal of Chemical Information and Modeling
Lucy Kerns
In risk assessment, it is often desired to make inferences on the risk at certain low doses or on the dose(s) at which a specific benchmark risk (BMR) is attained. At times, [Formula: see text] dose levels or BMRs are of interest, and some form of multiplicity adjustment is necessary to ensure a valid [Formula: see text] simultaneous inference. Bonferroni correction is often employed in practice for such purposes. Though relative simple to implement, the Bonferroni strategy can suffer from extreme conservatism (Nitcheva et al...
March 15, 2018: Journal of Biopharmaceutical Statistics
Patric Schmitz, Julian Hildebrandt, Andre Calero Valdez, Leif Kobbelt, Martina Ziefle
In virtual environments, the space that can be explored by real walking is limited by the size of the tracked area. To enable unimpeded walking through large virtual spaces in small real-world surroundings, redirection techniques are used. These unnoticeably manipulate the user's virtual walking trajectory. It is important to know how strongly such techniques can be applied without the user noticing the manipulation-or getting cybersick. Previously, this was estimated by measuring a detection threshold (DT) in highly-controlled psychophysical studies, which experimentally isolate the effect but do not aim for perceived immersion in the context of VR applications...
April 2018: IEEE Transactions on Visualization and Computer Graphics
Tianzhu Zhang, Si Liu, Changsheng Xu, Bin Liu, Ming-Hsuan Yang
In this paper, we propose a novel correlation particle filter (CPF) for robust visual tracking. Instead of a simple combination of a correlation filter and a particle filter, we exploit and complement the strength of each one. Compared with existing tracking methods based on correlation filters and particle filters, the proposed tracker has four major advantages: 1) it is robust to partial and total occlusions, and can recover from lost tracks by maintaining multiple hypotheses; 2) it can effectively handle large-scale variation via a particle sampling strategy; 3) it can efficiently maintain multiple modes in the posterior density using fewer particles than conventional particle filters, resulting in low computational cost; and 4) it can shepherd the sampled particles toward the modes of the target state distribution using a mixture of correlation filters, resulting in robust tracking performance...
June 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Wei Wang, Yan Yan, Feiping Nie, Shuicheng Yan, Nicu Sebe
Graph-based dimensionality reduction techniques have been widely and successfully applied to clustering and classification tasks. The basis of these algorithms is the constructed graph which dictates their performance. In general, the graph is defined by the input affinity matrix. However, the affinity matrix derived from the data is sometimes suboptimal for dimension reduction as the data used are very noisy. To address this issue, we propose the projective unsupervised flexible embedding models with optimal graph (PUFE-OG)...
June 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Jinlong Liu, Yao Zheng, Yan Jiao, Zhenyu Wang, Zhouguang Lu, Anthony Vasileff, Shi-Zhang Qiao
Conventional development of nanomaterials for efficient electrocatalysis is largely based on performance-oriented trial-and-error/iterative approaches, while a rational design approach at the atomic/molecular level is yet to be found. Here, inspired by a fundamental understanding of the mechanism for both oxygen and hydrogen evolution half reactions (OER/HER), a unique strategy is presented to engineer RuO2 for superior alkaline water electrolysis through coupling with NiO as an efficient bifunctional promoter...
March 15, 2018: Small
S Kharchoufi, J Gomez, C Lasanta, R Castro, F Sainz, M Hamdi
BACKGROUND: There is growing interest in the beneficial health effects of certain fruits, such as pomegranate, and their by-products, like vinegar. Vinegars contain antioxidant compounds such as polyphenols, which can scavenge free radicals in the body. In this study, the antioxidant properties (ABTS and DPPH scavenging capacities) and global polyphenolic composition of a new functional product, namely a pomegranate vinegar produced in the laboratory from the Gabsi variety, were evaluated and compared with those of commercial wine vinegars (Sherry and Rioja red wine Spanish vinegars)...
March 15, 2018: Journal of the Science of Food and Agriculture
Hanna Ferløv Schwensen, Carol Kan, Janet Treasure, Niels Høiby, Magnus Sjögren
PURPOSE: Anorexia nervosa (AN) is a poorly understood and often chronic condition. Deviations in the gut microbiota have been reported to influence the gut-brain axis in other disorders. Therefore, if present in AN, it may impact on symptoms and illness progression. A review of the gut microbiota studies in AN is presented. METHOD: A literature search on PubMed yielded 27 articles; 14 were selected and based on relevance, 9 articles were included. The findings were interpreted in the larger context of preclinical research and clinical observations...
March 14, 2018: Eating and Weight Disorders: EWD
Eric Michoulier, Jennifer A Noble, Aude Simon, Joëlle Mascetti, Céline Toubin
Polycyclic Aromatic Hydrocarbons (PAHs) are a family of molecules which represent the best candidates to explain the observation of one set of features in the Interstellar Medium (ISM): the Aromatic Interstellar Bands (AIBs). They could also contribute to the Diffuse Interstellar Bands (DIBs). In dense molecular clouds, PAHs may condense onto interstellar grains, contributing to the complex chemistry occurring in their icy mantles, composed essentially of water. In this context, the adsorption of various aromatic molecules, from benzene to ovalene, on different ices - both amorphous and crystalline - is investigated by means of classical molecular dynamics simulations...
March 15, 2018: Physical Chemistry Chemical Physics: PCCP
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