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Shahidul Islam, Ping Ge, Shaojie Zhang
The analysis of RNA tertiary structure is hindered by the fact that not too many structural data are available and a significant amount of them are in low resolution. Due to the atomic coordinate errors posed by the limitations of low-resolution RNA three-dimensional structures, it becomes a critical challenge to extract key geometric characteristics of RNA, particularly, the interaction of bases. To address this issue, we have devised a comparative method, named CompAnnotate, that utilizes more precise structural information of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structures, by aligning and making comparative geometric assessments...
June 21, 2017: Nucleic Acids Research
Jérôme Defosse, Mark Schieren, Torsten Loop, Cerstin Arndt, Rainer Röhrig, Erich Stoelben, Corinna Ludwig, Alexander Schleppers, Frank Wappler, Mark Gerbershagen, Alberto Lopez-Pastorini
The collection of clinical treatment data in registry databases is an important aspect of health services research. It allows for a critical evaluation of the safety, efficacy and cost-effectiveness of clinical treatment concepts in large patient populations. The findings of registry research represent real-world patients and treatment structures as they are not limited by strict inclusion criteria or unrealistic conditions as applied in prospective clinical trials. The implementation of the German Thorax Registry has enabled the collection and analysis of data on the interdisciplinary care (thoracic surgery, anaesthesiology, intensive care, pain management) of patients undergoing thoracic surgery...
June 2017: Zentralblatt Für Chirurgie
Sheng Xin Zhang, Shao Yong Zheng, Li Ming Zheng
Differential evolution (DE) is recognized as a simple but powerful algorithm in the family of evolutionary algorithms. Over the past two decades, many advanced DE variants with significantly improved performance have been proposed. However, the variants may only achieve the best performance on a certain type of functions. Moreover, a specific optimizer may not always be suitable for the whole optimization process. To overcome these weaknesses, this paper proposes a multiple variants coordination (MVC) framework with two mechanisms, namely, the multiple variants adaptive selecting mechanism and the multiple variants adaptive solutions preserving mechanisms (MV-APM)...
June 19, 2017: IEEE Transactions on Cybernetics
Liliana Ironi, Ettore Lanzarone
Computational and mathematical models have significantly contributed to the rapid progress in the study of gene regulatory networks (GRN), but researchers still lack a reliable model-based framework for computer-aided analysis and design. Such tool should both reveal the relation between network structure and dynamics and find parameter values and/or constraints that enable the simulated dynamics to reproduce specific behaviors. This paper addresses these issues and proposes a computational framework that facilitates network analysis or design...
June 19, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Shaoliang Peng, Shunyun Yang, Wenhe Su, Xiaoyu Zhang, Tenglilang Zhang, Weiguo Liu, Xingming Zhao
Molecular Dynamics (MD) is the simulation of the dynamic behavior of atoms and molecules. As the most popular software for molecular dynamics, GROMACS cannot work on large-scale data because of limit computing resources. In this paper, we propose a CPU and Intel® Xeon Phi Many Integrated Core (MIC) collaborated parallel framework to accelerate GROMACS using the offload mode on a MIC coprocessor, with which the performance of GROMACS is improved significantly, especially with the utility of Tianhe-2 supercomputer...
June 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Hong Tao, Chenping Hou, Feiping Nie, Jubo Zhu, Dongyun Yi
With the advent of multi-view data, multi-view learning has become an important research direction in machine learning and image processing. Considering the difficulty of obtaining labeled data in many machine learning applications, we focus on the multi-view semi-supervised classification problem. In this paper, we propose an algorithm named Multi-View Semi-Supervised Classification via Adaptive Regression (MVAR) to address this problem. Specifically, regression based loss functions with ℓ2,1 matrix norm are adopted for each view and the final objective function is formulated as the linear weighted combination of all the loss functions...
June 19, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Csaba Benedek
In this paper we introduce a probabilistic approach for extracting complex hierarchical object structures from digital images used by various vision applications. The proposed framework extends conventional Marked Point Process (MPP) models by (i) admitting object-subobject ensembles in parent-child relationships and (ii) allowing corresponding objects to form coherent object groups, by a Bayesian segmentation of the population. Different from earlier, highly domain specific attempts on MPP generalization, the proposed model is defined at an abstract level, providing clear interfaces for applications in various domains...
June 15, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Tao Wang, Haibin Ling
Matching-based algorithms have been commonly used in planar object tracking. They often model a planar object as a set of keypoints, and then find correspondences between keypoint sets via descriptor matching. In previous work, unary constraints on appearances or locations are usually used to guide the matching. However, these approaches rarely utilize structure information of the object, and are thus suffering from various perturbation factors. In this paper, we proposed a graph-based tracker, named Gracker, which is able to fully explore the structure information of the object to enhance tracking performance...
June 16, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
Austin M Faught, Scott E Davidson, Jonas Fontenot, Stephen F Kry, Carol Etzel, Geoffrey S Ibbott, David S Followill
PURPOSE: The Imaging and Radiation Oncology Core Houston (IROC-H) (formerly the Radiological Physics Center) has reported varying levels of agreement in their anthropomorphic phantom audits. There is reason to believe one source of error in this observed disagreement is the accuracy of the dose calculation algorithms and heterogeneity corrections used. To audit this component of the radiotherapy treatment process an independent dose calculation tool is needed. METHODS: Monte Carlo multiple source models for Elekta 6MV and 10MV therapeutic x-ray beams were commissioned based on measurement of central axis depth dose data for a 10 x 10 cm(2) field size and dose profiles for a 40 x 40 cm(2) field size...
June 22, 2017: Medical Physics
Gregory Shaun Watson, David W Green, Bronwen W Cribb, Christopher Leslie Brown, Christopher Merritt, Mark James Tobin, Jitraporn Vongsvivut, Ming-Xia Sun, Alping Liang, Jolanta Anna Watson
Nature has produced many intriguing and spectacular surfaces at the micro and nanoscales. These small surface decorations act for a singular or, in most cases, a range of functions. The minute landscape found on the lotus leaf is one such example, displaying anti-wetting behaviour and low adhesion with foreign particulate matter. Indeed the lotus leaf has often been considered the 'benchmark' for such properties. One could expect that there are animal counterparts of this self-drying and self-cleaning surface system...
June 22, 2017: ACS Applied Materials & Interfaces
Laura E Ritchey, Zhao Su, Yin Tang, David C Tack, Sarah M Assmann, Philip C Bevilacqua
RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage...
June 16, 2017: Nucleic Acids Research
Ruibang Luo, Michael C Schatz, Steven L Salzberg
16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy for calling indels as compared to the GATK HaplotypeCaller. 16GT is available at
June 15, 2017: GigaScience
Shweta Purawat, Pek U Ieong, Robert D Malmstrom, Garrett J Chan, Alan K Yeung, Ross C Walker, Ilkay Altintas, Rommie E Amaro
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine...
June 20, 2017: Biophysical Journal
Riccardo Spezia, Stefan Knecht, Benedetta Mennucci
Carotenoids can play multiple roles in biological photoreceptors thanks to their rich photophysics. In the present work, we have investigated six of the most common carbonyl containing carotenoids: echinenone, canthaxanthin, astaxanthin, fucoxanthin, capsanthin and capsorubin. Their excitation properties are investigated by means of a hybrid density functional theory (DFT) and multireference configuration interaction (MRCI) approach to elucidate the role of the carbonyl group: the bright transition is of ππ* character, as expected, but the presence of a C[double bond, length as m-dash]O moiety reduces the energy of nπ* transitions which may become closer to the ππ* transition, in particular as the conjugation chain decreases...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
Woon Yong Sohn, Sana Habka, Eric Gloaguen, Michel Mons
The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, was assessed by the comparison of protein structures with relevant isolated model peptides. Gas phase laser spectroscopy, combined with relevant quantum chemistry methods, was used to characterize the γ- and β-turn structures in these model peptides. A conformer-selective NH stretch infrared study provided evidence for the formation in vacuo of two types of short-range H-bonded motifs, labelled ε-6(δ) and δ-(δ)7/π(H), bridging the His side chain (in its gauche+ rotamer) to the neighbouring NH(i) and CO(i) sites of the backbone; each side chain-backbone motif was found to be specific of the tautomer (ε or δ) adopted by the His side chain in its neutral form...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
Stephanie Schiffer, Karsten Liber
Elevated vanadium (V) concentrations in oil sands coke, which is produced and stored on the site of some major Athabasca Oil Sands companies, could pose a risk to aquatic ecosystems in northern Alberta, Canada, depending on its future storage and utilization. In the present study, V toxicity was determined in reconstituted Athabasca River water to various freshwater organisms, including 2 midge species (Chironomus dilutus and Chironomus riparius; 4-d and 30- to 40-d exposures) and 2 freshwater fish species (Oncorhynchus mykiss and Pimephales promelas; 4-d and 28-d exposures) to facilitate estimation of water quality benchmarks...
June 21, 2017: Environmental Toxicology and Chemistry
J C Buchan, W H Dean, A Foster, M J Burton
PURPOSE: The quality of cataract surgery delivered in sub-Saharan Africa (SSA) is a significant constraint to achieving the elimination of avoidable blindness. No published reports from routine SSA cataract services attain the WHO benchmarks for visual outcomes; poor outcomes (<6/60) often comprise 20% in published case series. This Delphi exercise aimed to identify and prioritise potential interventions for improving the quality of cataract surgery in SSA to guide research and eye health programme development...
June 20, 2017: International Ophthalmology
Harry S Geggel
PURPOSE: To determine the best method to minimize postoperative hyperopia and achieve mild myopia in patients requiring low-powered (<6.00 D) MN60MA intraocular lenses (IOLs). METHODS: This retrospective non-comparative case series consists of 32 eyes (20 patients). Postoperative spherical equivalent (SE) refractions were compared using four methods: standard formulas with varying target refractions (Haigis -1.00 D, Hoffer Q -1.75 D, Holladay 1 -1.50 D and SRK/T -1...
June 20, 2017: International Ophthalmology
Xingwang Huang, Xuewen Zeng, Rui Han
Binary bat algorithm (BBA) is a binary version of the bat algorithm (BA). It has been proven that BBA is competitive compared to other binary heuristic algorithms. Since the update processes of velocity in the algorithm are consistent with BA, in some cases, this algorithm also faces the premature convergence problem. This paper proposes an improved binary bat algorithm (IBBA) to solve this problem. To evaluate the performance of IBBA, standard benchmark functions and zero-one knapsack problems have been employed...
2017: Computational Intelligence and Neuroscience
Marc G Chevrette, Fabian Aicheler, Oliver Kohlbacher, Cameron R Currie, Marnix H Medema
Summary: Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use...
June 19, 2017: Bioinformatics
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