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Determining crystal structures through crowdsourcing and coursework (vol 7, 12549, 2016)

NATURE COMMUNICATIONS 2016年第1期7卷 1-11页

作者： Horowitz, Scott Koepnick, Brian Martin, Raoul Tymieniecki, Agnes Winburn, Amanda A. Cooper, Seth Flatten, Jeff Rogawski, David S. Koropatkin, Nicole M. Hailu, Tsinatkeab T. Jain, Neha Koldewey, Philipp Ahlstrom, Logan S. Chapman, Matthew R. Sikkema, Andrew P. Skiba, Meredith A. Maloney, Finn P. Beinlich, Felix R. M. Players, Foldit Department of Molecular Cellular and Developmental Biology University of Michigan Ann Arbor Michigan 48109 USA. Howard Hughes Medical Institute University of Michigan Ann Arbor Michigan 48109 USA. Department of Biochemistry University of Washington Seattle Washington 98195 USA. Biophysics Graduate Group University of California Berkeley California 94720 USA. Center for Complex Networks and Systems Research Department of Informatics Indiana University Bloomington Indiana 47408 USA. Program in Cognitive Science Indiana University 1900 E 10th Street Bloomington Indiana 47406 USA. Northeastern University College of Computer and Information Science Boston Massachusetts 02115 USA. Department of Computer Science and Engineering Center for Game Science University of Washington Seattle Washington 98195 USA. Department of Pathology University of Michigan Ann Arbor Michigan 48109 USA. Department of Microbiology and Immunology University of Michigan Ann Arbor Michigan 48109 USA. ProQR Therapeutics NV. 2333 Leiden The Netherlands. Department of Biological Chemistry and Life Sciences Institute University of Michigan Ann Arbor Michigan 48109 USA. Chemical Biology Doctoral Program University of Michigan Ann Arbor Michigan 48109 USA. Institute of Complex Systems Cellular Biophysics (ICS-4) Forschungszentrum D-52428 Jülich Germany. Institute for Protein Design University of Washington Seattle Washington 98195 USA. Howard Hughes Medical Institute University of Washington Seattle Washington 98195 USA. Department of Computer and Information Science University of Massachusetts Dartmouth Dartmouth Massachusetts 02747 USA.

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

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Incorporating OMA Lightweight M2M protocol in IoT/M2M standard architecture

Incorporating OMA Lightweight M2M protocol in IoT/M2M standa...

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IEEE World Forum on Internet of Things (WF-IoT)

作者： Christian Antonia Lusiarta Putera Fuchun Joseph Lin EECS International Graduate Program National Chiao Tung University Hsinchu Taiwan Department of Computer Science National Chiao Tung University Hsinchu Taiwan

ISBN: (纸本)9781509003679

IoT/M2M aims to integrate a large number of heterogeneous devices which are constantly required to be discovered and reconfigured in order to bring them up to date or to recover from their failures. A device management protocol enables the abstraction of an IoT/M2M device as a managed object to ease the management of the device. The M2M standards, such as ETSI and OneM2M, have adopted the use of OMA Lightweight M2M Device Management Protocol to manage and configure the IoT/M2M devices from the IoT/M2M platform. However, how to incorporate and do resource mapping of OMA LWM2M in the IoT/M2M standard architecture is not well addressed by those standards. In this paper, we present and analyze how to incorporate the OMA LWM2M in the IoT/M2M standard architecture. Through this seamless incorporation, an IoT/M2M application is enabled to manage IoT/M2M devices from the IoT/M2M service platform at a higher level of abstraction.

关键词： Protocols Servers Standards computer architecture Performance evaluation Authorization

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Optimization Process of Glycerol Esterification Using Real Time Adaptive Control

Optimization Process of Glycerol Esterification Using Real T...

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International Conference on Advanced computer science and Information Systems

作者： Iwan Aang Soenandi Ani Suryani Taufik Djatna Irzaman Post Graduate Program of Agro-industrial Technology Bogor Agricultural University Dramaga Indonesia Lecturer Faculty of Engineering and Computer Science Krida Wacana Christian University Post Graduate Program of Agro-industrial Technology Bogor Agricultural University. Dramaga Indonesia Post Graduate Program of Agro-industrial Technology and Graduate Program of Computer Science Bogor Agricultural University. Dramaga Indonesia Department of Physics Faculty Mathematics and Natural Sciences Bogor Agricultural University. Dramaga Indonesia

ISBN: (纸本)9781509003648

The synthesis reaction used in esterification needs high energy consumption and a precise processing time to get the best yield of target. In this study, a model was formulated to optimize glycerol esterification process by minimizing the time needed for the process and maximizing the yield of Mono-glycerides. This optimization has gained importance for boosting the esterification industry and improving the production efficiency. Optimization through adaptive monitoring and control has provided significant advances in the process efficiency, a lower energy consumption and a better product quality. This paper presents the optimization with a computational algorithm in real time and adaptive control (RTAC), as compared to the conventional (traditional) methods to monitor and control of glycerol esterification processes. The identification of esterification status based on temperature and time are evaluated to strengthen the optimization. An adaptive method as feature selection to select wavelength IR sensors at specified intervals was carried out with Relief algorithm and Adaptive Pillar K-means clustering method to set the parameter control was proposed in this paper. Many combinations were evaluated from real time condition process, to achieve the best optimization results. The experimental results demonstrate that real time adaptive control can be achieved by using three clusters, which are heating up, stabilizing and finishing. In RTAC, each cluster has its own parameter to set the control point by the servo motor that was attached to magnetic stirrer-heater. By using optimization parameter for each cluster, esterification process time can be shortened by 15-20 minutes with a higher yield (7% or more), lower range stirrer rotation (300rpm-450 rpm) and a lower final temperature of 200℃ - 210℃.

关键词： Optimization Real Time Adaptive Control Glycerol Esterification

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FragGeneScan-plus for scalable high-throughput short-read open reading frame prediction

FragGeneScan-plus for scalable high-throughput short-read op...

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IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology (CIBCB)

作者： Dongjae Kim Aria S. Hahn Shang-Ju Wu Niels W. Hanson Kishori M. Konwar Steven J. Hallam Department of Computer Science University of British Columbia Vancouver Canada Department of Microbiology University of British Columbia Vancouver Canada Graduate Program in Bioinformatics University of British Columbia Vancouver Canada

A fundamental step in the analysis of environmental sequence information is the prediction of potential genes or open reading frames (ORFs) encoding the metabolic potential of individual cells and entire microbial communities. FragGeneScan, a software designed to predict intact and incomplete ORFs on short sequencing reads combines codon usage bias, sequencing error models and start/stop codon patterns in a hidden Markov model to find the most likely path of hidden states from a given input sequence, provides a promising route for gene recovery in environmental datasets with incomplete assemblies. However, the current implementation of FragGeneScan does not scale efficiently with increasing input data size. Thus, FragGeneScan cannot be applied to contemporary environmental datasets that can exceed 100s of Gb. Here, we present FragGeneScan-Plus, an improved implementation of the FragGeneScan gene prediction model that leverages algorithmic thread synchronization and efficient in-memory data management to utilize multiple CPU cores without blocking I/O operations. FragGeneScan-Plus can process data approximately 5-times faster than FragGeneScan using a single core and approximately 50-times faster using eight hyper-threaded cores when benchmarked against simulated and real world environmental datasets.

关键词： Instruction sets Buffer storage Hidden Markov models Synchronization Predictive models Prediction algorithms Soil

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Assembly independent functional annotation of short-read data using SOFA: Short-ORF functional annotation

Assembly independent functional annotation of short-read dat...

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IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology (CIBCB)

作者： Aria S. Hahn Niels W. Hanson Dongjae Kim Kishori M. Konwar Steven J. Hallam Department of Microbiology University of British Columbia Vancouver Canada Graduate Program in Bioinformatics University of British Columbia Vancouver Canada Department of Computer Science University of British Columbia Vancouver Canada

Accurate description of the microbial communities driving matter and energy transformations in complex ecosystems such as soils cannot yet be effectively accomplished using assembly-based approaches despite the rise of next generation sequencing technologies. Here we present SOFA, an open source pipeline enabling comparative functional annotation of unassembled short-read data. The pipeline attempts to merge mate pairs in fastq files, predicts open reading frames (ORFs) on merged and unmerged reads as small as 70 bps, and completes an additional step, we term `deduplication'. Deduplication prevents the double counting of ORFs predicted from unmerged paired-end reads by checking for homologous annotations that span the same ORF, allowing for quantitatively accurate predictions. The effectiveness of SOFA is validated with both simulated and bone fide soil metagenomes, and empirical results are compared to existing strategies for obtaining accurate ORF counts, and an analytical model of read duplication. SOFA enables downstream processing stages within the existing MetaPathways pipeline, and is available for download as a stand alone application at https://*** under the MIT license.

关键词： Bioinformatics Pipelines Genomics Databases Soil Proteins Assembly

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Intrinsic Raman signatures of pristine hybrid perovskite CH3NH3PbI3 and its multiple stages of structure transformation

Intrinsic Raman signatures of pristine hybrid perovskite CH3...

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2016 IEEE 43rd Photovoltaic Specialists Conference (PVSC)

作者： Qiong Chen Henan Liu Hui-Seon Kim Yucheng Liu Mengjin Yang Naili Yue Gang Ren Kai Zhu Shengzhong Frank Liu Nam-Gyu Park Yong Zhang Department of Electrical and Computer Engineering The University of North Carolina at Charlotte Charlotte NC USA Optical Science and Engineering graduate program The University of North Carolina at Charlotte Charlotte NC USA Department of Energy Science Sungkyunkwan University Suwon South Korea National Ministry of Education Shaanxi Normal University Xi'an China Chemical and Materials Science Center National Renewable Energy Laboratory CO USA Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA USA Key Laboratory of Applied Surface and Colloid Chemistry National Ministry of Education Shaanxi Normal University Xi'an Shaanxi CN School of Chemical Engineering Sungkyunkwan University Suwon South Korea University of North Carolina at Charlotte Charlotte NC US

By performing spatially resolved Raman and photoluminescence spectroscopy with different illumination conditions, we have achieved a unified understanding towards the spectroscopy signatures of the organic-inorganic hybrid perovskite, transforming from the pristine state (CH 3 NH 3 PbI 3 or MAPbI 3 ) to fully degraded state (i.e., PbI 2 ), for samples with varying crystalline domain size from mesoscopic scale to macroscopic size, synthesized by three different techniques.

关键词： Measurement by laser beam Density measurement Chemistry Lighting Optical films Degradation Spectroscopy

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Abstracts and Workshops 7th National Spinal Cord Injury Conference November 9-11, 2017 Fallsview Casino Resort Niagara Falls, Ontario, Canada Abstracts

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JOURNAL OF SPINAL CORD MEDICINE 2017年第6期40卷 813-869页

作者： [Anonymous] a NET Team Toronto Rehabilitation Institute - University Health Network Toronto ON Canada. fo Neural Engineering and Therapeutic Team Lyndhurst Centre Toronto Rehabilitation Institute - University Health Network Toronto ON Canada. c Rick Hansen Institute Vancouver BC Canada. ev Rick Hansen Institute Vancouver BC Canada. fc Stan Cassidy Hospital University of New Brunswick Fredericton NB Canada. fd Dalhousie University Halifax NS Canada. e University of Saskatchewan Saskatoon SK Canada. aa University of Calgary Calgary AB Canada. y Dalhousie University Halifax NS Canada. fa Health Sciences Centre Winnipeg MB Canada. fb University of Manitoba Winnipeg MB Canada. h University of Alberta Edmonton AB Canada. i Universite Laval Quebe c City QC Canada. bd Rick Hansen Institute Vancouver BC Canada. fz Clinician Investigator Lyndhurst Centre Toronto Rehabilitation Institute University Health Network and Assistant Professor Department of Medicine Division of Physical Medicine and Rehabilitation University of Toronto. v University of Toront o Toronto ON Canada. n Institute of Biomaterials and Biomedical Engineering University of Toronto Toronto ON Canada. o Toronto Rehabilitation Institute - University Health Network Toronto ON Canada. ga Clinical Scientist Lyndhurst Centre Toronto Rehabilitation Institute University Health Network and Assistant Professor Department of Physical Therapy University of Toronto. dx Department of Electrical and Computer Engineering University of Toronto Toronto ON Canada. fm Lawson Health Research Institute London ON Canada. r Parkwood Institute London ON Canada. bi Parkwood Institute London ON Canada. s University of British Columbia Vancouver BC Canada. t Simon Fraser University Burnaby BC Canada. u DeltaQuest Foundation Concord MA USA. z Institut national d'excellence en santé et en services sociaux (INESSS) Quebec City QC Ca

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Erratum: An intrinsic mechanism controls reactivation of neural stem cells by spindle matrix proteins

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Nature communications 2017年第1期8卷 1298页

作者： Song Li Chwee Tat Koe Su Ting Tay Angie Lay Keng Tan Shenli Zhang Yingjie Zhang Patrick Tan Wing-Kin Sung Hongyan Wang Neuroscience and Behavioural Disorders Program Duke-NUS Medical School 8 College Road Singapore 169857 Singapore. Cancer and Stem Cell Biology Program Duke-NUS Medical School 8 College Road Singapore 169857 Singapore. NUS Graduate School for Integrative Sciences and Engineering National University of Singapore 28 Medical Drive Singapore 117456 Singapore. Cellular and Molecular Research National Cancer Centre Singapore 169610 Singapore. Cancer Science Institute of Singapore National University of Singapore Singapore 119074 Singapore. Genome Institute of Singapore 60 Biopolis Street Genome 02-01 Singapore 138672 Singapore. Department of Computer Science National University of Singapore Singapore 117417 Singapore. Neuroscience and Behavioural Disorders Program Duke-NUS Medical School 8 College Road Singapore 169857 Singapore. hongyan.wang@duke-nus.edu.sg. NUS Graduate School for Integrative Sciences and Engineering National University of Singapore 28 Medical Drive Singapore 117456 Singapore. hongyan.wang@duke-nus.edu.sg. Department of Physiology Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore. hongyan.wang@duke-nus.edu.sg.

A correction to this article has been published and is linked from the HTML version of this article.

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Customer-oriented diagnosis of memory provisioning for IaaS clouds

Customer-oriented diagnosis of memory provisioning for IaaS ...

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Brazilian Symposium on computer System Engineering, SBESC 2013

作者： Pfitscher, Ricardo J. Pillon, Mauricio A. Obelheiro, Rafael R. Santa Catarina State University Graduate Program in Applied Computing Department of Computer Science Brazil

Infrastructure-as-a-service clouds enable customers to use computing resources in a flexible manner to satisfy their needs, and pay only for the allocated resources. One challenge for IaaS customers is the correct provisioning of their resources. Many users end up underprovisioning, hurting application performance, or overprovisioning, paying for resources that are not really necessary. Memory is an essential resource for any computing system, and is frequently a performance-limiting factor in cloud environments. In this work, we propose a model that enables cloud customers to determine whether the memory allocated to their virtual machines is correctly provisioned, underprovisioned, or overprovisioned. The model uses two metrics collected inside a VM, resident and committed memory, and defines thresholds for these metrics that characterize each provisioning level. Experimental results with Linux guests on Xen, running four benchmarks with different workloads and varying memory capacity, show that the model was able to accurately diagnose memory provisioning in 98% of the scenarios evaluated. Copyright 2013 by the Authors.

关键词： Customer satisfaction

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Optimal resource allocation for survivable virtual infrastructures

Optimal resource allocation for survivable virtual infrastru...

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10th International Conference on Design of Reliable Communication Networks, DRCN 2014

作者： De S. Cavalcanti, Gustavo A. Obelheiro, Rafael R. Koslovski, Guilherme Graduate Program in Applied Computing Department of Computer Science Santa Catarina State University Brazil

ISBN: (纸本)9781479940097

Virtual infrastructures (VIs) consolidated the dynamic provisioning of computing and communication resources. A VI is a set of virtual machines interconnected by virtual links and switches/routers. Infrastructure providers (InPs) manage the physical substrates in which virtual resources requested by VIs (such as CPU, disk, memory, bandwidth) are reserved and allocated. Resource allocation is a complex problem that needs to satisfy different goals: users expect to run their applications on survivable VIs, while InPs aim to maximize profits, minimize costs and reduce substrate fragmentation. However, there is a dichotomy between minimizing substrate fragmentation, by co-locating VIs, and maximizing VI survivability, by sparsely allocating resources in order to decrease the impact of substrate failures. In this context, this paper discusses VI survivability and its impact on substrate fragmentation. We propose a mixed integer linear programming model to allocate resources considering the joint coordination of fragmentation and survivability. Experimental results suggest that it is possible to enhance VI survivability without significantly impacting substrate fragmentation. © 2014 IEEE.

关键词： Substrates

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