Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

The EC2KEGG output for the RV1423 analysis sorted in ascending order by the FDR value. (XLSX 58 kb

A cascade of classifiers for extracting medication information from discharge summaries

<p>Abstract</p> <p>Background</p> <p>Extracting medication information from clinical records has many potential applications, and recently published research, systems, and competitions reflect an interest therein. Much of the early extraction work involved rules and lexicons, but more recently machine learning has been applied to the task.</p> <p>Methods</p> <p>We present a hybrid system consisting of two parts. The first part, field detection, uses a cascade of statistical classifiers to identify medication-related named entities. The second part uses simple heuristics to link those entities into medication events.</p> <p>Results</p> <p>The system achieved performance that is comparable to other approaches to the same task. This performance is further improved by adding features that reference external medication name lists.</p> <p>Conclusions</p> <p>This study demonstrates that our hybrid approach outperforms purely statistical or rule-based systems. The study also shows that a cascade of classifiers works better than a single classifier in extracting medication information. The system is available as is upon request from the first author.</p

필리핀 클락그린시티 프로젝트 벤치마크로서 한국 송도 유-시티(U-City) 모델의 정책 이동성 연구

학위논문 (석사)-- 서울대학교 환경대학원 : 환경계획학과(도시및지역계획전공), 2016. 8. 김경민.대한민국은 한국 전쟁의 폐허 속에서 오늘날 세계에서 가장 발전한 나라 중 하나로 변화하였다. 이러한 변화는 전 세계의 많은 정책 입안자들로부터 찬사를 받아왔다. 이들 정책 입안자들은 한국의 과거 경험과 교훈, 최선의 방안 등을 통해서 자국이 직면한 문제점을 해결하기 위한 잠재적 해법을 이끌어내기 위해 한국을 찾는다. 동시에 한국 정책 입안자들은 개발도상국들을 원조하는 일환으로 한국적 경험을 패키지화하고 공유하고자 한다. 이는 한국이 성공을 다른 곳으로 복제하기를 원하는 과정으로 볼 수 있다. 본 연구는 필리핀 뉴(新)클락그린시티 프로젝트의 모델로서 송도국제지구의 적용을 살펴보고자 한다. 이는 한국식 U-City를 필리핀의 첫 녹색, 지능, 글로벌 도시 건설에 적용하는 예이기도 하다. 심층 인터뷰, 문헌 조사, 참여자 관찰을 통해, 정책 입안자들을 관찰을 통해, 뉴클락시티 프로젝트에 대한 도시계획 정책 입안자들의 이해와 이와 관련하여 송도국제지구에 대해 어떤 시각을 가지고 있는지를 관찰했다. 정책 이동성 접근은 특별히 민간 부문에서 강력하게 통제된 정책 이동성에도 불구하고, 시간이 지남에 따라 정책 입안자들에 의해 적용된 정책 체득의 변화를 보여준다. 이는 한국, 혹은 서울의 개발 경험을 공유하기를 열망하는 국가와 도시들의 정책 영향을 줄 것이다.South Koreas transition from the destruction of the Korean War to being one of the worlds most advanced economies has gained the admiration of policymakers all over the world. They come to Korea to seek out lessons learned from past experiences, and best practices to potentially derive policy solutions for problems they encounter within their policy contexts. At the same time, Korean policymakers are attempting to package and share the Korean Experience as part of their aid to developing countries. This is a process that hopes on the replication of success from one context to another. This study follows the adoption of Songdo International Business District as a model for the new Clark Green City Project in the Philippines. It is an example of exporting a Korea-Style U-City or ubiquitous city to assist the Philippines in building its first green, intelligent and global city. Through a series of in-depth interviews, document reviews, and participant observations, it has been observed that the line between formal and informal spaces of mobilizing policies can become blurred. Secondly, urban policymakers perspectives on what to draw from mobilized policies evolve in parallel with the understanding of their own project. Third is that policymakers understand new policies based on their own experiences in studying and living in other places. They are then more partial to policies that come from those places or echo their own experiences. These have policy implications for countries like Korea or cities like Seoul who are eager to share their own development experiences.1. Introduction 1 1.1. Research purpose and research questions 2 1.2. Thesis statement 4 1.3. Structure and organization 5 2. Literature review and theoretical background 7 2.1. Microspaces and micropractices 8 2.2. Curation within policy tourism 11 3. Case Description 13 3.1. Songdo International Business District 14 3.2. Clark Green City 17 4. Methodology 21 4.1. Informal interviews and selection process 23 4.2. Archival analysis, site visits, and participant observations 27 5. Findings and discussions 28 5.1. Non-state actors and Songdos beginnings at CGC 29 5.2. Moving on from Songdo 35 5.3. Personal knowledge and experience of policy mobilizing elites 42 6. Discussions 44 6.1. Contributions to the literature 45 6.2. Theoretical implications 46 6.3. Policy implications 48 7. Conclusion 50 7.1. Research summary 50 7.2. Research limitations and opportunities for future research 53 8. Works cited 55 9. Appendices 65 9.1. Stakeholder mapping for interviewee identification 65 9.2. Interview request email (sample) 66 9.3. Photos from the Clark Green City site visit (26 FEB 2016) 67 9.4. NXCities conference schedule (08 MAR 2016) 69 9.5. Songdos current masterplan 72 9.6. Clark Green City 2013 Masterplan 73 9.7. 2015 Conceptual Masterplan for Clark Green City prepared by AECOM 74 9.8. Clark Green City key performance indicators 75 10. Abstract in Korean 76Maste

Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types

<p>Abstract</p> <p>Background</p> <p>Genes conferring antibiotic resistance to groups of bacterial pathogens are cause for considerable concern, as many once-reliable antibiotics continue to see a reduction in efficacy. The recent discovery of the metallo β-lactamase <it>blaNDM-1 </it>gene, which appears to grant antibiotic resistance to a variety of Enterobacteriaceae <it>via </it>a mobile plasmid, is one example of this distressing trend. The following work describes a computational analysis of pathogen-borne MBLs that focuses on the structural aspects of characterized proteins.</p> <p>Results</p> <p>Using both sequence and structural analyses, we examine residues and structural features specific to various pathogen-borne MBL types. This analysis identifies a linker region within MBL-like folds that may act as a discriminating structural feature between these proteins, and specifically resistance-associated acquirable MBLs. Recently released crystal structures of the newly emerged NDM-1 protein were aligned against related MBL structures using a variety of global and local structural alignment methods, and the overall fold conformation is examined for structural conservation. Conservation appears to be present in most areas of the protein, yet is strikingly absent within a linker region, making NDM-1 unique with respect to a linker-based classification scheme. Variability analysis of the NDM-1 crystal structure highlights unique residues in key regions as well as identifying several characteristics shared with other transferable MBLs.</p> <p>Conclusions</p> <p>A discriminating linker region identified in MBL proteins is highlighted and examined in the context of NDM-1 and primarily three other MBL types: IMP-1, VIM-2 and ccrA. The presence of an unusual linker region variant and uncommon amino acid composition at specific structurally important sites may help to explain the unusually broad kinetic profile of NDM-1 and may aid in directing research attention to areas of this protein, and possibly other MBLs, that may be targeted for inactivation or attenuation of enzymatic activity.</p

Challenges of Volcanic Crises on Small Islands States

International audienc

Place- and age-responsive disaster risk reduction for Hong Kong: Collaborative Place Audit and Social Vulnerability Index for elders

published_or_final_versio

Evaluating the accuracy of a functional SNP annotation system

Many common and chronic diseases are influenced at some level by genetic variation. Research done in population genetics, specifically in the area of single nucleotide polymorphisms (SNPs) is critical to understanding human genetic variation. A key element in assessing role of a given SNP is determining if the variation is likely to result in change in function. The SNP Integration Tool (SNPit) is a comprehensive tool that integrates diverse, existing predictors of SNP functionality, providing the user with information for improved association study analysis. To evaluate the SNPit system, we developed an alternative gold standard to measure accuracy using sensitivity and specificity. The results of our evaluation demonstrated that our alternative gold standard produced encouraging results

Remote Data Retrieval for Bioinformatics Applications: An Agent Migration Approach

Some of the approaches have been developed to retrieve data automatically from one or multiple remote biological data sources. However, most of them require researchers to remain online and wait for returned results. The latter not only requires highly available network connection, but also may cause the network overload. Moreover, so far none of the existing approaches has been designed to address the following problems when retrieving the remote data in a mobile network environment: (1) the resources of mobile devices are limited; (2) network connection is relatively of low quality; and (3) mobile users are not always online. To address the aforementioned problems, we integrate an agent migration approach with a multi-agent system to overcome the high latency or limited bandwidth problem by moving their computations to the required resources or services. More importantly, the approach is fit for the mobile computing environments. Presented in this paper are also the system architecture, the migration strategy, as well as the security authentication of agent migration. As a demonstration, the remote data retrieval from GenBank was used to illustrate the feasibility of the proposed approach

The genome sequence of Trypanosoma cruzi, etiologic agent of chagas disease

Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.Fil: El-Sayed, Najib M.. The George Washington University; Estados Unidos. The Institute for Genomic Research; Estados UnidosFil: Myler, Peter J.. University of Washington; Estados Unidos. Seattle Biomedical Research Institute; Estados Unidos. University Of Washington School Of Public Health And Community Medicine; Estados UnidosFil: Bartholomeu, Daniella C.. The Institute for Genomic Research; Estados UnidosFil: Nilsson, Daniel. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Aggarwal, Gautam. Seattle Biomedical Research Institute; Estados UnidosFil: Tran, Anh-Nhi. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Ghedin, Elodie. The George Washington University; Estados Unidos. The Institute for Genomic Research; Estados UnidosFil: Worthey, Elizabeth A.. Seattle Biomedical Research Institute; Estados UnidosFil: Delcher, Arthur L.. The Institute for Genomic Research; Estados UnidosFil: Blandin, Gaëlle. The Institute for Genomic Research; Estados UnidosFil: Westenberger, Scott J.. The Institute for Genomic Research; Estados Unidos. University of California at Los Angeles; Estados UnidosFil: Caler, Elisabet. The Institute for Genomic Research; Estados UnidosFil: Cerqueira, Gustavo C.. The Institute for Genomic Research; Estados Unidos. Universidade Federal de Minas Gerais; BrasilFil: Branche, Carole. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Haas, Brian. The Institute for Genomic Research; Estados UnidosFil: Anupama, Atashi. Seattle Biomedical Research Institute; Estados UnidosFil: Arner, Erik. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Åslund, Lena. Uppsala Universitet; SueciaFil: Attipoe, Philip. Seattle Biomedical Research Institute; Estados UnidosFil: Bontempi, Esteban. Karolinska Huddinge Hospital. Karolinska Institutet; Suecia. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; ArgentinaFil: Bringaud, Frédéric. Centre National de la Recherche Scientifique; FranciaFil: Burton, Peter. University of Glasgow; Reino UnidoFil: Cadag, Eithon. Seattle Biomedical Research Institute; Estados UnidosFil: Campbell, David A.. University of California at Los Angeles; Estados UnidosFil: Carrington, Mark. University of Cambridge; Estados UnidosFil: Crabtree, Jonathan. The Institute for Genomic Research; Estados UnidosFil: Darban, Hamid. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Da Silveira, Jose Franco. Universidade Federal de Sao Paulo; BrasilFil: De Jong, Pieter. Children's Hospital Oakland Research Institute; Estados UnidosFil: Edwards, Kimberly. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Englund, Paul T.. The Johns Hopkins School Of Medicine; Estados UnidosFil: Fazelina, Gholam. Seattle Biomedical Research Institute; Estados UnidosFil: Feldblyum, Tamara. The Institute for Genomic Research; Estados UnidosFil: Ferella, Marcela. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Frasch, Alberto Carlos C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Gull, Keith. University of Oxford; Reino UnidoFil: Horn, David. London School of Hygiene and Tropical Medicine; Reino UnidoFil: Hou, Lihua. The Institute for Genomic Research; Estados UnidosFil: Huang, Yiting. Seattle Biomedical Research Institute; Estados UnidosFil: Kindlund, Ellen. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Klingbeil, Michele. University Of Massachusetts; Estados UnidosFil: Kluge, Sindy. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Koo, Hean. The Institute for Genomic Research; Estados UnidosFil: Lacerda, Daniela. Fundación Oswaldo Cruz; Brasil. The Institute for Genomic Research; Estados UnidosFil: Levin, Mariano Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Lorenzi, Hernan. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Louie, Tin. Seattle Biomedical Research Institute; Estados UnidosFil: Machado, Carlos Renato. Universidade Federal de Minas Gerais; BrasilFil: McCulloch, Richard. University of Glasgow; Reino UnidoFil: McKenna, Alan. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Mizuno, Yumi. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Mottram, Jeremy C.. University of Glasgow; Reino UnidoFil: Nelson, Siri. Seattle Biomedical Research Institute; Estados UnidosFil: Ochaya, Stephen. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Osoegawa, Kazutoyo. Children's Hospital Oakland Research Institute; Estados UnidosFil: Pai, Grace. The Institute for Genomic Research; Estados UnidosFil: Parsons, Marilyn. Seattle Biomedical Research Institute; Estados Unidos. University Of Washington School Of Public Health And Community Medicine; Estados UnidosFil: Pentony, Martin. Seattle Biomedical Research Institute; Estados UnidosFil: Pettersson, Ulf. Uppsala Universitet; SueciaFil: Pop, Mihai. The Institute for Genomic Research; Estados UnidosFil: Ramirez, Jose Luis. Universidad Central de Venezuela, Facultad de Ciencias; VenezuelaFil: Rinta, Joel. Seattle Biomedical Research Institute; Estados UnidosFil: Robertson, Laura. Seattle Biomedical Research Institute; Estados UnidosFil: Salzberg, Steven L.. The Institute for Genomic Research; Estados UnidosFil: Sanchez, Daniel Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Seyler, Amber. Seattle Biomedical Research Institute; Estados UnidosFil: Sharma, Reuben. University of Cambridge; Estados UnidosFil: Shetty, Jyoti. The Institute for Genomic Research; Estados UnidosFil: Simpson, Anjana J.. The Institute for Genomic Research; Estados UnidosFil: Sisk, Ellen. Seattle Biomedical Research Institute; Estados UnidosFil: Tammi, Martti T.. Karolinska Huddinge Hospital. Karolinska Institutet; Suecia. National University Of Singapore; SingapurFil: Tarleton, Rick. University of Georgia; Estados UnidosFil: Teixeira, Santuza. Universidade Federal de Minas Gerais; BrasilFil: Van Aken, Susan. The Institute for Genomic Research; Estados UnidosFil: Vogt, Christy. Seattle Biomedical Research Institute; Estados UnidosFil: Ward, Pauline N.. University of Glasgow; Reino UnidoFil: Wickstead, Bill. Sir William Dunn School Of Pathology; Reino UnidoFil: Wortman, Jennifer. The Institute for Genomic Research; Estados UnidosFil: White, Owen. The Institute for Genomic Research; Estados UnidosFil: Fraser, Claire M.. The Institute for Genomic Research; Estados UnidosFil: Stuart, Kenneth D.. Seattle Biomedical Research Institute; Estados Unidos. University Of Washington School Of Public Health And Community Medicine; Estados UnidosFil: Andersson, Björn. Karolinska Huddinge Hospital. Karolinska Institutet; Sueci