1
|
|
2
|
Wei Y, Ye Z, Cui M, Wei X. COVID-19 prevention and control in China: grid governance. J Public Health (Oxf) 2021; 43:76-81. [PMID: 32978620 PMCID: PMC7543388 DOI: 10.1093/pubmed/fdaa175] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 11/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has spread worldwide and caused negative economic and health effects. China is one of the most seriously affected countries, and it has adopted grid governance measures at the basic level of society, which include city lockdown, household survey and resident quarantine. By the end of April, China had basically brought the pandemic under control within its own borders, and residents' lives and factory production gradually began to return to normal. In referring to the specific cases of different communities, schools, and enterprises in the four cities of Anhui, Beijing, Shenzhen and Zibo, we analyze grid-based governance measures and we summarize the effectiveness and shortcomings of these measures and discuss foundations and future challenges of grid governance. We do so in the expectation (and hope) that the world will gain a comprehensive understanding of China's situation and introduce effective measures that enable the prevention and control of COVID-19.
Collapse
Affiliation(s)
- Yujun Wei
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
- Department of Public Governance, Qianhai Institute for Innovative Research, Shenzhen 518052, China
| | - Zhonghua Ye
- School of Public Policy and Management, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Cui
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaokun Wei
- School of Mathematics and Physics, Anhui Polytechnic University, Wuhu 241000, China
| |
Collapse
|
3
|
Stamatakos G, Dionysiou D, Lunzer A, Belleman R, Kolokotroni E, Georgiadi E, Erdt M, Pukacki J, Rueping S, Giatili S, d'Onofrio A, Sfakianakis S, Marias K, Desmedt C, Tsiknakis M, Graf N. The Technologically Integrated Oncosimulator: Combining Multiscale Cancer Modeling With Information Technology in the In Silico Oncology Context. IEEE J Biomed Health Inform 2014; 18:840-54. [DOI: 10.1109/jbhi.2013.2284276] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Georgios Stamatakos
- Institute of Communication and Computer Systems, National Technical University of Athens, In Silico Oncology Group, 9 Iroon Polytechniou, Zografos, Greece
| | - Dimitra Dionysiou
- Oncology Group, Institute of Communication and Computer Systems, National Technical University of Athens, GR , Greece
| | | | | | - Eleni Kolokotroni
- Oncology Group, Institute of Communication and Computer Systems, National Technical University of Athens, GR , Greece
| | - Eleni Georgiadi
- Oncology Group, Institute of Communication and Computer Systems, National Technical University of Athens, GR , Greece
| | | | - Juliusz Pukacki
- Poznan Supercomputing and Networking Center (PSNC), Poznan, Poland
| | - Stefan Rueping
- Fraunhofer IAIS, Schloss Birlinghoven, St. Augustin, Germany
| | - Stavroula Giatili
- Oncology Group, Institute of Communication and Computer Systems, National Technical University of Athens, GR , Greece
| | | | | | - Kostas Marias
- Foundation for Research and Technology Hellas, Heraklion, Greece
| | | | - Manolis Tsiknakis
- Department of Informatics Engineering, TEI Crete and the Computational Medicine Laboratory, Institute of Computer Science, FORTH , Heraklion, Greece
| | - Norbert Graf
- University Hospital of the Saarland, Pediatric Haematology and Oncology, Homburg, Germany
| |
Collapse
|
4
|
Koumakis L, Moustakis V, Tsiknakis M, Kafetzopoulos D, Potamias G. Supporting genotype-to-phenotype association studies with grid-enabled knowledge discovery workflows. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2009:6958-62. [PMID: 19964717 DOI: 10.1109/iembs.2009.5333882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Web Services and Grid-enabled scientific workflows are of paramount importance for the realization of efficient and secure knowledge discovery scenarios. This paper presents a Grid-enabled Genotype-to-Phenotype discovery scenario (GG2P), which is realized by a respective scientific workflow. GG2P supports the seamless integration of SNP genotype data sources, and the discovery of indicative and predictive genotype-to-phenotype association models - all wrapped around custom-made Web Services. GG2P is applied on a whole-genome SNP-genotyping experiment (breast cancer vs. normal/control phenotypes). A set of about 100 indicative SNPs are induced with very high classification performance. The biological relevance of the findings is supported by the relevant literature.
Collapse
Affiliation(s)
- Lefteris Koumakis
- Institute of Computer Science, FORTH, N. Plastira 100, 70013 Heraklion, Crete, Greece.
| | | | | | | | | |
Collapse
|
5
|
Tsiknakis M, Sfakianakis S, Zacharioudakis G, Umakis L, Kanterakis A, Potamias G, Kafetzopoulos D. A semantically aware platform for the authoring and secure enactment of bioinformatics workflows. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2009:5625-8. [PMID: 19964401 DOI: 10.1109/iembs.2009.5333787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent advances in the field of bioinformatics present a number of challenges in the secure and efficient management and analysis of biological data resources. Workflow technologies aim to assist scientists and domain experts in the design of complex, long running, data and computing intensive experiments that involve many data processing and analysis tasks with the objective of generating new knowledge or formulate new hypothesis. In this paper we present a bioinformatics workflow authoring and execution environment that intends to greatly facilitate the whole lifecycle of such experiments. Emphasis is given on the security and ethical requirements of these scenarios and the corresponding technological response. In addition we present our semantic framework used for supporting specific user-requirements related to the reasoning and inference capabilities of the environment.
Collapse
Affiliation(s)
- M Tsiknakis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.
| | | | | | | | | | | | | |
Collapse
|
6
|
Redolfi A, McClatchey R, Anjum A, Zijdenbos A, Manset D, Barkhof F, Spenger C, Legré Y, Wahlund LO, di San Pietro CB, Frisoni GB. Grid infrastructures for computational neuroscience: the neuGRID example. FUTURE NEUROLOGY 2009. [DOI: 10.2217/fnl.09.53] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neuroscience is increasingly making use of statistical and mathematical tools to extract information from images of biological tissues. Computational neuroimaging tools require substantial computational resources and the increasing availability of large image datasets will further enhance this need. Many efforts have been directed towards creating brain image repositories including the recent US Alzheimer Disease Neuroimaging Initiative. Multisite-distributed computing infrastructures have been launched with the goal of fostering shared resources and facilitating data analysis in the study of neurodegenerative diseases. Currently, some Grid- and non-Grid-based projects are aiming to establish distributed e-infrastructures, interconnecting compatible imaging datasets and to supply neuroscientists with the most advanced information and communication technologies tools to study markers of Alzheimer’s and other brain diseases, but they have so far failed to make a difference in the larger neuroscience community. NeuGRID is an Europeon comission-funded effort arising from the needs of the Alzheimer’s disease imaging community, which will allow the collection and archiving of large amounts of imaging data coupled with Grid-based algorithms and sufficiently powered computational resources. The major benefit will be the faster discovery of new disease markers that will be valuable for earlier diagnosis and development of innovative drugs. The initial setup of neuGRID will feature three nodes equipped with supercomputer capabilities and resources of more than 300 processor cores, 300 GB of RAM memory and approximately 20 TB of physical space. The scope of this article is highlights the new perspectives and potential for the study of the neurodegenerative disorders using the emerging Grid technology.
Collapse
Affiliation(s)
- Alberto Redolfi
- Fatebenefratelli – Centro San Giovanni di Dio, Laboratory of Epidemiology & Neuroimaging, Via Pilastroni 4, I-25125 Brescia, Italy
| | - Richard McClatchey
- University of the West of England, The Centre for Complex Cooperative Systems, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Ashiq Anjum
- University of the West of England, The Centre for Complex Cooperative Systems, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Alex Zijdenbos
- Prodema Medical, Industriestrasse 6B, PO Box 51, 9620 Bronschhofen, Switzerland
| | - David Manset
- maat Gknowledge, Immeuble Alliance Entrée A, 74160 Archamps, France
| | - Frederik Barkhof
- VU University Medical Center, Department of Radiology, De Boelelaan 1118, 1081 HV Amsterdam, The Netherlands
| | - Christian Spenger
- Prodema Medical, Industriestrasse 6B, PO Box 51, 9620 Bronschhofen, Switzerland
| | - Yannik Legré
- HealthGrid, 36 rue Charles de Montesquieu, F-63430 Pont-du-Château, France
| | - Lars-Olof Wahlund
- Karolinska Institutet, Stockholm, Department of Neurobiology, Caring Sciences & Society, Division of Clinical Geriatrics Novum 5th floor, 141 86 Stockholm, Sweden
| | - Chiara Barattieri di San Pietro
- Fatebenefratelli – Centro San Giovanni di Dio, Laboratory of Epidemiology & Neuroimaging, Via Pilastroni 4, I-25125 Brescia, Italy
| | - Giovanni B Frisoni
- Fatebenefratelli – Centro San Giovanni di Dio, Laboratory of Epidemiology & Neuroimaging, Via Pilastroni 4, I-25125 Brescia, Italy
| |
Collapse
|
7
|
Small SL, Wilde M, Kenny S, Andric M, Hasson U. Database-managed grid-enabled analysis of neuroimaging data: the CNARI framework. Int J Psychophysiol 2009; 73:62-72. [PMID: 19233234 DOI: 10.1016/j.ijpsycho.2009.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 01/13/2009] [Accepted: 01/13/2009] [Indexed: 11/16/2022]
Abstract
Functional magnetic resonance imaging (fMRI) has led to an enormous growth in the study of cognitive neuroanatomy, and combined with advances in high-field electrophysiology (and other methods), has led to a fast-growing field of human neuroscience. Technological advances in both hardware and software will lead to an ever more promising future for fMRI. We have developed a new computational framework that facilitates fMRI experimentation and analysis, and which has led to some rethinking of the nature of experimental design and analysis. The Computational Neuroscience Applications Research Infrastructure (CNARI) incorporates novel methods for maintaining, serving, and analyzing massive amounts of fMRI data. By using CNARI, it is possible to perform naturalistic, network-based, statistically valid experiments in systems neuroscience on a very large scale, with ease of data manipulation and analysis, within reasonable computational time scales. In this article, we describe this infrastructure and then illustrate its use on a number of actual examples in both cognitive neuroscience and neurological research. We believe that these advanced computational approaches will fundamentally change the future shape of cognitive brain imaging with fMRI.
Collapse
Affiliation(s)
- Steven L Small
- Department of Neurology, The University of Chicago, United States.
| | | | | | | | | |
Collapse
|
8
|
|
9
|
Abstract
The increased generation of data in the pharmaceutical R&D process has failed to generate the expected returns in terms of enhanced productivity and pipelines. The inability of existing integration strategies to organize and apply the available knowledge to the range of real scientific and business issues is impacting on not only productivity but also transparency of information in crucial safety and regulatory applications. The new range of semantic technologies based on ontologies enables the proper integration of knowledge in a way that is reusable by several applications across businesses, from discovery to corporate affairs.
Collapse
|
10
|
Affiliation(s)
- John S Mattick
- ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.
| | | |
Collapse
|
11
|
Van Horn JD, Wolfe J, Agnoli A, Woodward J, Schmitt M, Dobson J, Schumacher S, Vance B. Neuroimaging databases as a resource for scientific discovery. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2005; 66:55-87. [PMID: 16387200 DOI: 10.1016/s0074-7742(05)66002-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
12
|
Van Horn JD, Grafton ST, Rockmore D, Gazzaniga MS. Sharing neuroimaging studies of human cognition. Nat Neurosci 2004; 7:473-81. [PMID: 15114361 DOI: 10.1038/nn1231] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
After more than a decade of collecting large neuroimaging datasets, neuroscientists are now working to archive these studies in publicly accessible databases. In particular, the fMRI Data Center (fMRIDC), a high-performance computing center managed by computer and brain scientists, seeks to catalogue and openly disseminate the data from published fMRI studies to the community. This repository enables experimental validation and allows researchers to combine and examine patterns of brain activity beyond that of any single study. As with some biological databases, early scientific, technical and sociological concerns hindered initial acceptance of the fMRIDC. However, with the continued growth of this and other neuroscience archives, researchers are recognizing the potential of such resources for identifying new knowledge about cognitive and neural activity. Thus, the field of neuroimaging is following the lead of biology and chemistry, mining its accumulating body of knowledge and moving toward a 'discovery science' of brain function.
Collapse
Affiliation(s)
- John Darrell Van Horn
- Center for Cognitive Neuroscience, Dartmouth College, Hanover, New Hampshire 03755, USA.
| | | | | | | |
Collapse
|
13
|
Tepas JJ. The national pediatric trauma registry: a legacy of commitment to control of childhood injury. Semin Pediatr Surg 2004; 13:126-32. [PMID: 15362283 DOI: 10.1053/j.sempedsurg.2004.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The National Pediatric Trauma Registry represents almost 15 years of effective collaboration among hospitals committed to improving care for the injured child. Its design of providing a "physiologic snapshot" of the injured child on presentation has supported numerous studies that have helped define the epidemiology of childhood injury and refine principles of management. Global analysis of the 103,434 records included in this database suggest that mortality is significantly higher in the very young, that vehicular injury remains a major pediatric public health challenge, and that shock is just as devastating in the child as the adult. Based on this foundation of collaborative commitment, future versions of a pediatric trauma database must harness the emerging internet technology that combines information accrual with human thought, and must extend this effort to include all the children of our world.
Collapse
Affiliation(s)
- Joseph J Tepas
- Department of Surgery and Pediatrics, University of Florida College of Medicine, University of Florida Health Science Center Jacksonville, 655 West 8th Street, Jacksonville, FL 32209, USA
| |
Collapse
|
14
|
Fleming K, Müller A, MacCallum RM, Sternberg MJE. 3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. Nucleic Acids Res 2004; 32:D245-50. [PMID: 14681404 PMCID: PMC308798 DOI: 10.1093/nar/gkh064] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The 3D-GENOMICS database (http://www.sbg.bio. ic.ac.uk/3dgenomics/) provides structural annotations for proteins from sequenced genomes. In August 2003 the database included data for 93 proteomes. The annotations stored in the database include homologous sequences from various sequence databases, domains from SCOP and Pfam, patterns from Prosite and other predicted sequence features such as transmembrane regions and coiled coils. In addition to annotations at the sequence level, several precomputed cross- proteome comparative analyses are available based on SCOP domain superfamily composition. Annotations are available to the user via a web interface to the database. Multiple points of entry are available so that a user is able to: (i) directly access annotations for a single protein sequence via keywords or accession codes, (ii) examine a sequence of interest chosen from a summary of annotations for a particular proteome, or (iii) access precomputed frequency-based cross-proteome comparative analyses.
Collapse
Affiliation(s)
- Keiran Fleming
- Department of Biological Sciences and Centre for Bioinformatics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | | | | | |
Collapse
|