Journal of biomedical discovery and collaboration最新文献

{"title":"Tracking the current rise of chinese pharmaceutical bionanotechnology.","authors":"Tim Lenoir,&nbsp;Patrick Herron","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>THE CONTEXT AND PURPOSE OF THE STUDY: Over the last decade China has emerged as a major producer of scientific publications, currently ranking second behind the US. During that time Chinese strategic policy initiatives have placed indigenous innovation at the heart of its economy while focusing internal R&D investments and the attraction of foreign investment in nanotechnology as one of their four top areas. China's scientific research publication and nanotechnology research publication production has reached a rank of second in the world, behind only the US. Despite these impressive gains, some scholars argue that the quality of Chinese nanotech research is inferior to US research quality due to lower overall times cited rates, suggesting that the US is still the world leader. We combine citation analysis, text mining, mapping, and data visualization to gauge the development and application of nanotechnology in China, particularly in biopharmananotechnology, and to measure the impact of Chinese policy on nanotechnology research production.</p><p><strong>Results, the main findings: </strong>Our text mining-based methods provide results that counter existing claims about Chinese nanotechnology research quality. Due in large part to its strategic innovation policy, China's output of nanotechnology publications is on pace to surpass US production in or around 2012.A closer look at Chinese nanotechnology research literature reveals a large increase in research activity in China's biopharmananotechnology research since the implementation in January, 2006 of China's Medium & Long Term Scientific and Technological Development Plan Guidelines for the period 2006-2020 (\"MLP\").</p><p><strong>Conclusions, brief summary and potential implications: </strong>Since the implementation of the MLP, China has enjoyed a great deal of success producing bionano research findings while attracting a great deal of foreign investment from pharmaceutical corporations setting up advanced drug discovery operations. Given the combination of current scientific production growth as well as economic growth, a relatively low scientific capacity, and the ability of its policy to enhance such trends, China is in some sense already the new world leader in nanotechnology. Further, the Chinese national innovation system may be the new standard by which other national S&T policies should be measured.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"4 ","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2009-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28444264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tracking the Current Rise of Chinese Pharmaceutical Bionanotechnology","authors":"T. Lenoir, Patrick Herron","doi":"10.5210/DISCO.V4I0.2491","DOIUrl":"https://doi.org/10.5210/DISCO.V4I0.2491","url":null,"abstract":"ABSTRACT Background: The Context and Purpose of the Study Over the last decade China has emerged as a major producer of scientific publications, currently ranking second behind the US. During that time Chinese strategic policy initiatives have placed indigenous innovation at the heart of its economy while focusing internal R&D investments and the attraction of foreign investment in nanotechnology as one of their four top areas. China’s scientific research publication and nanotechnology research publication production has reached a rank of second in the world, behind only the US. Despite these impressive gains, some scholars argue that the quality of Chinese nanotech research is inferior to US research quality due to lower overall times cited rates, suggesting that the US is still the world leader. We combine citation analysis, text mining, mapping, and data visualization to gauge the development and application of nanotechnology in China, particularly in biopharmananotechnology, and to measure the impact of Chinese policy on nanotechnology research production. Results, the main findings Our text mining-based methods provide results that counter existing claims about Chinese nanotechnology research quality. Due in large part to its strategic innovation policy, China’s output of nanotechnology publications is on pace to surpass US production in or around 2012.A closer look at Chinese nanotechnology research literature reveals a large increase in research activity in China’s biopharmananotechnology research since the implementation in January, 2006 of China’s Medium & Long Term Scientific and Technological Development Plan Guidelines for the period 2006-2020 (“MLP”). Since the implementation of the MLP, China has enjoyed a great deal of success producing bionano research findings while attracting a great deal of foreign investment from pharmaceutical corporations setting up advanced drug discovery operations. Given the combination of current scientific production growth as well as economic growth, a relatively low scientific capacity, and the ability of its policy to enhance such trends, China is in some sense already the new world leader in nanotechnology. Further, the Chinese national innovation system may be the new standard by which other national S&T policies should be measured.","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"30 1","pages":"8 - 8"},"PeriodicalIF":0.0,"publicationDate":"2009-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70827186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Concepts and synonymy in the UMLS Metathesaurus.","authors":"Gary H Merrill","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This paper advances a detailed exploration of the complex relationships among terms, concepts, and synonymy in the UMLS Metathesaurus, and proposes the study and understanding of the Metathesaurus from a model-theoretic perspective. Initial sections provide the background and motivation for such an approach, and a careful informal treatment of these notions is offered as a context and basis for the formal analysis. What emerges from this is a set of puzzles and confusions in the Metathesaurus and its literature pertaining to synonymy and its relation to terms and concepts. A model theory for a segment of the Metathesaurus is then constructed, and its adequacy relative to the informal treatment is demonstrated. Finally, it is shown how this approach clarifies and addresses the puzzles educed from the informal discussion, and how the model-theoretic perspective may be employed to evaluate some fundamental criticisms of the Metathesaurus. For users of the UMLS, two significant results of this analysis are a rigorous clarification of the different senses of synonymy that appear in treatments of the Metathesaurus and an illustration of the dangers in computing inferences involving ambiguous terms.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"4 ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2009-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28444263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Open Access Publishing – A New Path","authors":"Neil R Smalheiser, Sandra L De Groote, Mary M. Case","doi":"10.5210/DISCO.V4I0.2574","DOIUrl":"https://doi.org/10.5210/DISCO.V4I0.2574","url":null,"abstract":"Editorial The open‐access movement in journal publishing has generally been equated with the author‐pays model, and contrasted with the subscription or reader‐pays model. Yet there is a third possible path that has received scant public attention: For example, at the University of Illinois at Chicago, the Library system is hosting several peer‐reviewed, open‐access journals that do not charge any fees from authors or readers. These include First Monday, a leading information‐science journal, and Journal of Biomedical Discovery and Collaboration, a multi‐disciplinary journal that is indexed in PubMed. Virginia Polytechnic Institute also hosts a variety of free peer‐reviewed open‐access journals (http://scholar.lib.vt.edu/), and many journals produced using Open Journal Systems software fall into this category as well (http://pkp.sfu.ca/ojs‐journals/). The actual costs of supporting online journals are surprisingly modest ‐ for minimal costs one can host servers providing open access journal management software and layout software, resources that can be shared by all journals in the same system. The efforts of editors and peer reviewers are non‐compensated, as is true even in commercial ventures. Copyeditors can be hired to edit articles for spelling, grammar and journal style, but this is optional ‐‐ note that PLOS ONE and most Biomed Central journals charge article fees yet do not provide copyediting services for authors. It is natural for institutional libraries to take a leading position in open‐access publishing, since they bear the brunt of skyrocketing subscription fees under the reader‐pays","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"4 1","pages":"6 - 6"},"PeriodicalIF":0.0,"publicationDate":"2009-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70827279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Open-access publishing - a new path.","authors":"Neil Smalheiser,&nbsp;Sandra L De Groote,&nbsp;Mary M Case","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"4 ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2009-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28249724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Life science research and drug discovery at the turn of the 21st century: the experience of SwissBioGrid.","authors":"Matthijs den Besten,&nbsp;Arthur J Thomas,&nbsp;Ralph Schroeder","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>It is often said that the life sciences are transforming into an information science. As laboratory experiments are starting to yield ever increasing amounts of data and the capacity to deal with those data is catching up, an increasing share of scientific activity is seen to be taking place outside the laboratories, sifting through the data and modelling \"in silico\" the processes observed \"in vitro.\" The transformation of the life sciences and similar developments in other disciplines have inspired a variety of initiatives around the world to create technical infrastructure to support the new scientific practices that are emerging. The e-Science programme in the United Kingdom and the NSF Office for Cyberinfrastructure are examples of these. In Switzerland there have been no such national initiatives. Yet, this has not prevented scientists from exploring the development of similar types of computing infrastructures. In 2004, a group of researchers in Switzerland established a project, SwissBioGrid, to explore whether Grid computing technologies could be successfully deployed within the life sciences. This paper presents their experiences as a case study of how the life sciences are currently operating as an information science and presents the lessons learned about how existing institutional and technical arrangements facilitate or impede this operation.</p><p><strong>Results: </strong>SwissBioGrid gave rise to two pilot projects: one for proteomics data analysis and the other for high-throughput molecular docking (\"virtual screening\") to find new drugs for neglected diseases (specifically, for dengue fever). The proteomics project was an example of a data management problem, applying many different analysis algorithms to Terabyte-sized datasets from mass spectrometry, involving comparisons with many different reference databases; the virtual screening project was more a purely computational problem, modelling the interactions of millions of small molecules with a limited number of protein targets on the coat of the dengue virus. Both present interesting lessons about how scientific practices are changing when they tackle the problems of large-scale data analysis and data management by means of creating a novel technical infrastructure.</p><p><strong>Conclusions: </strong>In the experience of SwissBioGrid, data intensive discovery has a lot to gain from close collaboration with industry and harnessing distributed computing power. Yet the diversity in life science research implies only a limited role for generic infrastructure; and the transience of support means that researchers need to integrate their efforts with others if they want to sustain the benefits of their success, which are otherwise lost.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"4 ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2009-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28239617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"3D medical collaboration technology to enhance emergency healthcare.","authors":"Gregory F Welch, Diane H Sonnenwald, Henry Fuchs, Bruce Cairns, Ketan Mayer-Patel, Hanna M Söderholm, Ruigang Yang, Andrei State, Herman Towles, Adrian Ilie, Manoj K Ampalam, Srinivas Krishnan, Vincent Noel, Michael Noland, James E Manning","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Two-dimensional (2D) videoconferencing has been explored widely in the past 15-20 years to support collaboration in healthcare. Two issues that arise in most evaluations of 2D videoconferencing in telemedicine are the difficulty obtaining optimal camera views and poor depth perception. To address these problems, we are exploring the use of a small array of cameras to reconstruct dynamic three-dimensional (3D) views of a remote environment and of events taking place within. The 3D views could be sent across wired or wireless networks to remote healthcare professionals equipped with fixed displays or with mobile devices such as personal digital assistants (PDAs). The remote professionals' viewpoints could be specified manually or automatically (continuously) via user head or PDA tracking, giving the remote viewers head-slaved or hand-slaved virtual cameras for monoscopic or stereoscopic viewing of the dynamic reconstructions. We call this idea remote 3D medical collaboration. In this article we motivate and explain the vision for 3D medical collaboration technology; we describe the relevant computer vision, computer graphics, display, and networking research; we present a proof-of-concept prototype system; and we present evaluation results supporting the general hypothesis that 3D remote medical collaboration technology could offer benefits over conventional 2D videoconferencing in emergency healthcare.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"4 ","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2009-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28240249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The continuity of scientific discovery and its communication: the example of Michael Faraday.","authors":"Alan G Gross","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This paper documents the cognitive strategies that led to Faraday's first significant scientific discovery. For Faraday, discovery is essentially a matter seeing as, of substituting for the eye all possess the eye of analysis all scientists must develop. In the process of making his first significant discovery, Faraday learns to dismiss the magnetic attractions and repulsions he and others had observed; by means of systematic variations in his experimental set-up, he learns to see these motions as circular: it is the first indication that an electro-magnetic field exists. In communicating his discoveries, Faraday, of course, takes into consideration his various audiences' varying needs and their differences in scientific competence; but whatever his audience, Faraday learns to convey what it feels like to do science, to shift from seeing to seeing as, from sight to insight.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"4 ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2009-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28096914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Supporting cognition in systems biology analysis: findings on users' processes and design implications.","authors":"Barbara Mirel","doi":"10.1186/1747-5333-4-2","DOIUrl":"https://doi.org/10.1186/1747-5333-4-2","url":null,"abstract":"<p><strong>Background: </strong>Current usability studies of bioinformatics tools suggest that tools for exploratory analysis support some tasks related to finding relationships of interest but not the deep causal insights necessary for formulating plausible and credible hypotheses. To better understand design requirements for gaining these causal insights in systems biology analyses a longitudinal field study of 15 biomedical researchers was conducted. Researchers interacted with the same protein-protein interaction tools to discover possible disease mechanisms for further experimentation.</p><p><strong>Results: </strong>Findings reveal patterns in scientists' exploratory and explanatory analysis and reveal that tools positively supported a number of well-structured query and analysis tasks. But for several of scientists' more complex, higher order ways of knowing and reasoning the tools did not offer adequate support. Results show that for a better fit with scientists' cognition for exploratory analysis systems biology tools need to better match scientists' processes for validating, for making a transition from classification to model-based reasoning, and for engaging in causal mental modelling.</p><p><strong>Conclusion: </strong>As the next great frontier in bioinformatics usability, tool designs for exploratory systems biology analysis need to move beyond the successes already achieved in supporting formulaic query and analysis tasks and now reduce current mismatches with several of scientists' higher order analytical practices. The implications of results for tool designs are discussed.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"4 ","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2009-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1747-5333-4-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27985298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Basic Blue Skies Research in the UK: Are we losing out?","authors":"Belinda Linden","doi":"10.1186/1747-5333-3-3","DOIUrl":"10.1186/1747-5333-3-3","url":null,"abstract":"<p><strong>Background: </strong>The term blue skies research implies a freedom to carry out flexible, curiosity-driven research that leads to outcomes not envisaged at the outset. This research often challenges accepted thinking and introduces new fields of study. Science policy in the UK has given growing support for short-term goal-oriented scientific research projects, with pressure being applied on researchers to demonstrate the future application of their work. These policies carry the risk of restricting freedom, curbing research direction, and stifling rather than stimulating the creativity needed for scientific discovery.</p><p><strong>Methods: </strong>This study tracks the tortuous routes that led to three major discoveries in cardiology. It then investigates the constraints in current research, and opportunities that may be lost with existing funding processes, by interviewing selected scientists and fund providers for their views on curiosity-driven research and the freedom needed to allow science to flourish. The transcripts were analysed using a grounded theory approach to gather recurrent themes from the interviews.</p><p><strong>Results: </strong>The results from these interviews suggest that scientists often cannot predict the future applications of research. Constraints such as lack of scientific freedom, and a narrow focus on relevance and accountability were believed to stifle the discovery process. Although it was acknowledged that some research projects do need a clear and measurable framework, the interviewees saw a need for inquisitive, blue skies research to be managed in a different way. They provided examples of situations where money allocated to 'safe' funding was used for more innovative research.</p><p><strong>Conclusion: </strong>This sample of key UK scientists and grant providers acknowledge the importance of basic blue skies research. Yet the current evaluation process often requires that scientists predict their likely findings and estimate short-term impact, which does not permit freedom of research direction. There is a vital need for prominent scientists and for universities to help the media, the public, and policy makers to understand the importance of innovative thought along with the need for scientists to have the freedom to challenge accepted thinking. Encouraging an avenue for blue skies research could have immense influence over future scientific discoveries.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"3 ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2008-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1747-5333-3-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27298768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}