WorldWideScience

Sample records for de-identified biomedical information

  1. The development of large-scale de-identified biomedical databases in the age of genomics-principles and challenges.

    Science.gov (United States)

    Dankar, Fida K; Ptitsyn, Andrey; Dankar, Samar K

    2018-04-10

    Contemporary biomedical databases include a wide range of information types from various observational and instrumental sources. Among the most important features that unite biomedical databases across the field are high volume of information and high potential to cause damage through data corruption, loss of performance, and loss of patient privacy. Thus, issues of data governance and privacy protection are essential for the construction of data depositories for biomedical research and healthcare. In this paper, we discuss various challenges of data governance in the context of population genome projects. The various challenges along with best practices and current research efforts are discussed through the steps of data collection, storage, sharing, analysis, and knowledge dissemination.

  2. Biomedical information retrieval across languages.

    Science.gov (United States)

    Daumke, Philipp; Markü, Kornél; Poprat, Michael; Schulz, Stefan; Klar, Rüdiger

    2007-06-01

    This work presents a new dictionary-based approach to biomedical cross-language information retrieval (CLIR) that addresses many of the general and domain-specific challenges in current CLIR research. Our method is based on a multilingual lexicon that was generated partly manually and partly automatically, and currently covers six European languages. It contains morphologically meaningful word fragments, termed subwords. Using subwords instead of entire words significantly reduces the number of lexical entries necessary to sufficiently cover a specific language and domain. Mediation between queries and documents is based on these subwords as well as on lists of word-n-grams that are generated from large monolingual corpora and constitute possible translation units. The translations are then sent to a standard Internet search engine. This process makes our approach an effective tool for searching the biomedical content of the World Wide Web in different languages. We evaluate this approach using the OHSUMED corpus, a large medical document collection, within a cross-language retrieval setting.

  3. A system architecture for sharing de-identified, research-ready brain scans and health information across clinical imaging centers.

    Science.gov (United States)

    Chervenak, Ann L; van Erp, Theo G M; Kesselman, Carl; D'Arcy, Mike; Sobell, Janet; Keator, David; Dahm, Lisa; Murry, Jim; Law, Meng; Hasso, Anton; Ames, Joseph; Macciardi, Fabio; Potkin, Steven G

    2012-01-01

    Progress in our understanding of brain disorders increasingly relies on the costly collection of large standardized brain magnetic resonance imaging (MRI) data sets. Moreover, the clinical interpretation of brain scans benefits from compare and contrast analyses of scans from patients with similar, and sometimes rare, demographic, diagnostic, and treatment status. A solution to both needs is to acquire standardized, research-ready clinical brain scans and to build the information technology infrastructure to share such scans, along with other pertinent information, across hospitals. This paper describes the design, deployment, and operation of a federated imaging system that captures and shares standardized, de-identified clinical brain images in a federation across multiple institutions. In addition to describing innovative aspects of the system architecture and our initial testing of the deployed infrastructure, we also describe the Standardized Imaging Protocol (SIP) developed for the project and our interactions with the Institutional Review Board (IRB) regarding handling patient data in the federated environment.

  4. Proof of concept: concept-based biomedical information retrieval

    NARCIS (Netherlands)

    Trieschnigg, Rudolf Berend

    2010-01-01

    In this thesis we investigate the possibility to integrate domain-specific knowledge into biomedical information retrieval (IR). Recent decades have shown a fast growing interest in biomedical research, reflected by an exponential growth in scientific literature. An important problem for biomedical

  5. Information Retrieval in Biomedical Research: From Articles to Datasets

    Science.gov (United States)

    Wei, Wei

    2017-01-01

    Information retrieval techniques have been applied to biomedical research for a variety of purposes, such as textual document retrieval and molecular data retrieval. As biomedical research evolves over time, information retrieval is also constantly facing new challenges, including the growing number of available data, the emerging new data types,…

  6. Mining biomarker information in biomedical literature

    Directory of Open Access Journals (Sweden)

    Younesi Erfan

    2012-12-01

    Full Text Available Abstract Background For selection and evaluation of potential biomarkers, inclusion of already published information is of utmost importance. In spite of significant advancements in text- and data-mining techniques, the vast knowledge space of biomarkers in biomedical text has remained unexplored. Existing named entity recognition approaches are not sufficiently selective for the retrieval of biomarker information from the literature. The purpose of this study was to identify textual features that enhance the effectiveness of biomarker information retrieval for different indication areas and diverse end user perspectives. Methods A biomarker terminology was created and further organized into six concept classes. Performance of this terminology was optimized towards balanced selectivity and specificity. The information retrieval performance using the biomarker terminology was evaluated based on various combinations of the terminology's six classes. Further validation of these results was performed on two independent corpora representing two different neurodegenerative diseases. Results The current state of the biomarker terminology contains 119 entity classes supported by 1890 different synonyms. The result of information retrieval shows improved retrieval rate of informative abstracts, which is achieved by including clinical management terms and evidence of gene/protein alterations (e.g. gene/protein expression status or certain polymorphisms in combination with disease and gene name recognition. When additional filtering through other classes (e.g. diagnostic or prognostic methods is applied, the typical high number of unspecific search results is significantly reduced. The evaluation results suggest that this approach enables the automated identification of biomarker information in the literature. A demo version of the search engine SCAIView, including the biomarker retrieval, is made available to the public through http

  7. An information technology emphasis in biomedical informatics education.

    Science.gov (United States)

    Kane, Michael D; Brewer, Jeffrey L

    2007-02-01

    Unprecedented growth in the interdisciplinary domain of biomedical informatics reflects the recent advancements in genomic sequence availability, high-content biotechnology screening systems, as well as the expectations of computational biology to command a leading role in drug discovery and disease characterization. These forces have moved much of life sciences research almost completely into the computational domain. Importantly, educational training in biomedical informatics has been limited to students enrolled in the life sciences curricula, yet much of the skills needed to succeed in biomedical informatics involve or augment training in information technology curricula. This manuscript describes the methods and rationale for training students enrolled in information technology curricula in the field of biomedical informatics, which augments the existing information technology curriculum and provides training on specific subjects in Biomedical Informatics not emphasized in bioinformatics courses offered in life science programs, and does not require prerequisite courses in the life sciences.

  8. Improve Biomedical Information Retrieval using Modified Learning to Rank Methods.

    Science.gov (United States)

    Xu, Bo; Lin, Hongfei; Lin, Yuan; Ma, Yunlong; Yang, Liang; Wang, Jian; Yang, Zhihao

    2016-06-14

    In these years, the number of biomedical articles has increased exponentially, which becomes a problem for biologists to capture all the needed information manually. Information retrieval technologies, as the core of search engines, can deal with the problem automatically, providing users with the needed information. However, it is a great challenge to apply these technologies directly for biomedical retrieval, because of the abundance of domain specific terminologies. To enhance biomedical retrieval, we propose a novel framework based on learning to rank. Learning to rank is a series of state-of-the-art information retrieval techniques, and has been proved effective in many information retrieval tasks. In the proposed framework, we attempt to tackle the problem of the abundance of terminologies by constructing ranking models, which focus on not only retrieving the most relevant documents, but also diversifying the searching results to increase the completeness of the resulting list for a given query. In the model training, we propose two novel document labeling strategies, and combine several traditional retrieval models as learning features. Besides, we also investigate the usefulness of different learning to rank approaches in our framework. Experimental results on TREC Genomics datasets demonstrate the effectiveness of our framework for biomedical information retrieval.

  9. Semantic reasoning with XML-based biomedical information models.

    Science.gov (United States)

    O'Connor, Martin J; Das, Amar

    2010-01-01

    The Extensible Markup Language (XML) is increasingly being used for biomedical data exchange. The parallel growth in the use of ontologies in biomedicine presents opportunities for combining the two technologies to leverage the semantic reasoning services provided by ontology-based tools. There are currently no standardized approaches for taking XML-encoded biomedical information models and representing and reasoning with them using ontologies. To address this shortcoming, we have developed a workflow and a suite of tools for transforming XML-based information models into domain ontologies encoded using OWL. In this study, we applied semantics reasoning methods to these ontologies to automatically generate domain-level inferences. We successfully used these methods to develop semantic reasoning methods for information models in the HIV and radiological image domains.

  10. NAMED ENTITY RECOGNITION FROM BIOMEDICAL TEXT -AN INFORMATION EXTRACTION TASK

    Directory of Open Access Journals (Sweden)

    N. Kanya

    2016-07-01

    Full Text Available Biomedical Text Mining targets the Extraction of significant information from biomedical archives. Bio TM encompasses Information Retrieval (IR and Information Extraction (IE. The Information Retrieval will retrieve the relevant Biomedical Literature documents from the various Repositories like PubMed, MedLine etc., based on a search query. The IR Process ends up with the generation of corpus with the relevant document retrieved from the Publication databases based on the query. The IE task includes the process of Preprocessing of the document, Named Entity Recognition (NER from the documents and Relationship Extraction. This process includes Natural Language Processing, Data Mining techniques and machine Language algorithm. The preprocessing task includes tokenization, stop word Removal, shallow parsing, and Parts-Of-Speech tagging. NER phase involves recognition of well-defined objects such as genes, proteins or cell-lines etc. This process leads to the next phase that is extraction of relationships (IE. The work was based on machine learning algorithm Conditional Random Field (CRF.

  11. [The system of biomedical scientific information of Serbia].

    Science.gov (United States)

    Dacić, M

    1995-09-01

    Building of the System of biomedical scientific information of Yugoslavia (SBMSI YU) began, by the end of 1980, and the system became operative officially in 1986. After the political disintegration of former Yugoslavia SBMSI of Serbia was formed. SBMSI is developed according to the policy of developing of the System of scientific technologic information of Serbia (SSTI S), and with technical support of SSTI S. Reconstruction of the System is done by using former SBMSI YU as a model. Unlike the former SBMSI YU, SBMSI S owns besides the database Biomedicina Serbica, three important databases: database of doctoral dissertations promoted at University Medical School in Belgrade in the period from 1955-1993, database of Master's theses promoted at the University School of Medicine in Belgrade from 1965-1993; A database of foreign biomedical periodicals in libraries of Serbia.

  12. Development of an information retrieval tool for biomedical patents.

    Science.gov (United States)

    Alves, Tiago; Rodrigues, Rúben; Costa, Hugo; Rocha, Miguel

    2018-06-01

    The volume of biomedical literature has been increasing in the last years. Patent documents have also followed this trend, being important sources of biomedical knowledge, technical details and curated data, which are put together along the granting process. The field of Biomedical text mining (BioTM) has been creating solutions for the problems posed by the unstructured nature of natural language, which makes the search of information a challenging task. Several BioTM techniques can be applied to patents. From those, Information Retrieval (IR) includes processes where relevant data are obtained from collections of documents. In this work, the main goal was to build a patent pipeline addressing IR tasks over patent repositories to make these documents amenable to BioTM tasks. The pipeline was developed within @Note2, an open-source computational framework for BioTM, adding a number of modules to the core libraries, including patent metadata and full text retrieval, PDF to text conversion and optical character recognition. Also, user interfaces were developed for the main operations materialized in a new @Note2 plug-in. The integration of these tools in @Note2 opens opportunities to run BioTM tools over patent texts, including tasks from Information Extraction, such as Named Entity Recognition or Relation Extraction. We demonstrated the pipeline's main functions with a case study, using an available benchmark dataset from BioCreative challenges. Also, we show the use of the plug-in with a user query related to the production of vanillin. This work makes available all the relevant content from patents to the scientific community, decreasing drastically the time required for this task, and provides graphical interfaces to ease the use of these tools. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. The Influence of Biomedical Information and Childhood History on Sentencing.

    Science.gov (United States)

    Kim, JongHan; Boytos, Abby; Seong, Yoori; Park, Kwangbai

    2015-01-01

    A recent trend in court is for defense attorneys to introduce brain scans and other forms of biomedical information (BI) into criminal trials as mitigating evidence. The present study investigates how BI, when considered in combination with a defendant's childhood information (CI), can influence the length of a defendant's sentence. We hypothesized that certain combinations of BI and CI result in shorter sentences because they suggest that the defendant poses less of a threat to society. Participants were asked to read accounts of the trial of a murder suspect and, based on the information therein, recommend a sentence as if they were the judge. The defendant was diagnosed with psychopathy, but biomedical information regarding that diagnosis was included or excluded depending on the BI condition. The defendant was further described as growing up in either a loving or abusive family. The results showed that, if BI was present in the trial account, the defendant from an abusive family was perceived as less of a threat to society and received a shorter recommended sentence than if the defendant had been from a loving family. If BI was absent from the account, the pattern was reversed: the defendant from a loving family was perceived as less of a threat to society and received a shorter recommended sentence than if he had been from an abusive family. Implications for the use of BI and CI in court trials are discussed, as well as their relationship to free will and the function of punishment as retribution and utility. Copyright © 2015 John Wiley & Sons, Ltd.

  14. MIMI: multimodality, multiresource, information integration environment for biomedical core facilities.

    Science.gov (United States)

    Szymanski, Jacek; Wilson, David L; Zhang, Guo-Qiang

    2009-10-01

    The rapid expansion of biomedical research has brought substantial scientific and administrative data management challenges to modern core facilities. Scientifically, a core facility must be able to manage experimental workflow and the corresponding set of large and complex scientific data. It must also disseminate experimental data to relevant researchers in a secure and expedient manner that facilitates collaboration and provides support for data interpretation and analysis. Administratively, a core facility must be able to manage the scheduling of its equipment and to maintain a flexible and effective billing system to track material, resource, and personnel costs and charge for services to sustain its operation. It must also have the ability to regularly monitor the usage and performance of its equipment and to provide summary statistics on resources spent on different categories of research. To address these informatics challenges, we introduce a comprehensive system called MIMI (multimodality, multiresource, information integration environment) that integrates the administrative and scientific support of a core facility into a single web-based environment. We report the design, development, and deployment experience of a baseline MIMI system at an imaging core facility and discuss the general applicability of such a system in other types of core facilities. These initial results suggest that MIMI will be a unique, cost-effective approach to addressing the informatics infrastructure needs of core facilities and similar research laboratories.

  15. MIMI: Multimodality, Multiresource, Information Integration Environment for Biomedical Core Facilities

    OpenAIRE

    Szymanski, Jacek; Wilson, David L.; Zhang, Guo-Qiang

    2007-01-01

    The rapid expansion of biomedical research has brought substantial scientific and administrative data management challenges to modern core facilities. Scientifically, a core facility must be able to manage experimental workflow and the corresponding set of large and complex scientific data. It must also disseminate experimental data to relevant researchers in a secure and expedient manner that facilitates collaboration and provides support for data interpretation and analysis. Administrativel...

  16. A Semantics-Based Approach to Retrieving Biomedical Information

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik; Zambach, Sine

    2011-01-01

    This paper describes an approach to representing, organising, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative ontol...... of data mining of texts identifying paraphrases and concept relations and measuring distances between key concepts in texts. Thus, the project is distinct in its attempt to provide a formal underpinning of conceptual similarity or relatedness of meaning.......This paper describes an approach to representing, organising, and accessing conceptual content of biomedical texts using a formal ontology. The ontology is based on UMLS resources supplemented with domain ontologies developed in the project. The approach introduces the notion of ‘generative...... ontologies’, i.e., ontologies providing increasingly specialised concepts reflecting the phrase structure of natural language. Furthermore, we propose a novel so called ontological semantics which maps noun phrases from texts and queries into nodes in the generative ontology. This enables an advanced form...

  17. PASSIM – an open source software system for managing information in biomedical studies

    Directory of Open Access Journals (Sweden)

    Neogi Sudeshna

    2007-02-01

    Full Text Available Abstract Background One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to large-scale, expensive commercial Laboratory Information Management Systems (LIMS. Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweight open source systems for patient and sample information management. Results We present a web-based tool for submission, management and retrieval of sample and research subject data. The system secures confidentiality by separating anonymized sample information from individuals' records. It is simple and generic, and can be customised for various biomedical studies. Information can be both entered and accessed using the same web interface. User groups and their privileges can be defined. The system is open-source and is supplied with an on-line tutorial and necessary documentation. It has proven to be successful in a large international collaborative project. Conclusion The presented system closes the gap between the need and the availability of lightweight software solutions for managing information in biomedical studies involving human research subjects.

  18. Strategies for Disseminating Information on Biomedical Research on Autism to Hispanic Parents

    Science.gov (United States)

    Lajonchere, Clara M.; Wheeler, Barbara Y.; Valente, Thomas W.; Kreutzer, Cary; Munson, Aron; Narayanan, Shrikanth; Kazemzadeh, Abe; Cruz, Roxana; Martinez, Irene; Schrager, Sheree M.; Schweitzer, Lisa; Chklovski, Tara; Hwang, Darryl

    2016-01-01

    Low income Hispanic families experience multiple barriers to accessing evidence-based information on Autism Spectrum Disorders (ASD). This study utilized a mixed-strategy intervention to create access to information in published bio-medical research articles on ASD by distilling the content into parent-friendly English- and Spanish-language ASD…

  19. Cloud computing: a new business paradigm for biomedical information sharing.

    Science.gov (United States)

    Rosenthal, Arnon; Mork, Peter; Li, Maya Hao; Stanford, Jean; Koester, David; Reynolds, Patti

    2010-04-01

    We examine how the biomedical informatics (BMI) community, especially consortia that share data and applications, can take advantage of a new resource called "cloud computing". Clouds generally offer resources on demand. In most clouds, charges are pay per use, based on large farms of inexpensive, dedicated servers, sometimes supporting parallel computing. Substantial economies of scale potentially yield costs much lower than dedicated laboratory systems or even institutional data centers. Overall, even with conservative assumptions, for applications that are not I/O intensive and do not demand a fully mature environment, the numbers suggested that clouds can sometimes provide major improvements, and should be seriously considered for BMI. Methodologically, it was very advantageous to formulate analyses in terms of component technologies; focusing on these specifics enabled us to bypass the cacophony of alternative definitions (e.g., exactly what does a cloud include) and to analyze alternatives that employ some of the component technologies (e.g., an institution's data center). Relative analyses were another great simplifier. Rather than listing the absolute strengths and weaknesses of cloud-based systems (e.g., for security or data preservation), we focus on the changes from a particular starting point, e.g., individual lab systems. We often find a rough parity (in principle), but one needs to examine individual acquisitions--is a loosely managed lab moving to a well managed cloud, or a tightly managed hospital data center moving to a poorly safeguarded cloud? 2009 Elsevier Inc. All rights reserved.

  20. Use of systematic review to inform the infection risk for biomedical engineers and technicians servicing biomedical devices

    International Nuclear Information System (INIS)

    Smith, Anne-Louise

    2011-01-01

    Full text: Many microorganisms responsible for hospital acquired infections are able to stay viable on surfaces with no visible sign of contamination, in dry conditions and on non-porous surfaces. The infection risk to biomedical staff when servicing biomedical devices is not documented. An indirect approach has been used to examine the different aspects that will affect the risk of infection including a systematic review of microbial contamination and transmission relating to biomedical devices. A systematic review found 58% of biomedical devices have microbial contamination with 13% having at least one pathogenic organism. These microbes can persist for some months. Occupational-infections of biomedical service staff are low compared to other healthcare workers. A biomedical device with contaminated surface or dust was identified as the source of patient outbreaks in 13 papers. The cleaning agent most tested for removal of micro-organisms from devices was alcohol swabs, but sterile water swabs were also effective. However, manufacturers mainly recommend (74%) cleaning devices with water and detergent. Biomedical engineers and technicians have a small risk of being exposed to dangerous micro-organisms on most biomedical devices, but without skin breakage, this exposure is unlikely to cause ill-health. It is recommended that biomedical staff follow good infection control practices, wipe devices with detergent, sterile water or alcohol swabs as recommended by the manufacturer before working on them, and keep alcohol hand rubs accessible at all benches. (author)

  1. Conflicts of interests and access to information resulting from biomedical research: an international legal perspective.

    Science.gov (United States)

    Byk, Christian

    2002-07-01

    Recently adopted international texts have given a new focus on conflicts of interests and access to information resulting from biomedical research. They confirmed ethical review committees as a central point to guarantee individual rights and the effective application of ethical principles. Therefore specific attention should be paid in giving such committees all the facilities necessary to keep them independent and qualified.

  2. Developing a search engine for pharmacotherapeutic information that is not published in biomedical journals.

    Science.gov (United States)

    Do Pazo-Oubiña, F; Calvo Pita, C; Puigventós Latorre, F; Periañez-Párraga, L; Ventayol Bosch, P

    2011-01-01

    To identify publishers of pharmacotherapeutic information not found in biomedical journals that focuses on evaluating and providing advice on medicines and to develop a search engine to access this information. Compiling web sites that publish information on the rational use of medicines and have no commercial interests. Free-access web sites in Spanish, Galician, Catalan or English. Designing a search engine using the Google "custom search" application. Overall 159 internet addresses were compiled and were classified into 9 labels. We were able to recover the information from the selected sources using a search engine, which is called "AlquimiA" and available from http://www.elcomprimido.com/FARHSD/AlquimiA.htm. The main sources of pharmacotherapeutic information not published in biomedical journals were identified. The search engine is a useful tool for searching and accessing "grey literature" on the internet. Copyright © 2010 SEFH. Published by Elsevier Espana. All rights reserved.

  3. [Biomedical information on the internet using search engines. A one-year trial].

    Science.gov (United States)

    Corrao, Salvatore; Leone, Francesco; Arnone, Sabrina

    2004-01-01

    The internet is a communication medium and content distributor that provide information in the general sense but it could be of great utility regarding as the search and retrieval of biomedical information. Search engines represent a great deal to rapidly find information on the net. However, we do not know whether general search engines and meta-search ones are reliable in order to find useful and validated biomedical information. The aim of our study was to verify the reproducibility of a search by key-words (pediatric or evidence) using 9 international search engines and 1 meta-search engine at the baseline and after a one year period. We analysed the first 20 citations as output of each searching. We evaluated the formal quality of Web-sites and their domain extensions. Moreover, we compared the output of each search at the start of this study and after a one year period and we considered as a criterion of reliability the number of Web-sites cited again. We found some interesting results that are reported throughout the text. Our findings point out an extreme dynamicity of the information on the Web and, for this reason, we advice a great caution when someone want to use search and meta-search engines as a tool for searching and retrieve reliable biomedical information. On the other hand, some search and meta-search engines could be very useful as a first step searching for defining better a search and, moreover, for finding institutional Web-sites too. This paper allows to know a more conscious approach to the internet biomedical information universe.

  4. [Biomedical informatics].

    Science.gov (United States)

    Capurro, Daniel; Soto, Mauricio; Vivent, Macarena; Lopetegui, Marcelo; Herskovic, Jorge R

    2011-12-01

    Biomedical Informatics is a new discipline that arose from the need to incorporate information technologies to the generation, storage, distribution and analysis of information in the domain of biomedical sciences. This discipline comprises basic biomedical informatics, and public health informatics. The development of the discipline in Chile has been modest and most projects have originated from the interest of individual people or institutions, without a systematic and coordinated national development. Considering the unique features of health care system of our country, research in the area of biomedical informatics is becoming an imperative.

  5. Organization of Biomedical Data for Collaborative Scientific Research: A Research Information Management System.

    Science.gov (United States)

    Myneni, Sahiti; Patel, Vimla L

    2010-06-01

    Biomedical researchers often work with massive, detailed and heterogeneous datasets. These datasets raise new challenges of information organization and management for scientific interpretation, as they demand much of the researchers' time and attention. The current study investigated the nature of the problems that researchers face when dealing with such data. Four major problems identified with existing biomedical scientific information management methods were related to data organization, data sharing, collaboration, and publications. Therefore, there is a compelling need to develop an efficient and user-friendly information management system to handle the biomedical research data. This study evaluated the implementation of an information management system, which was introduced as part of the collaborative research to increase scientific productivity in a research laboratory. Laboratory members seemed to exhibit frustration during the implementation process. However, empirical findings revealed that they gained new knowledge and completed specified tasks while working together with the new system. Hence, researchers are urged to persist and persevere when dealing with any new technology, including an information management system in a research laboratory environment.

  6. Institute for Scientific Information-indexed biomedical journals of Saudi Arabia

    Science.gov (United States)

    Rohra, Dileep K.; Rohra, Vikram K.; Cahusac, Peter

    2016-01-01

    Objectives: To compare the journal impact factor (JIF) and Eigenfactor score (ES) of Institute for Scientific Information (ISI)-indexed biomedical journals published from the Kingdom of Saudi Arabia (KSA) over the last 8 years. Methods: This is a retrospective study, conducted at Alfaisal University, Riyadh, KSA from January to March 2016. The Journal Citation Reports of ISI Web of Knowledge were accessed, and 6 Saudi biomedical journals were included for analysis. Results: All Saudi journals have improved their IF compared with their baseline. However, the performance of the Journal of Pharmaceutical Sciences and Neurosciences has been exceptionally good. The biggest improvement in percent growth in JIF was seen in the Saudi Pharmaceutical Journal (approximately 887%) followed by Neurosciences (approximately 462%). Interestingly, the ES of all biomedical journals, except Saudi Journal of Gastroenterology and Saudi Medical Journal, increased over the years. The greatest growth in ES (more than 5 fold) was noted for Neurosciences and Saudi Pharmaceutical Journal. Conclusion: This study shows that the overall quality of all Saudi biomedical journals has improved in the last 8 years. PMID:27761565

  7. Method for detecting core malware sites related to biomedical information systems.

    Science.gov (United States)

    Kim, Dohoon; Choi, Donghee; Jin, Jonghyun

    2015-01-01

    Most advanced persistent threat attacks target web users through malicious code within landing (exploit) or distribution sites. There is an urgent need to block the affected websites. Attacks on biomedical information systems are no exception to this issue. In this paper, we present a method for locating malicious websites that attempt to attack biomedical information systems. Our approach uses malicious code crawling to rearrange websites in the order of their risk index by analyzing the centrality between malware sites and proactively eliminates the root of these sites by finding the core-hub node, thereby reducing unnecessary security policies. In particular, we dynamically estimate the risk index of the affected websites by analyzing various centrality measures and converting them into a single quantified vector. On average, the proactive elimination of core malicious websites results in an average improvement in zero-day attack detection of more than 20%.

  8. Method for Detecting Core Malware Sites Related to Biomedical Information Systems

    Directory of Open Access Journals (Sweden)

    Dohoon Kim

    2015-01-01

    Full Text Available Most advanced persistent threat attacks target web users through malicious code within landing (exploit or distribution sites. There is an urgent need to block the affected websites. Attacks on biomedical information systems are no exception to this issue. In this paper, we present a method for locating malicious websites that attempt to attack biomedical information systems. Our approach uses malicious code crawling to rearrange websites in the order of their risk index by analyzing the centrality between malware sites and proactively eliminates the root of these sites by finding the core-hub node, thereby reducing unnecessary security policies. In particular, we dynamically estimate the risk index of the affected websites by analyzing various centrality measures and converting them into a single quantified vector. On average, the proactive elimination of core malicious websites results in an average improvement in zero-day attack detection of more than 20%.

  9. A System for Information Management in BioMedical Studies—SIMBioMS

    Science.gov (United States)

    Krestyaninova, Maria; Zarins, Andris; Viksna, Juris; Kurbatova, Natalja; Rucevskis, Peteris; Neogi, Sudeshna Guha; Gostev, Mike; Perheentupa, Teemu; Knuuttila, Juha; Barrett, Amy; Lappalainen, Ilkka; Rung, Johan; Podnieks, Karlis; Sarkans, Ugis; McCarthy, Mark I; Brazma, Alvis

    2009-01-01

    Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented. Availability: The source code, documentation and initialization scripts are available at http://simbioms.org. Contact: support@simbioms.org; mariak@ebi.ac.uk PMID:19633095

  10. Improving validity of informed consent for biomedical research in Zambia using a laboratory exposure intervention.

    Science.gov (United States)

    Zulu, Joseph Mumba; Lisulo, Mpala Mwanza; Besa, Ellen; Kaonga, Patrick; Chisenga, Caroline C; Chomba, Mumba; Simuyandi, Michelo; Banda, Rosemary; Kelly, Paul

    2014-01-01

    Complex biomedical research can lead to disquiet in communities with limited exposure to scientific discussions, leading to rumours or to high drop-out rates. We set out to test an intervention designed to address apprehensions commonly encountered in a community where literacy is uncommon, and where complex biomedical research has been conducted for over a decade. We aimed to determine if it could improve the validity of consent. Data were collected using focus group discussions, key informant interviews and observations. We designed an intervention that exposed participants to a detailed demonstration of laboratory processes. Each group was interviewed twice in a day, before and after exposure to the intervention in order to assess changes in their views. Factors that motivated people to participate in invasive biomedical research included a desire to stay healthy because of the screening during the recruitment process, regular advice from doctors, free medical services, and trust in the researchers. Inhibiting factors were limited knowledge about samples taken from their bodies during endoscopic procedures, the impact of endoscopy on the function of internal organs, and concerns about the use of biomedical samples. The belief that blood can be used for Satanic practices also created insecurities about drawing of blood samples. Further inhibiting factors included a fear of being labelled as HIV positive if known to consult heath workers repeatedly, and gender inequality. Concerns about the use and storage of blood and tissue samples were overcome by a laboratory exposure intervention. Selecting a group of members from target community and engaging them in a laboratory exposure intervention could be a useful tool for enhancing specific aspects of consent for biomedical research. Further work is needed to determine the extent to which improved understanding permeates beyond the immediate group participating in the intervention.

  11. Improving validity of informed consent for biomedical research in Zambia using a laboratory exposure intervention.

    Directory of Open Access Journals (Sweden)

    Joseph Mumba Zulu

    Full Text Available Complex biomedical research can lead to disquiet in communities with limited exposure to scientific discussions, leading to rumours or to high drop-out rates. We set out to test an intervention designed to address apprehensions commonly encountered in a community where literacy is uncommon, and where complex biomedical research has been conducted for over a decade. We aimed to determine if it could improve the validity of consent.Data were collected using focus group discussions, key informant interviews and observations. We designed an intervention that exposed participants to a detailed demonstration of laboratory processes. Each group was interviewed twice in a day, before and after exposure to the intervention in order to assess changes in their views.Factors that motivated people to participate in invasive biomedical research included a desire to stay healthy because of the screening during the recruitment process, regular advice from doctors, free medical services, and trust in the researchers. Inhibiting factors were limited knowledge about samples taken from their bodies during endoscopic procedures, the impact of endoscopy on the function of internal organs, and concerns about the use of biomedical samples. The belief that blood can be used for Satanic practices also created insecurities about drawing of blood samples. Further inhibiting factors included a fear of being labelled as HIV positive if known to consult heath workers repeatedly, and gender inequality. Concerns about the use and storage of blood and tissue samples were overcome by a laboratory exposure intervention.Selecting a group of members from target community and engaging them in a laboratory exposure intervention could be a useful tool for enhancing specific aspects of consent for biomedical research. Further work is needed to determine the extent to which improved understanding permeates beyond the immediate group participating in the intervention.

  12. Implementation and management of a biomedical observation dictionary in a large healthcare information system.

    Science.gov (United States)

    Vandenbussche, Pierre-Yves; Cormont, Sylvie; André, Christophe; Daniel, Christel; Delahousse, Jean; Charlet, Jean; Lepage, Eric

    2013-01-01

    This study shows the evolution of a biomedical observation dictionary within the Assistance Publique Hôpitaux Paris (AP-HP), the largest European university hospital group. The different steps are detailed as follows: the dictionary creation, the mapping to logical observation identifier names and codes (LOINC), the integration into a multiterminological management platform and, finally, the implementation in the health information system. AP-HP decided to create a biomedical observation dictionary named AnaBio, to map it to LOINC and to maintain the mapping. A management platform based on methods used for knowledge engineering has been put in place. It aims at integrating AnaBio within the health information system and improving both the quality and stability of the dictionary. This new management platform is now active in AP-HP. The AnaBio dictionary is shared by 120 laboratories and currently includes 50 000 codes. The mapping implementation to LOINC reaches 40% of the AnaBio entries and uses 26% of LOINC records. The results of our work validate the choice made to develop a local dictionary aligned with LOINC. This work constitutes a first step towards a wider use of the platform. The next step will support the entire biomedical production chain, from the clinician prescription, through laboratory tests tracking in the laboratory information system to the communication of results and the use for decision support and biomedical research. In addition, the increase in the mapping implementation to LOINC ensures the interoperability allowing communication with other international health institutions.

  13. Modeling and mining term association for improving biomedical information retrieval performance.

    Science.gov (United States)

    Hu, Qinmin; Huang, Jimmy Xiangji; Hu, Xiaohua

    2012-06-11

    The growth of the biomedical information requires most information retrieval systems to provide short and specific answers in response to complex user queries. Semantic information in the form of free text that is structured in a way makes it straightforward for humans to read but more difficult for computers to interpret automatically and search efficiently. One of the reasons is that most traditional information retrieval models assume terms are conditionally independent given a document/passage. Therefore, we are motivated to consider term associations within different contexts to help the models understand semantic information and use it for improving biomedical information retrieval performance. We propose a term association approach to discover term associations among the keywords from a query. The experiments are conducted on the TREC 2004-2007 Genomics data sets and the TREC 2004 HARD data set. The proposed approach is promising and achieves superiority over the baselines and the GSP results. The parameter settings and different indices are investigated that the sentence-based index produces the best results in terms of the document-level, the word-based index for the best results in terms of the passage-level and the paragraph-based index for the best results in terms of the passage2-level. Furthermore, the best term association results always come from the best baseline. The tuning number k in the proposed recursive re-ranking algorithm is discussed and locally optimized to be 10. First, modelling term association for improving biomedical information retrieval using factor analysis, is one of the major contributions in our work. Second, the experiments confirm that term association considering co-occurrence and dependency among the keywords can produce better results than the baselines treating the keywords independently. Third, the baselines are re-ranked according to the importance and reliance of latent factors behind term associations. These latent

  14. Mediator infrastructure for information integration and semantic data integration environment for biomedical research.

    Science.gov (United States)

    Grethe, Jeffrey S; Ross, Edward; Little, David; Sanders, Brian; Gupta, Amarnath; Astakhov, Vadim

    2009-01-01

    This paper presents current progress in the development of semantic data integration environment which is a part of the Biomedical Informatics Research Network (BIRN; http://www.nbirn.net) project. BIRN is sponsored by the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). A goal is the development of a cyberinfrastructure for biomedical research that supports advance data acquisition, data storage, data management, data integration, data mining, data visualization, and other computing and information processing services over the Internet. Each participating institution maintains storage of their experimental or computationally derived data. Mediator-based data integration system performs semantic integration over the databases to enable researchers to perform analyses based on larger and broader datasets than would be available from any single institution's data. This paper describes recent revision of the system architecture, implementation, and capabilities of the semantically based data integration environment for BIRN.

  15. Data integration and knowledge discovery in biomedical databases. Reliable information from unreliable sources

    Directory of Open Access Journals (Sweden)

    A Mitnitski

    2003-01-01

    Full Text Available To better understand information about human health from databases we analyzed three datasets collected for different purposes in Canada: a biomedical database of older adults, a large population survey across all adult ages, and vital statistics. Redundancy in the variables was established, and this led us to derive a generalized (macroscopic state variable, being a fitness/frailty index that reflects both individual and group health status. Evaluation of the relationship between fitness/frailty and the mortality rate revealed that the latter could be expressed in terms of variables generally available from any cross-sectional database. In practical terms, this means that the risk of mortality might readily be assessed from standard biomedical appraisals collected for other purposes.

  16. Semantics-driven modelling of user preferences for information retrieval in the biomedical domain.

    Science.gov (United States)

    Gladun, Anatoly; Rogushina, Julia; Valencia-García, Rafael; Béjar, Rodrigo Martínez

    2013-03-01

    A large amount of biomedical and genomic data are currently available on the Internet. However, data are distributed into heterogeneous biological information sources, with little or even no organization. Semantic technologies provide a consistent and reliable basis with which to confront the challenges involved in the organization, manipulation and visualization of data and knowledge. One of the knowledge representation techniques used in semantic processing is the ontology, which is commonly defined as a formal and explicit specification of a shared conceptualization of a domain of interest. The work presented here introduces a set of interoperable algorithms that can use domain and ontological information to improve information-retrieval processes. This work presents an ontology-based information-retrieval system for the biomedical domain. This system, with which some experiments have been carried out that are described in this paper, is based on the use of domain ontologies for the creation and normalization of lightweight ontologies that represent user preferences in a determined domain in order to improve information-retrieval processes.

  17. A service-oriented distributed semantic mediator: integrating multiscale biomedical information.

    Science.gov (United States)

    Mora, Oscar; Engelbrecht, Gerhard; Bisbal, Jesus

    2012-11-01

    Biomedical research continuously generates large amounts of heterogeneous and multimodal data spread over multiple data sources. These data, if appropriately shared and exploited, could dramatically improve the research practice itself, and ultimately the quality of health care delivered. This paper presents DISMED (DIstributed Semantic MEDiator), an open source semantic mediator that provides a unified view of a federated environment of multiscale biomedical data sources. DISMED is a Web-based software application to query and retrieve information distributed over a set of registered data sources, using semantic technologies. It also offers a userfriendly interface specifically designed to simplify the usage of these technologies by non-expert users. Although the architecture of the software mediator is generic and domain independent, in the context of this paper, DISMED has been evaluated for managing biomedical environments and facilitating research with respect to the handling of scientific data distributed in multiple heterogeneous data sources. As part of this contribution, a quantitative evaluation framework has been developed. It consist of a benchmarking scenario and the definition of five realistic use-cases. This framework, created entirely with public datasets, has been used to compare the performance of DISMED against other available mediators. It is also available to the scientific community in order to evaluate progress in the domain of semantic mediation, in a systematic and comparable manner. The results show an average improvement in the execution time by DISMED of 55% compared to the second best alternative in four out of the five use-cases of the experimental evaluation.

  18. Biomedical and health informatics education and research at the Information Technology Institute in Egypt.

    Science.gov (United States)

    Hussein, R; Khalifa, A

    2011-01-01

    During the last decade, Egypt has experienced a revolution in the field of Information and Communication Technology (ICT) that has had a corresponding impact on the field of healthcare. Since 1993, the Information Technology Institute (ITI) has been leading the development of the Information Technology (IT) professional training and education in Egypt to produce top quality IT professionals who are considered now the backbone of the IT revolution in Egypt. For the past five years, ITI has been adopting the objective of building high caliber health professionals who can effectively serve the ever-growing information society. Academic links have been established with internationally renowned universities, e.g., Oregon Health and Science University (OHSU) in US, University of Leipzig in Germany, in addition those with the Egyptian Fellowship Board in order to enrich ITI Medical Informatics Education and Research. The ITI Biomedical and Health Informatics (BMHI) education and training programs target fresh graduates as well as life-long learners. Therefore, the program's learning objectives are framed within the context of the four specialization tracks: Healthcare Management (HCM), Biomedical Informatics Research (BMIR), Bioinformatics Professional (BIP), and Healthcare Professional (HCP). The ITI BMHI research projects tackle a wide-range of current challenges in this field, such as knowledge management in healthcare, providing tele-consultation services for diagnosis and treatment of infectious diseases for underserved regions in Egypt, and exploring the cultural and educational aspects of Nanoinformatics. Since 2006, ITI has been positively contributing to develop the discipline of BMHI in Egypt in order to support improved healthcare services.

  19. Architecture for biomedical multimedia information delivery on the World Wide Web

    Science.gov (United States)

    Long, L. Rodney; Goh, Gin-Hua; Neve, Leif; Thoma, George R.

    1997-10-01

    Research engineers at the National Library of Medicine are building a prototype system for the delivery of multimedia biomedical information on the World Wide Web. This paper discuses the architecture and design considerations for the system, which will be used initially to make images and text from the third National Health and Nutrition Examination Survey (NHANES) publicly available. We categorized our analysis as follows: (1) fundamental software tools: we analyzed trade-offs among use of conventional HTML/CGI, X Window Broadway, and Java; (2) image delivery: we examined the use of unconventional TCP transmission methods; (3) database manager and database design: we discuss the capabilities and planned use of the Informix object-relational database manager and the planned schema for the HNANES database; (4) storage requirements for our Sun server; (5) user interface considerations; (6) the compatibility of the system with other standard research and analysis tools; (7) image display: we discuss considerations for consistent image display for end users. Finally, we discuss the scalability of the system in terms of incorporating larger or more databases of similar data, and the extendibility of the system for supporting content-based retrieval of biomedical images. The system prototype is called the Web-based Medical Information Retrieval System. An early version was built as a Java applet and tested on Unix, PC, and Macintosh platforms. This prototype used the MiniSQL database manager to do text queries on a small database of records of participants in the second NHANES survey. The full records and associated x-ray images were retrievable and displayable on a standard Web browser. A second version has now been built, also a Java applet, using the MySQL database manager.

  20. A Part-Of-Speech term weighting scheme for biomedical information retrieval.

    Science.gov (United States)

    Wang, Yanshan; Wu, Stephen; Li, Dingcheng; Mehrabi, Saeed; Liu, Hongfang

    2016-10-01

    In the era of digitalization, information retrieval (IR), which retrieves and ranks documents from large collections according to users' search queries, has been popularly applied in the biomedical domain. Building patient cohorts using electronic health records (EHRs) and searching literature for topics of interest are some IR use cases. Meanwhile, natural language processing (NLP), such as tokenization or Part-Of-Speech (POS) tagging, has been developed for processing clinical documents or biomedical literature. We hypothesize that NLP can be incorporated into IR to strengthen the conventional IR models. In this study, we propose two NLP-empowered IR models, POS-BoW and POS-MRF, which incorporate automatic POS-based term weighting schemes into bag-of-word (BoW) and Markov Random Field (MRF) IR models, respectively. In the proposed models, the POS-based term weights are iteratively calculated by utilizing a cyclic coordinate method where golden section line search algorithm is applied along each coordinate to optimize the objective function defined by mean average precision (MAP). In the empirical experiments, we used the data sets from the Medical Records track in Text REtrieval Conference (TREC) 2011 and 2012 and the Genomics track in TREC 2004. The evaluation on TREC 2011 and 2012 Medical Records tracks shows that, for the POS-BoW models, the mean improvement rates for IR evaluation metrics, MAP, bpref, and P@10, are 10.88%, 4.54%, and 3.82%, compared to the BoW models; and for the POS-MRF models, these rates are 13.59%, 8.20%, and 8.78%, compared to the MRF models. Additionally, we experimentally verify that the proposed weighting approach is superior to the simple heuristic and frequency based weighting approaches, and validate our POS category selection. Using the optimal weights calculated in this experiment, we tested the proposed models on the TREC 2004 Genomics track and obtained average of 8.63% and 10.04% improvement rates for POS-BoW and POS

  1. Improving biomedical information retrieval by linear combinations of different query expansion techniques.

    Science.gov (United States)

    Abdulla, Ahmed AbdoAziz Ahmed; Lin, Hongfei; Xu, Bo; Banbhrani, Santosh Kumar

    2016-07-25

    Biomedical literature retrieval is becoming increasingly complex, and there is a fundamental need for advanced information retrieval systems. Information Retrieval (IR) programs scour unstructured materials such as text documents in large reserves of data that are usually stored on computers. IR is related to the representation, storage, and organization of information items, as well as to access. In IR one of the main problems is to determine which documents are relevant and which are not to the user's needs. Under the current regime, users cannot precisely construct queries in an accurate way to retrieve particular pieces of data from large reserves of data. Basic information retrieval systems are producing low-quality search results. In our proposed system for this paper we present a new technique to refine Information Retrieval searches to better represent the user's information need in order to enhance the performance of information retrieval by using different query expansion techniques and apply a linear combinations between them, where the combinations was linearly between two expansion results at one time. Query expansions expand the search query, for example, by finding synonyms and reweighting original terms. They provide significantly more focused, particularized search results than do basic search queries. The retrieval performance is measured by some variants of MAP (Mean Average Precision) and according to our experimental results, the combination of best results of query expansion is enhanced the retrieved documents and outperforms our baseline by 21.06 %, even it outperforms a previous study by 7.12 %. We propose several query expansion techniques and their combinations (linearly) to make user queries more cognizable to search engines and to produce higher-quality search results.

  2. Generic information can retrieve known biological associations: implications for biomedical knowledge discovery.

    Directory of Open Access Journals (Sweden)

    Herman H H B M van Haagen

    Full Text Available MOTIVATION: Weighted semantic networks built from text-mined literature can be used to retrieve known protein-protein or gene-disease associations, and have been shown to anticipate associations years before they are explicitly stated in the literature. Our text-mining system recognizes over 640,000 biomedical concepts: some are specific (i.e., names of genes or proteins others generic (e.g., 'Homo sapiens'. Generic concepts may play important roles in automated information retrieval, extraction, and inference but may also result in concept overload and confound retrieval and reasoning with low-relevance or even spurious links. Here, we attempted to optimize the retrieval performance for protein-protein interactions (PPI by filtering generic concepts (node filtering or links to generic concepts (edge filtering from a weighted semantic network. First, we defined metrics based on network properties that quantify the specificity of concepts. Then using these metrics, we systematically filtered generic information from the network while monitoring retrieval performance of known protein-protein interactions. We also systematically filtered specific information from the network (inverse filtering, and assessed the retrieval performance of networks composed of generic information alone. RESULTS: Filtering generic or specific information induced a two-phase response in retrieval performance: initially the effects of filtering were minimal but beyond a critical threshold network performance suddenly drops. Contrary to expectations, networks composed exclusively of generic information demonstrated retrieval performance comparable to unfiltered networks that also contain specific concepts. Furthermore, an analysis using individual generic concepts demonstrated that they can effectively support the retrieval of known protein-protein interactions. For instance the concept "binding" is indicative for PPI retrieval and the concept "mutation abnormality" is

  3. A passage retrieval method based on probabilistic information retrieval model and UMLS concepts in biomedical question answering.

    Science.gov (United States)

    Sarrouti, Mourad; Ouatik El Alaoui, Said

    2017-04-01

    Passage retrieval, the identification of top-ranked passages that may contain the answer for a given biomedical question, is a crucial component for any biomedical question answering (QA) system. Passage retrieval in open-domain QA is a longstanding challenge widely studied over the last decades. However, it still requires further efforts in biomedical QA. In this paper, we present a new biomedical passage retrieval method based on Stanford CoreNLP sentence/passage length, probabilistic information retrieval (IR) model and UMLS concepts. In the proposed method, we first use our document retrieval system based on PubMed search engine and UMLS similarity to retrieve relevant documents to a given biomedical question. We then take the abstracts from the retrieved documents and use Stanford CoreNLP for sentence splitter to make a set of sentences, i.e., candidate passages. Using stemmed words and UMLS concepts as features for the BM25 model, we finally compute the similarity scores between the biomedical question and each of the candidate passages and keep the N top-ranked ones. Experimental evaluations performed on large standard datasets, provided by the BioASQ challenge, show that the proposed method achieves good performances compared with the current state-of-the-art methods. The proposed method significantly outperforms the current state-of-the-art methods by an average of 6.84% in terms of mean average precision (MAP). We have proposed an efficient passage retrieval method which can be used to retrieve relevant passages in biomedical QA systems with high mean average precision. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. De-identifying an EHR Database

    DEFF Research Database (Denmark)

    Lauesen, Søren; Pantazos, Kostas; Lippert, Søren

    2011-01-01

    -identified a Danish EHR database with 437,164 patients. The goal was to generate a version with real medical records, but related to artificial persons. We developed a de-identification algorithm that uses lists of named entities, simple language analysis, and special rules. Our algorithm consists of 3 steps: collect...... lists of identifiers from the database and external resources, define a replacement for each identifier, and replace identifiers in structured data and free text. Some patient records could not be safely de-identified, so the de-identified database has 323,122 patient records with an acceptable degree...... of anonymity, readability and correctness (F-measure of 95%). The algorithm has to be adjusted for each culture, language and database....

  5. The caCORE Software Development Kit: Streamlining construction of interoperable biomedical information services

    Directory of Open Access Journals (Sweden)

    Warzel Denise

    2006-01-01

    Full Text Available Abstract Background Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs. The National Cancer Institute (NCI developed the cancer common ontologic representation environment (caCORE to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. Results The caCORE SDK requires a Unified Modeling Language (UML tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has

  6. Information sources in biomedical science and medical journalism: methodological approaches and assessment.

    Science.gov (United States)

    Miranda, Giovanna F; Vercellesi, Luisa; Bruno, Flavia

    2004-09-01

    Throughout the world the public is showing increasing interest in medical and scientific subjects and journalists largely spread this information, with an important impact on knowledge and health. Clearly, therefore, the relationship between the journalist and his sources is delicate: freedom and independence of information depend on the independence and truthfulness of the sources. The new "precision journalism" holds that scientific methods should be applied to journalism, so authoritative sources are a common need for journalists and scientists. We therefore compared the individual classifications and methods of assessing of sources in biomedical science and medical journalism to try to extrapolate scientific methods of evaluation to journalism. In journalism and science terms used to classify sources of information show some similarities, but their meanings are different. In science primary and secondary classes of information, for instance, refer to the levels of processing, but in journalism to the official nature of the source itself. Scientists and journalists must both always consult as many sources as possible and check their authoritativeness, reliability, completeness, up-to-dateness and balance. In journalism, however, there are some important differences and limits: too many sources can sometimes diminish the quality of the information. The sources serve a first filter between the event and the journalist, who is not providing the reader with the fact, but with its projection. Journalists have time constraints and lack the objective criteria for searching, the specific background knowledge, and the expertise to fully assess sources. To assist in understanding the wealth of sources of information in journalism, we have prepared a checklist of items and questions. There are at least four fundamental points that a good journalist, like any scientist, should know: how to find the latest information (the sources), how to assess it (the quality and

  7. Mutual-Information-Based Incremental Relaying Communications for Wireless Biomedical Implant Systems

    Directory of Open Access Journals (Sweden)

    Yangzhe Liao

    2018-02-01

    Full Text Available Network lifetime maximization of wireless biomedical implant systems is one of the major research challenges of wireless body area networks (WBANs. In this paper, a mutual information (MI-based incremental relaying communication protocol is presented where several on-body relay nodes and one coordinator are attached to the clothes of a patient. Firstly, a comprehensive analysis of a system model is investigated in terms of channel path loss, energy consumption, and the outage probability from the network perspective. Secondly, only when the MI value becomes smaller than the predetermined threshold is data transmission allowed. The communication path selection can be either from the implanted sensor to the on-body relay then forwards to the coordinator or from the implanted sensor to the coordinator directly, depending on the communication distance. Moreover, mathematical models of quality of service (QoS metrics are derived along with the related subjective functions. The results show that the MI-based incremental relaying technique achieves better performance in comparison to our previous proposed protocol techniques regarding several selected performance metrics. The outcome of this paper can be applied to intra-body continuous physiological signal monitoring, artificial biofeedback-oriented WBANs, and telemedicine system design.

  8. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

    Science.gov (United States)

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

  9. Active learning-based information structure analysis of full scientific articles and two applications for biomedical literature review.

    Science.gov (United States)

    Guo, Yufan; Silins, Ilona; Stenius, Ulla; Korhonen, Anna

    2013-06-01

    Techniques that are capable of automatically analyzing the information structure of scientific articles could be highly useful for improving information access to biomedical literature. However, most existing approaches rely on supervised machine learning (ML) and substantial labeled data that are expensive to develop and apply to different sub-fields of biomedicine. Recent research shows that minimal supervision is sufficient for fairly accurate information structure analysis of biomedical abstracts. However, is it realistic for full articles given their high linguistic and informational complexity? We introduce and release a novel corpus of 50 biomedical articles annotated according to the Argumentative Zoning (AZ) scheme, and investigate active learning with one of the most widely used ML models-Support Vector Machines (SVM)-on this corpus. Additionally, we introduce two novel applications that use AZ to support real-life literature review in biomedicine via question answering and summarization. We show that active learning with SVM trained on 500 labeled sentences (6% of the corpus) performs surprisingly well with the accuracy of 82%, just 2% lower than fully supervised learning. In our question answering task, biomedical researchers find relevant information significantly faster from AZ-annotated than unannotated articles. In the summarization task, sentences extracted from particular zones are significantly more similar to gold standard summaries than those extracted from particular sections of full articles. These results demonstrate that active learning of full articles' information structure is indeed realistic and the accuracy is high enough to support real-life literature review in biomedicine. The annotated corpus, our AZ classifier and the two novel applications are available at http://www.cl.cam.ac.uk/yg244/12bioinfo.html

  10. Efficient Techniques of Sparse Signal Analysis for Enhanced Recovery of Information in Biomedical Engineering and Geosciences

    KAUST Repository

    Sana, Furrukh

    2016-11-01

    Sparse signals are abundant among both natural and man-made signals. Sparsity implies that the signal essentially resides in a small dimensional subspace. The sparsity of the signal can be exploited to improve its recovery from limited and noisy observations. Traditional estimation algorithms generally lack the ability to take advantage of signal sparsity. This dissertation considers several problems in the areas of biomedical engineering and geosciences with the aim of enhancing the recovery of information by exploiting the underlying sparsity in the problem. The objective is to overcome the fundamental bottlenecks, both in terms of estimation accuracies and required computational resources. In the first part of dissertation, we present a high precision technique for the monitoring of human respiratory movements by exploiting the sparsity of wireless ultra-wideband signals. The proposed technique provides a novel methodology of overcoming the Nyquist sampling constraint and enables robust performance in the presence of noise and interferences. We also present a comprehensive framework for the important problem of extracting the fetal electrocardiogram (ECG) signals from abdominal ECG recordings of pregnant women. The multiple measurement vectors approach utilized for this purpose provides an efficient mechanism of exploiting the common structure of ECG signals, when represented in sparse transform domains, and allows leveraging information from multiple ECG electrodes under a joint estimation formulation. In the second part of dissertation, we adopt sparse signal processing principles for improved information recovery in large-scale subsurface reservoir characterization problems. We propose multiple new algorithms for sparse representation of the subsurface geological structures, incorporation of useful prior information in the estimation process, and for reducing computational complexities of the problem. The techniques presented here enable significantly

  11. BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction

    OpenAIRE

    Jonnalagadda, Siddhartha; Gonzalez, Graciela

    2011-01-01

    BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification for improving human readability). The model is based on a "shot-gun" approach that produces many different (simpler) versions of the original sentence by combining variants of its constituent elements. This tool is optimized for processing biomedical scien...

  12. KISTI at TREC 2014 Clinical Decision Support Track: Concept-based Document Re-ranking to Biomedical Information Retrieval

    Science.gov (United States)

    2014-11-01

    sematic type. Injury or Poisoning inpo T037 Anatomical Abnormality anab T190 Given a document D, a concept vector = {1, 2, … , ...integrating biomedical terminology . Nucleic acids research 32, Database issue (2004), 267–270. 5. Chapman, W.W., Hillert, D., Velupillai, S., et...Conference (TREC), (2011). 9. Koopman, B. and Zuccon, G. Understanding negation and family history to improve clinical information retrieval. Proceedings

  13. A de-identifier for medical discharge summaries.

    Science.gov (United States)

    Uzuner, Ozlem; Sibanda, Tawanda C; Luo, Yuan; Szolovits, Peter

    2008-01-01

    Clinical records contain significant medical information that can be useful to researchers in various disciplines. However, these records also contain personal health information (PHI) whose presence limits the use of the records outside of hospitals. The goal of de-identification is to remove all PHI from clinical records. This is a challenging task because many records contain foreign and misspelled PHI; they also contain PHI that are ambiguous with non-PHI. These complications are compounded by the linguistic characteristics of clinical records. For example, medical discharge summaries, which are studied in this paper, are characterized by fragmented, incomplete utterances and domain-specific language; they cannot be fully processed by tools designed for lay language. In this paper, we show that we can de-identify medical discharge summaries using a de-identifier, Stat De-id, based on support vector machines and local context (F-measure=97% on PHI). Our representation of local context aids de-identification even when PHI include out-of-vocabulary words and even when PHI are ambiguous with non-PHI within the same corpus. Comparison of Stat De-id with a rule-based approach shows that local context contributes more to de-identification than dictionaries combined with hand-tailored heuristics (F-measure=85%). Comparison with two well-known named entity recognition (NER) systems, SNoW (F-measure=94%) and IdentiFinder (F-measure=36%), on five representative corpora show that when the language of documents is fragmented, a system with a relatively thorough representation of local context can be a more effective de-identifier than systems that combine (relatively simpler) local context with global context. Comparison with a Conditional Random Field De-identifier (CRFD), which utilizes global context in addition to the local context of Stat De-id, confirms this finding (F-measure=88%) and establishes that strengthening the representation of local context may be more

  14. A Study of the Information Literacy of Biomedical Graduate Students: Based on the Thesis Topic Discovery Process in Molecular Biology Research

    Directory of Open Access Journals (Sweden)

    Jhao-Yen Huang

    2014-06-01

    Full Text Available The biomedical information environment is in a state of constant and rapid change due to the increase in research data and rapid technological advances. In Taiwan, few research has investigated the information literacy of biomedical graduate students. This exploratory study examined the information literacy abilities and training of biomedical graduate students in Taiwan. Semi-structured interviews based on the Association of College and Research Libraries Information Literacy Competency Standards for Science and Engineering/Technology were conducted with 20 molecular biological graduate students. The interview inquired about their information-seeking channels and information literacy education. The findings show that the biomedical graduate students developed a workable thesis topic with their advisors. Through various information-seeking channels and retrieval strategies, they obtained and critically evaluated information to address different information needs for their thesis research. Through seminars, annual conferences and papers, the interviewees were informed of current developments in their field. Subsequently, through written or oral communications, they were able to integrate and exchange the information. Most interviewees cared about the social, economic, legal, and ethical issues surrounding the use of information. College courses and labs were the main information literacy education environment for them to learn about research skills and knowledge. The study concludes four areas to address for the information literacy of biomedical graduate students, i.e., using professional information, using the current information, efficiency in assessing the domain information, and utilization of diverse information channels. Currently, the interviewees showed rather low usage of library resources, which is a concern for biomedical educators and libraries. [Article content in Chinese

  15. [Human rights. Right to health. Right to health information. The Venezuelan biomedical journals].

    Science.gov (United States)

    Stegemann, Herbert

    2013-06-01

    Venezuelan Biomedical journals have been confronting, for several years, a gradual decline both, from the standpoint of their management and in the quality of their editorial content. At its highest level, Venezuela had about sixty different titles. But irregular financial support, as well as the lack of a clear official policy, regarding these scientific activities, were some of the reasons that have contributed to this decline. Several recent Venezuelan and international documents provide an important legal support for the design of new official policies and government responsibilities. There is now a valid opportunity to profit from new tools to evaluate and improve the quality of our scientific and editorial activities.

  16. BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction.

    Science.gov (United States)

    Jonnalagadda, Siddhartha; Gonzalez, Graciela

    2010-11-13

    BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification for improving human readability). The model is based on a "shot-gun" approach that produces many different (simpler) versions of the original sentence by combining variants of its constituent elements. This tool is optimized for processing biomedical scientific literature such as the abstracts indexed in PubMed. We tested our tool on its impact to the task of PPI extraction and it improved the f-score of the PPI tool by around 7%, with an improvement in recall of around 20%. The BioSimplify tool and test corpus can be downloaded from https://biosimplify.sourceforge.net.

  17. An Effective Approach to Biomedical Information Extraction with Limited Training Data

    Science.gov (United States)

    Jonnalagadda, Siddhartha

    2011-01-01

    In the current millennium, extensive use of computers and the internet caused an exponential increase in information. Few research areas are as important as information extraction, which primarily involves extracting concepts and the relations between them from free text. Limitations in the size of training data, lack of lexicons and lack of…

  18. Preserving Privacy by De-identifying Facial Images

    National Research Council Canada - National Science Library

    Newton, Elaine; Sweeney, Latanya; Malin, Bradley

    2003-01-01

    .... A trivial solution to de-identifying faces involves blacking out each face. This thwarts any possible face recognition, but because all facial details are obscured, the result is of limited use...

  19. Why not just Google it? An assessment of information literacy skills in a biomedical science curriculum

    Directory of Open Access Journals (Sweden)

    Stewart Tanis

    2011-04-01

    Full Text Available Abstract Background Few issues in higher education are as fundamental as the ability to search for, evaluate, and synthesize information. The need to develop information literacy, the process of finding, retrieving, organizing, and evaluating the ever-expanding collection of online information, has precipitated the need for training in skill-based competencies in higher education, as well as medical and dental education. Methods The current study evaluated the information literacy skills of first-year dental students, consisting of two, consecutive dental student cohorts (n = 160. An assignment designed to evaluate information literacy skills was conducted. In addition, a survey of student online search engine or database preferences was conducted to identify any significant associations. Subsequently, an intervention was developed, based upon the results of the assessment and survey, to address any deficiencies in information literacy. Results Nearly half of students (n = 70/160 or 43% missed one or more question components that required finding an evidence-based citation. Analysis of the survey revealed a significantly higher percentage of students who provided incorrect responses (n = 53/70 or 75.7% reported using Google as their preferred online search method (p Conclusions This study confirmed that information literacy among this student population was lacking and that integration of modules within the curriculum can help students to filter and establish the quality of online information, a critical component in the training of new health care professionals. Furthermore, incorporation of these modules early in the curriculum may be of significant value to other dental, medical, health care, and professional schools with similar goals of incorporating the evidence base into teaching and learning activities.

  20. Using the weighted keyword model to improve information retrieval for answering biomedical questions.

    Science.gov (United States)

    Yu, Hong; Cao, Yong-Gang

    2009-03-01

    Physicians ask many complex questions during the patient encounter. Information retrieval systems that can provide immediate and relevant answers to these questions can be invaluable aids to the practice of evidence-based medicine. In this study, we first automatically identify topic keywords from ad hoc clinical questions with a Condition Random Field model that is trained over thousands of manually annotated clinical questions. We then report on a linear model that assigns query weights based on their automatically identified semantic roles: topic keywords, domain specific terms, and their synonyms. Our evaluation shows that this weighted keyword model improves information retrieval from the Text Retrieval Conference Genomics track data.

  1. Biomedical image representation approach using visualness and spatial information in a concept feature space for interactive region-of-interest-based retrieval.

    Science.gov (United States)

    Rahman, Md Mahmudur; Antani, Sameer K; Demner-Fushman, Dina; Thoma, George R

    2015-10-01

    This article presents an approach to biomedical image retrieval by mapping image regions to local concepts where images are represented in a weighted entropy-based concept feature space. The term "concept" refers to perceptually distinguishable visual patches that are identified locally in image regions and can be mapped to a glossary of imaging terms. Further, the visual significance (e.g., visualness) of concepts is measured as the Shannon entropy of pixel values in image patches and is used to refine the feature vector. Moreover, the system can assist the user in interactively selecting a region-of-interest (ROI) and searching for similar image ROIs. Further, a spatial verification step is used as a postprocessing step to improve retrieval results based on location information. The hypothesis that such approaches would improve biomedical image retrieval is validated through experiments on two different data sets, which are collected from open access biomedical literature.

  2. Ontology-based retrieval of bio-medical information based on microarray text corpora

    DEFF Research Database (Denmark)

    Hansen, Kim Allan; Zambach, Sine; Have, Christian Theil

    are exponentially growing, the text corpora are sparse and inconsistent in spite of attempts to standardize the format. Ordinary keyword search may in some cases be insucient to nd rele- vant information and the potential benet of using a semantic approach in this context has only been investigated to a limited...

  3. Ethics Review Committee approval and informed consent: an analysis of biomedical publications originating from Sri Lanka

    Directory of Open Access Journals (Sweden)

    Siriwardhana Chesmal

    2008-02-01

    Full Text Available Abstract Background International guidelines on research have focused on protecting research participants. Ethical Research Committee (ERC approval and informed consent are the cornerstones. Externally sponsored research requires approval through ethical review in both the host and the sponsoring country. This study aimed to determine to what extent ERC approval and informed consent procedures are documented in locally and internationally published human subject research carried out in Sri Lanka. Methods We obtained ERC approval in Sri Lanka and the United Kingdom. Theses from 1985 to 2005 available at the Postgraduate Institute of Medicine (PGIM library affiliated to the University of Colombo were scrutinised using checklists agreed in consultation with senior research collaborators. A Medline search was carried out with MeSH major and minor heading 'Sri Lanka' as the search term for international publications originating in Sri Lanka during 1999 to 2004. All research publications from CMJ during 1999 to 2005 were also scrutinized. Results Of 291 theses, 34% documented ERC approvals and 61% documented obtaining consent. From the international journal survey, 250 publications originated from Sri Lanka of which only 79 full text original research publications could be accessed electronically. Of these 38% documented ERC approval and 39% documented obtaining consent. In the Ceylon Medical Journal 36% documented ERC approval and 37% documented obtaining consent. Conclusion Only one third of the publications scrutinized recorded ERC approval and procurement of informed consent. However, there is a positive trend in documenting these ethical requirements in local postgraduate research and in the local medical journal.

  4. Perceptions of the use of intelligent information access systems in university level active learning activities among teachers of biomedical subjects.

    Science.gov (United States)

    Aparicio, Fernando; Morales-Botello, María Luz; Rubio, Margarita; Hernando, Asunción; Muñoz, Rafael; López-Fernández, Hugo; Glez-Peña, Daniel; Fdez-Riverola, Florentino; de la Villa, Manuel; Maña, Manuel; Gachet, Diego; Buenaga, Manuel de

    2018-04-01

    Student participation and the use of active methodologies in classroom learning are being increasingly emphasized. The use of intelligent systems can be of great help when designing and developing these types of activities. Recently, emerging disciplines such as 'educational data mining' and 'learning analytics and knowledge' have provided clear examples of the importance of the use of artificial intelligence techniques in education. The main objective of this study was to gather expert opinions regarding the benefits of using complementary methods that are supported by intelligent systems, specifically, by intelligent information access systems, when processing texts written in natural language and the benefits of using these methods as companion tools to the learning activities that are employed by biomedical and health sciences teachers. Eleven teachers of degree courses who belonged to the Faculties of Biomedical Sciences (BS) and Health Sciences (HS) of a Spanish university in Madrid were individually interviewed. These interviews were conducted using a mixed methods questionnaire that included 66 predefined close-ended and open-ended questions. In our study, three intelligent information access systems (i.e., BioAnnote, CLEiM and MedCMap) were successfully used to evaluate the teacher's perceptions regarding the utility of these systems and their different methods in learning activities. All teachers reported using active learning methods in the classroom, most of which were computer programs that were used for initially designing and later executing learning activities. All teachers used case-based learning methods in the classroom, with a specific emphasis on case reports written in Spanish and/or English. In general, few or none of the teachers were familiar with the technical terms related to the technologies used for these activities such as "intelligent systems" or "concept/mental maps". However, they clearly realized the potential applicability of such

  5. Biomedical photonics handbook biomedical diagnostics

    CERN Document Server

    Vo-Dinh, Tuan

    2014-01-01

    Shaped by Quantum Theory, Technology, and the Genomics RevolutionThe integration of photonics, electronics, biomaterials, and nanotechnology holds great promise for the future of medicine. This topic has recently experienced an explosive growth due to the noninvasive or minimally invasive nature and the cost-effectiveness of photonic modalities in medical diagnostics and therapy. The second edition of the Biomedical Photonics Handbook presents fundamental developments as well as important applications of biomedical photonics of interest to scientists, engineers, manufacturers, teachers, studen

  6. Biomedical nanomaterials from design to implementation

    CERN Document Server

    Webster, Thomas

    2016-01-01

    Biomedical Nanomaterials brings together the engineering applications and challenges of using nanostructured surfaces and nanomaterials in healthcare in a single source. Each chapter covers important and new information in the biomedical applications of nanomaterials.

  7. Interpretation of the auto-mutual information rate of decrease in the context of biomedical signal analysis. Application to electroencephalogram recordings

    International Nuclear Information System (INIS)

    Escudero, Javier; Hornero, Roberto; Abásolo, Daniel

    2009-01-01

    The mutual information (MI) is a measure of both linear and nonlinear dependences. It can be applied to a time series and a time-delayed version of the same sequence to compute the auto-mutual information function (AMIF). Moreover, the AMIF rate of decrease (AMIFRD) with increasing time delay in a signal is correlated with its entropy and has been used to characterize biomedical data. In this paper, we aimed at gaining insight into the dependence of the AMIFRD on several signal processing concepts and at illustrating its application to biomedical time series analysis. Thus, we have analysed a set of synthetic sequences with the AMIFRD. The results show that the AMIF decreases more quickly as bandwidth increases and that the AMIFRD becomes more negative as there is more white noise contaminating the time series. Additionally, this metric detected changes in the nonlinear dynamics of a signal. Finally, in order to illustrate the analysis of real biomedical signals with the AMIFRD, this metric was applied to electroencephalogram (EEG) signals acquired with eyes open and closed and to ictal and non-ictal intracranial EEG recordings

  8. Interpretation of the auto-mutual information rate of decrease in the context of biomedical signal analysis. Application to electroencephalogram recordings.

    Science.gov (United States)

    Escudero, Javier; Hornero, Roberto; Abásolo, Daniel

    2009-02-01

    The mutual information (MI) is a measure of both linear and nonlinear dependences. It can be applied to a time series and a time-delayed version of the same sequence to compute the auto-mutual information function (AMIF). Moreover, the AMIF rate of decrease (AMIFRD) with increasing time delay in a signal is correlated with its entropy and has been used to characterize biomedical data. In this paper, we aimed at gaining insight into the dependence of the AMIFRD on several signal processing concepts and at illustrating its application to biomedical time series analysis. Thus, we have analysed a set of synthetic sequences with the AMIFRD. The results show that the AMIF decreases more quickly as bandwidth increases and that the AMIFRD becomes more negative as there is more white noise contaminating the time series. Additionally, this metric detected changes in the nonlinear dynamics of a signal. Finally, in order to illustrate the analysis of real biomedical signals with the AMIFRD, this metric was applied to electroencephalogram (EEG) signals acquired with eyes open and closed and to ictal and non-ictal intracranial EEG recordings.

  9. Three-dimensional biomedical imaging

    International Nuclear Information System (INIS)

    Robb, R.A.

    1985-01-01

    Scientists in biomedical imaging provide researchers, physicians, and academicians with an understanding of the fundamental theories and practical applications of three-dimensional biomedical imaging methodologies. Succinct descriptions of each imaging modality are supported by numerous diagrams and illustrations which clarify important concepts and demonstrate system performance in a variety of applications. Comparison of the different functional attributes, relative advantages and limitations, complementary capabilities, and future directions of three-dimensional biomedical imaging modalities are given. Volume 1: Introductions to Three-Dimensional Biomedical Imaging Photoelectronic-Digital Imaging for Diagnostic Radiology. X-Ray Computed Tomography - Basic Principles. X-Ray Computed Tomography - Implementation and Applications. X-Ray Computed Tomography: Advanced Systems and Applications in Biomedical Research and Diagnosis. Volume II: Single Photon Emission Computed Tomography. Position Emission Tomography (PET). Computerized Ultrasound Tomography. Fundamentals of NMR Imaging. Display of Multi-Dimensional Biomedical Image Information. Summary and Prognostications

  10. Biomedical nanotechnology.

    Science.gov (United States)

    Hurst, Sarah J

    2011-01-01

    This chapter summarizes the roles of nanomaterials in biomedical applications, focusing on those highlighted in this volume. A brief history of nanoscience and technology and a general introduction to the field are presented. Then, the chemical and physical properties of nanostructures that make them ideal for use in biomedical applications are highlighted. Examples of common applications, including sensing, imaging, and therapeutics, are given. Finally, the challenges associated with translating this field from the research laboratory to the clinic setting, in terms of the larger societal implications, are discussed.

  11. Biomedical Engineering

    CERN Document Server

    Suh, Sang C; Tanik, Murat M

    2011-01-01

    Biomedical Engineering: Health Care Systems, Technology and Techniques is an edited volume with contributions from world experts. It provides readers with unique contributions related to current research and future healthcare systems. Practitioners and researchers focused on computer science, bioinformatics, engineering and medicine will find this book a valuable reference.

  12. Biomedical Data Mining

    NARCIS (Netherlands)

    Peek, N.; Combi, C.; Tucker, A.

    2009-01-01

    Objective: To introduce the special topic of Methods of Information in Medicine on data mining in biomedicine, with selected papers from two workshops on Intelligent Data Analysis in bioMedicine (IDAMAP) held in Verona (2006) and Amsterdam (2007). Methods: Defining the field of biomedical data

  13. Controlled searching in reversibly de-identified medical imaging archives.

    Science.gov (United States)

    Silva, Jorge Miguel; Pinho, Eduardo; Monteiro, Eriksson; Silva, João Figueira; Costa, Carlos

    2018-01-01

    Nowadays, digital medical imaging in healthcare has become a fundamental tool for medical diagnosis. This growth has been accompanied by the development of technologies and standards, such as the DICOM standard and PACS. This environment led to the creation of collaborative projects where there is a need to share medical data between different institutions for research and educational purposes. In this context, it is necessary to maintain patient data privacy and provide an easy and secure mechanism for authorized personnel access. This paper presents a solution that fully de-identifies standard medical imaging objects, including metadata and pixel data, providing at the same time a reversible de-identifier mechanism that retains search capabilities from the original data. The last feature is important in some scenarios, for instance, in collaborative platforms where data is anonymized when shared with the community but searchable for data custodians or authorized entities. The solution was integrated into an open source PACS archive and validated in a multidisciplinary collaborative scenario. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Bio-medical CMOS ICs

    CERN Document Server

    Yoo, Hoi-Jun

    2011-01-01

    This book is based on a graduate course entitled, Ubiquitous Healthcare Circuits and Systems, that was given by one of the editors. It includes an introduction and overview to biomedical ICs and provides information on the current trends in research.

  15. Biomedical informatics and translational medicine

    Directory of Open Access Journals (Sweden)

    Sarkar Indra

    2010-02-01

    Full Text Available Abstract Biomedical informatics involves a core set of methodologies that can provide a foundation for crossing the "translational barriers" associated with translational medicine. To this end, the fundamental aspects of biomedical informatics (e.g., bioinformatics, imaging informatics, clinical informatics, and public health informatics may be essential in helping improve the ability to bring basic research findings to the bedside, evaluate the efficacy of interventions across communities, and enable the assessment of the eventual impact of translational medicine innovations on health policies. Here, a brief description is provided for a selection of key biomedical informatics topics (Decision Support, Natural Language Processing, Standards, Information Retrieval, and Electronic Health Records and their relevance to translational medicine. Based on contributions and advancements in each of these topic areas, the article proposes that biomedical informatics practitioners ("biomedical informaticians" can be essential members of translational medicine teams.

  16. Computational intelligence in biomedical imaging

    CERN Document Server

    2014-01-01

    This book provides a comprehensive overview of the state-of-the-art computational intelligence research and technologies in biomedical images with emphasis on biomedical decision making. Biomedical imaging offers useful information on patients’ medical conditions and clues to causes of their symptoms and diseases. Biomedical images, however, provide a large number of images which physicians must interpret. Therefore, computer aids are demanded and become indispensable in physicians’ decision making. This book discusses major technical advancements and research findings in the field of computational intelligence in biomedical imaging, for example, computational intelligence in computer-aided diagnosis for breast cancer, prostate cancer, and brain disease, in lung function analysis, and in radiation therapy. The book examines technologies and studies that have reached the practical level, and those technologies that are becoming available in clinical practices in hospitals rapidly such as computational inte...

  17. [Evidence-based medicine. 2. Research of clinically relevant biomedical information. Gruppo Italiano per la Medicina Basata sulle Evidenze--GIMBE].

    Science.gov (United States)

    Cartabellotta, A

    1998-05-01

    Evidence-based Medicine is a product of the electronic information age and there are several databases useful for practice it--MEDLINE, EMBASE, specialized compendiums of evidence (Cochrane Library, Best Evidence), practice guidelines--most of them free available through Internet, that offers a growing number of health resources. Because searching best evidence is a basic step to practice Evidence-based Medicine, this second review (the first one has been published in the issue of March 1998) has the aim to provide physicians tools and skills for retrieving relevant biomedical information. Therefore, we discuss about strategies for managing information overload, analyze characteristics, usefulness and limits of medical databases and explain how to use MEDLINE in day-to-day clinical practice.

  18. search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information.

    Science.gov (United States)

    Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Siążnik, Artur

    2013-03-01

    Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user's query, advanced data searching based on the specified user's query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. search GenBank extends standard capabilities of the

  19. Biomedical engineering and nanotechnology

    International Nuclear Information System (INIS)

    Pawar, S.H.; Khyalappa, R.J.; Yakhmi, J.V.

    2009-01-01

    This book is predominantly a compilation of papers presented in the conference which is focused on the development in biomedical materials, biomedical devises and instrumentation, biomedical effects of electromagnetic radiation, electrotherapy, radiotherapy, biosensors, biotechnology, bioengineering, tissue engineering, clinical engineering and surgical planning, medical imaging, hospital system management, biomedical education, biomedical industry and society, bioinformatics, structured nanomaterial for biomedical application, nano-composites, nano-medicine, synthesis of nanomaterial, nano science and technology development. The papers presented herein contain the scientific substance to suffice the academic directivity of the researchers from the field of biomedicine, biomedical engineering, material science and nanotechnology. Papers relevant to INIS are indexed separately

  20. Pathophysiologic mechanisms of biomedical nanomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Liming, E-mail: wangliming@ihep.ac.cn; Chen, Chunying, E-mail: chenchy@nanoctr.cn

    2016-05-15

    Nanomaterials (NMs) have been widespread used in biomedical fields, daily consuming, and even food industry. It is crucial to understand the safety and biomedical efficacy of NMs. In this review, we summarized the recent progress about the physiological and pathological effects of NMs from several levels: protein-nano interface, NM-subcellular structures, and cell–cell interaction. We focused on the detailed information of nano-bio interaction, especially about protein adsorption, intracellular trafficking, biological barriers, and signaling pathways as well as the associated mechanism mediated by nanomaterials. We also introduced related analytical methods that are meaningful and helpful for biomedical effect studies in the future. We believe that knowledge about pathophysiologic effects of NMs is not only significant for rational design of medical NMs but also helps predict their safety and further improve their applications in the future. - Highlights: • Rapid protein adsorption onto nanomaterials that affects biomedical effects • Nanomaterials and their interaction with biological membrane, intracellular trafficking and specific cellular effects • Nanomaterials and their interaction with biological barriers • The signaling pathways mediated by nanomaterials and related biomedical effects • Novel techniques for studying translocation and biomedical effects of NMs.

  1. Pathophysiologic mechanisms of biomedical nanomaterials

    International Nuclear Information System (INIS)

    Wang, Liming; Chen, Chunying

    2016-01-01

    Nanomaterials (NMs) have been widespread used in biomedical fields, daily consuming, and even food industry. It is crucial to understand the safety and biomedical efficacy of NMs. In this review, we summarized the recent progress about the physiological and pathological effects of NMs from several levels: protein-nano interface, NM-subcellular structures, and cell–cell interaction. We focused on the detailed information of nano-bio interaction, especially about protein adsorption, intracellular trafficking, biological barriers, and signaling pathways as well as the associated mechanism mediated by nanomaterials. We also introduced related analytical methods that are meaningful and helpful for biomedical effect studies in the future. We believe that knowledge about pathophysiologic effects of NMs is not only significant for rational design of medical NMs but also helps predict their safety and further improve their applications in the future. - Highlights: • Rapid protein adsorption onto nanomaterials that affects biomedical effects • Nanomaterials and their interaction with biological membrane, intracellular trafficking and specific cellular effects • Nanomaterials and their interaction with biological barriers • The signaling pathways mediated by nanomaterials and related biomedical effects • Novel techniques for studying translocation and biomedical effects of NMs

  2. De-identifying a public use microdata file from the Canadian national discharge abstract database

    Directory of Open Access Journals (Sweden)

    Paton David

    2011-08-01

    Full Text Available Abstract Background The Canadian Institute for Health Information (CIHI collects hospital discharge abstract data (DAD from Canadian provinces and territories. There are many demands for the disclosure of this data for research and analysis to inform policy making. To expedite the disclosure of data for some of these purposes, the construction of a DAD public use microdata file (PUMF was considered. Such purposes include: confirming some published results, providing broader feedback to CIHI to improve data quality, training students and fellows, providing an easily accessible data set for researchers to prepare for analyses on the full DAD data set, and serve as a large health data set for computer scientists and statisticians to evaluate analysis and data mining techniques. The objective of this study was to measure the probability of re-identification for records in a PUMF, and to de-identify a national DAD PUMF consisting of 10% of records. Methods Plausible attacks on a PUMF were evaluated. Based on these attacks, the 2008-2009 national DAD was de-identified. A new algorithm was developed to minimize the amount of suppression while maximizing the precision of the data. The acceptable threshold for the probability of correct re-identification of a record was set at between 0.04 and 0.05. Information loss was measured in terms of the extent of suppression and entropy. Results Two different PUMF files were produced, one with geographic information, and one with no geographic information but more clinical information. At a threshold of 0.05, the maximum proportion of records with the diagnosis code suppressed was 20%, but these suppressions represented only 8-9% of all values in the DAD. Our suppression algorithm has less information loss than a more traditional approach to suppression. Smaller regions, patients with longer stays, and age groups that are infrequently admitted to hospitals tend to be the ones with the highest rates of suppression

  3. Supporting Evidence-Informed Teaching in Biomedical and Health Professions Education Through Knowledge Translation: An Interdisciplinary Literature Review.

    Science.gov (United States)

    Tractenberg, Rochelle E; Gordon, Morris

    2017-01-01

    Phenomenon: The purpose of "systematic" reviews/reviewers of medical and health professions educational research is to identify best practices. This qualitative article explores the question of whether systematic reviews can support "evidence informed" teaching and contrasts traditional systematic reviewing with a knowledge translation (KT) approach to this objective. Degrees of freedom analysis (DOFA) is used to examine the alignment of systematic review methods with educational research and the pedagogical strategies and approaches that might be considered with a decision-making framework developed to support valid assessment. This method is also used to explore how KT can be used to inform teaching and learning. The nature of educational research is not compatible with most (11/14) methods for systematic review. The inconsistency of systematic reviewing with the nature of educational research impedes both the identification and implementation of "best-evidence" pedagogy and teaching. This is primarily because research questions that do support the purposes of review do not support educational decision making. By contrast to systematic reviews of the literature, both a DOFA and KT are fully compatible with informing teaching using evidence. A DOFA supports the translation of theory to a specific teaching or learning case, so could be considered a type of KT. The DOFA results in a test of alignment of decision options with relevant educational theory, and KT leads to interventions in teaching or learning that can be evaluated. Examples of how to structure evaluable interventions are derived from a KT approach that are simply not available from a systematic review. Insights: Systematic reviewing of current empirical educational research is not suitable for deriving or supporting best practices in education. However, both "evidence-informed" and scholarly approaches to teaching can be supported as KT projects, which are inherently evaluable and can generate

  4. The role of ethics in information technology decisions: a case-based approach to biomedical informatics education.

    Science.gov (United States)

    Anderson, James G

    2004-03-18

    The purpose of this paper is to propose a case-based approach to instruction regarding ethical issues raised by the use of information technology (IT) in healthcare. These issues are rarely addressed in graduate degree and continuing professional education programs in health informatics. There are important reasons why ethical issues need to be addressed in informatics training. Ethical issues raised by the introduction of information technology affect practice and are ubiquitous. These issues are frequently among the most challenging to young practitioners who are ill prepared to deal with them in practice. First, the paper provides an overview of methods of moral reasoning that can be used to identify and analyze ethical problems in health informatics. Second, we provide a framework for defining cases that involve ethical issues and outline major issues raised by the use of information technology. Specific cases are used as examples of new dilemmas that are posed by the introduction of information technology in healthcare. These cases are used to illustrate how ethics can be integrated with the other elements of informatics training. The cases discussed here reflect day-to-day situations that arise in health settings that require decisions. Third, an approach that can be used to teach ethics in health informatics programs is outlined and illustrated.

  5. Radiochemicals in biomedical research

    International Nuclear Information System (INIS)

    Evans, E.A.; Oldham, K.G.

    1988-01-01

    This volume describes the role of radiochemicals in biomedical research, as tracers in the development of new drugs, their interaction and function with receptor proteins, with the kinetics of binding of hormone - receptor interactions, and their use in cancer research and clinical oncology. The book also aims to identify future trends in this research, the main objective of which is to provide information leading to improvements in the quality of life, and to give readers a basic understanding of the development of new drugs, how they function in relation to receptor proteins and lead to a better understanding of the diagnosis and treatment of cancers. (author)

  6. Frontiers in biomedical engineering and biotechnology.

    Science.gov (United States)

    Liu, Feng; Goodarzi, Ali; Wang, Haifeng; Stasiak, Joanna; Sun, Jianbo; Zhou, Yu

    2014-01-01

    The 2nd International Conference on Biomedical Engineering and Biotechnology (iCBEB 2013), held in Wuhan on 11–13 October 2013, is an annual conference that aims at providing an opportunity for international and national researchers and practitioners to present the most recent advances and future challenges in the fields of Biomedical Information, Biomedical Engineering and Biotechnology. The papers published by this issue are selected from this conference, which witnesses the frontier in the field of Biomedical Engineering and Biotechnology, which particularly has helped improving the level of clinical diagnosis in medical work.

  7. Telemedicine optoelectronic biomedical data processing system

    Science.gov (United States)

    Prosolovska, Vita V.

    2010-08-01

    The telemedicine optoelectronic biomedical data processing system is created to share medical information for the control of health rights and timely and rapid response to crisis. The system includes the main blocks: bioprocessor, analog-digital converter biomedical images, optoelectronic module for image processing, optoelectronic module for parallel recording and storage of biomedical imaging and matrix screen display of biomedical images. Rated temporal characteristics of the blocks defined by a particular triggering optoelectronic couple in analog-digital converters and time imaging for matrix screen. The element base for hardware implementation of the developed matrix screen is integrated optoelectronic couples produced by selective epitaxy.

  8. LORD: a phenotype-genotype semantically integrated biomedical data tool to support rare disease diagnosis coding in health information systems.

    Science.gov (United States)

    Choquet, Remy; Maaroufi, Meriem; Fonjallaz, Yannick; de Carrara, Albane; Vandenbussche, Pierre-Yves; Dhombres, Ferdinand; Landais, Paul

    Characterizing a rare disease diagnosis for a given patient is often made through expert's networks. It is a complex task that could evolve over time depending on the natural history of the disease and the evolution of the scientific knowledge. Most rare diseases have genetic causes and recent improvements of sequencing techniques contribute to the discovery of many new diseases every year. Diagnosis coding in the rare disease field requires data from multiple knowledge bases to be aggregated in order to offer the clinician a global information space from possible diagnosis to clinical signs (phenotypes) and known genetic mutations (genotype). Nowadays, the major barrier to the coding activity is the lack of consolidation of such information scattered in different thesaurus such as Orphanet, OMIM or HPO. The Linking Open data for Rare Diseases (LORD) web portal we developed stands as the first attempt to fill this gap by offering an integrated view of 8,400 rare diseases linked to more than 14,500 signs and 3,270 genes. The application provides a browsing feature to navigate through the relationships between diseases, signs and genes, and some Application Programming Interfaces to help its integration in health information systems in routine.

  9. BIG: a Grid Portal for Biomedical Data and Images

    Directory of Open Access Journals (Sweden)

    Giovanni Aloisio

    2004-06-01

    Full Text Available Modern management of biomedical systems involves the use of many distributed resources, such as high performance computational resources to analyze biomedical data, mass storage systems to store them, medical instruments (microscopes, tomographs, etc., advanced visualization and rendering tools. Grids offer the computational power, security and availability needed by such novel applications. This paper presents BIG (Biomedical Imaging Grid, a Web-based Grid portal for management of biomedical information (data and images in a distributed environment. BIG is an interactive environment that deals with complex user's requests, regarding the acquisition of biomedical data, the "processing" and "delivering" of biomedical images, using the power and security of Computational Grids.

  10. Environmental/Biomedical Terminology Index

    Energy Technology Data Exchange (ETDEWEB)

    Huffstetler, J.K.; Dailey, N.S.; Rickert, L.W.; Chilton, B.D.

    1976-12-01

    The Information Center Complex (ICC), a centrally administered group of information centers, provides information support to environmental and biomedical research groups and others within and outside Oak Ridge National Laboratory. In-house data base building and development of specialized document collections are important elements of the ongoing activities of these centers. ICC groups must be concerned with language which will adequately classify and insure retrievability of document records. Language control problems are compounded when the complexity of modern scientific problem solving demands an interdisciplinary approach. Although there are several word lists, indexes, and thesauri specific to various scientific disciplines usually grouped as Environmental Sciences, no single generally recognized authority can be used as a guide to the terminology of all environmental science. If biomedical terminology for the description of research on environmental effects is also needed, the problem becomes even more complex. The building of a word list which can be used as a general guide to the environmental/biomedical sciences has been a continuing activity of the Information Center Complex. This activity resulted in the publication of the Environmental Biomedical Terminology Index (EBTI).

  11. Environmental/Biomedical Terminology Index

    International Nuclear Information System (INIS)

    Huffstetler, J.K.; Dailey, N.S.; Rickert, L.W.; Chilton, B.D.

    1976-12-01

    The Information Center Complex (ICC), a centrally administered group of information centers, provides information support to environmental and biomedical research groups and others within and outside Oak Ridge National Laboratory. In-house data base building and development of specialized document collections are important elements of the ongoing activities of these centers. ICC groups must be concerned with language which will adequately classify and insure retrievability of document records. Language control problems are compounded when the complexity of modern scientific problem solving demands an interdisciplinary approach. Although there are several word lists, indexes, and thesauri specific to various scientific disciplines usually grouped as Environmental Sciences, no single generally recognized authority can be used as a guide to the terminology of all environmental science. If biomedical terminology for the description of research on environmental effects is also needed, the problem becomes even more complex. The building of a word list which can be used as a general guide to the environmental/biomedical sciences has been a continuing activity of the Information Center Complex. This activity resulted in the publication of the Environmental Biomedical Terminology Index

  12. Biomedical engineering fundamentals

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

    Known as the bible of biomedical engineering, The Biomedical Engineering Handbook, Fourth Edition, sets the standard against which all other references of this nature are measured. As such, it has served as a major resource for both skilled professionals and novices to biomedical engineering.Biomedical Engineering Fundamentals, the first volume of the handbook, presents material from respected scientists with diverse backgrounds in physiological systems, biomechanics, biomaterials, bioelectric phenomena, and neuroengineering. More than three dozen specific topics are examined, including cardia

  13. Biomedical Imaging Principles and Applications

    CERN Document Server

    Salzer, Reiner

    2012-01-01

    This book presents and describes imaging technologies that can be used to study chemical processes and structural interactions in dynamic systems, principally in biomedical systems. The imaging technologies, largely biomedical imaging technologies such as MRT, Fluorescence mapping, raman mapping, nanoESCA, and CARS microscopy, have been selected according to their application range and to the chemical information content of their data. These technologies allow for the analysis and evaluation of delicate biological samples, which must not be disturbed during the profess. Ultimately, this may me

  14. Introduction to biomedical engineering

    CERN Document Server

    Enderle, John D; Blanchard, Susan M

    2005-01-01

    Under the direction of John Enderle, Susan Blanchard and Joe Bronzino, leaders in the field have contributed chapters on the most relevant subjects for biomedical engineering students. These chapters coincide with courses offered in all biomedical engineering programs so that it can be used at different levels for a variety of courses of this evolving field. Introduction to Biomedical Engineering, Second Edition provides a historical perspective of the major developments in the biomedical field. Also contained within are the fundamental principles underlying biomedical engineering design, analysis, and modeling procedures. The numerous examples, drill problems and exercises are used to reinforce concepts and develop problem-solving skills making this book an invaluable tool for all biomedical students and engineers. New to this edition: Computational Biology, Medical Imaging, Genomics and Bioinformatics. * 60% update from first edition to reflect the developing field of biomedical engineering * New chapters o...

  15. Preserving medical correctness, readability and consistency in de-identified health records

    DEFF Research Database (Denmark)

    Pantazos, Kostas; Lauesen, Søren; Lippert, Søren

    2016-01-01

    A health record database contains structured data fields that identify the patient, such as patient ID, patient name, e-mail and phone number. These data are fairly easy to de-identify, that is, replace with other identifiers. However, these data also occur in fields with doctors’ free-text notes...... database, ending up with 323,122 patient health records. We had to invent many methods for de-identifying potential identifiers in the free-text notes. The de-identified health records should be used with caution for statistical purposes because we removed health records that were so special...

  16. CNN-based ranking for biomedical entity normalization.

    Science.gov (United States)

    Li, Haodi; Chen, Qingcai; Tang, Buzhou; Wang, Xiaolong; Xu, Hua; Wang, Baohua; Huang, Dong

    2017-10-03

    Most state-of-the-art biomedical entity normalization systems, such as rule-based systems, merely rely on morphological information of entity mentions, but rarely consider their semantic information. In this paper, we introduce a novel convolutional neural network (CNN) architecture that regards biomedical entity normalization as a ranking problem and benefits from semantic information of biomedical entities. The CNN-based ranking method first generates candidates using handcrafted rules, and then ranks the candidates according to their semantic information modeled by CNN as well as their morphological information. Experiments on two benchmark datasets for biomedical entity normalization show that our proposed CNN-based ranking method outperforms traditional rule-based method with state-of-the-art performance. We propose a CNN architecture that regards biomedical entity normalization as a ranking problem. Comparison results show that semantic information is beneficial to biomedical entity normalization and can be well combined with morphological information in our CNN architecture for further improvement.

  17. Applications of computational intelligence in biomedical technology

    CERN Document Server

    Majernik, Jaroslav; Pancerz, Krzysztof; Zaitseva, Elena

    2016-01-01

    This book presents latest results and selected applications of Computational Intelligence in Biomedical Technologies. Most of contributions deal with problems of Biomedical and Medical Informatics, ranging from theoretical considerations to practical applications. Various aspects of development methods and algorithms in Biomedical and Medical Informatics as well as Algorithms for medical image processing, modeling methods are discussed. Individual contributions also cover medical decision making support, estimation of risks of treatments, reliability of medical systems, problems of practical clinical applications and many other topics  This book is intended for scientists interested in problems of Biomedical Technologies, for researchers and academic staff, for all dealing with Biomedical and Medical Informatics, as well as PhD students. Useful information is offered also to IT companies, developers of equipment and/or software for medicine and medical professionals.  .

  18. Biomedical engineering principles

    CERN Document Server

    Ritter, Arthur B; Valdevit, Antonio; Ascione, Alfred N

    2011-01-01

    Introduction: Modeling of Physiological ProcessesCell Physiology and TransportPrinciples and Biomedical Applications of HemodynamicsA Systems Approach to PhysiologyThe Cardiovascular SystemBiomedical Signal ProcessingSignal Acquisition and ProcessingTechniques for Physiological Signal ProcessingExamples of Physiological Signal ProcessingPrinciples of BiomechanicsPractical Applications of BiomechanicsBiomaterialsPrinciples of Biomedical Capstone DesignUnmet Clinical NeedsEntrepreneurship: Reasons why Most Good Designs Never Get to MarketAn Engineering Solution in Search of a Biomedical Problem

  19. Fundamental of biomedical engineering

    CERN Document Server

    Sawhney, GS

    2007-01-01

    About the Book: A well set out textbook explains the fundamentals of biomedical engineering in the areas of biomechanics, biofluid flow, biomaterials, bioinstrumentation and use of computing in biomedical engineering. All these subjects form a basic part of an engineer''s education. The text is admirably suited to meet the needs of the students of mechanical engineering, opting for the elective of Biomedical Engineering. Coverage of bioinstrumentation, biomaterials and computing for biomedical engineers can meet the needs of the students of Electronic & Communication, Electronic & Instrumenta

  20. International symposium on Biomedical Data Infrastructure (BDI 2013)

    CERN Document Server

    Dhillon, Sarinder; Advances in biomedical infrastructure 2013

    2013-01-01

    Current Biomedical Databases are independently administered in geographically distinct locations, lending them almost ideally to adoption of intelligent data management approaches. This book focuses on research issues, problems and opportunities in Biomedical Data Infrastructure identifying new issues and directions for future research in Biomedical Data and Information Retrieval, Semantics in Biomedicine, and Biomedical Data Modeling and Analysis. The book will be a useful guide for researchers, practitioners, and graduate-level students interested in learning state-of-the-art development in biomedical data management.

  1. Figure mining for biomedical research.

    Science.gov (United States)

    Rodriguez-Esteban, Raul; Iossifov, Ivan

    2009-08-15

    Figures from biomedical articles contain valuable information difficult to reach without specialized tools. Currently, there is no search engine that can retrieve specific figure types. This study describes a retrieval method that takes advantage of principles in image understanding, text mining and optical character recognition (OCR) to retrieve figure types defined conceptually. A search engine was developed to retrieve tables and figure types to aid computational and experimental research. http://iossifovlab.cshl.edu/figurome/.

  2. Biomedical applications engineering tasks

    Science.gov (United States)

    Laenger, C. J., Sr.

    1976-01-01

    The engineering tasks performed in response to needs articulated by clinicians are described. Initial contacts were made with these clinician-technology requestors by the Southwest Research Institute NASA Biomedical Applications Team. The basic purpose of the program was to effectively transfer aerospace technology into functional hardware to solve real biomedical problems.

  3. Statistics and Biomedical Informatics in Forensic Sciences

    Czech Academy of Sciences Publication Activity Database

    Zvárová, Jana

    2009-01-01

    Roč. 20, č. 6 (2009), s. 743-750 ISSN 1180-4009. [TIES 2007. Annual Meeting of the International Environmental Society /18./. Mikulov, 16.08.2007-20.08.2007] Institutional research plan: CEZ:AV0Z10300504 Keywords : biomedical informatics * biomedical statistics * genetic information * forensic dentistry Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 1.000, year: 2009

  4. The Ontology for Biomedical Investigations.

    Science.gov (United States)

    Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H; Bug, Bill; Chibucos, Marcus C; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Soldatova, Larisa N; Stoeckert, Christian J; Taylor, Chris F; Torniai, Carlo; Turner, Jessica A; Vita, Randi; Whetzel, Patricia L; Zheng, Jie

    2016-01-01

    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed

  5. Education of biomedical engineering in Taiwan.

    Science.gov (United States)

    Lin, Kang-Ping; Kao, Tsair; Wang, Jia-Jung; Chen, Mei-Jung; Su, Fong-Chin

    2014-01-01

    Biomedical Engineers (BME) play an important role in medical and healthcare society. Well educational programs are important to support the healthcare systems including hospitals, long term care organizations, manufacture industries of medical devices/instrumentations/systems, and sales/services companies of medical devices/instrumentations/system. In past 30 more years, biomedical engineering society has accumulated thousands people hold a biomedical engineering degree, and work as a biomedical engineer in Taiwan. Most of BME students can be trained in biomedical engineering departments with at least one of specialties in bioelectronics, bio-information, biomaterials or biomechanics. Students are required to have internship trainings in related institutions out of campus for 320 hours before graduating. Almost all the biomedical engineering departments are certified by IEET (Institute of Engineering Education Taiwan), and met the IEET requirement in which required mathematics and fundamental engineering courses. For BMEs after graduation, Taiwanese Society of Biomedical Engineering (TSBME) provides many continue-learning programs and certificates for all members who expect to hold the certification as a professional credit in his working place. In current status, many engineering departments in university are continuously asked to provide joint programs with BME department to train much better quality students. BME is one of growing fields in Taiwan.

  6. Biomedical applications of polymers

    CERN Document Server

    Gebelein, C G

    1991-01-01

    The biomedical applications of polymers span an extremely wide spectrum of uses, including artificial organs, skin and soft tissue replacements, orthopaedic applications, dental applications, and controlled release of medications. No single, short review can possibly cover all these items in detail, and dozens of books andhundreds of reviews exist on biomedical polymers. Only a few relatively recent examples will be cited here;additional reviews are listed under most of the major topics in this book. We will consider each of the majorclassifications of biomedical polymers to some extent, inclu

  7. Handbook of biomedical optics

    CERN Document Server

    Boas, David A

    2011-01-01

    Biomedical optics holds tremendous promise to deliver effective, safe, non- or minimally invasive diagnostics and targeted, customizable therapeutics. Handbook of Biomedical Optics provides an in-depth treatment of the field, including coverage of applications for biomedical research, diagnosis, and therapy. It introduces the theory and fundamentals of each subject, ensuring accessibility to a wide multidisciplinary readership. It also offers a view of the state of the art and discusses advantages and disadvantages of various techniques.Organized into six sections, this handbook: Contains intr

  8. Biomedical Engineering Desk Reference

    CERN Document Server

    Ratner, Buddy D; Schoen, Frederick J; Lemons, Jack E; Dyro, Joseph; Martinsen, Orjan G; Kyle, Richard; Preim, Bernhard; Bartz, Dirk; Grimnes, Sverre; Vallero, Daniel; Semmlow, John; Murray, W Bosseau; Perez, Reinaldo; Bankman, Isaac; Dunn, Stanley; Ikada, Yoshito; Moghe, Prabhas V; Constantinides, Alkis

    2009-01-01

    A one-stop Desk Reference, for Biomedical Engineers involved in the ever expanding and very fast moving area; this is a book that will not gather dust on the shelf. It brings together the essential professional reference content from leading international contributors in the biomedical engineering field. Material covers a broad range of topics including: Biomechanics and Biomaterials; Tissue Engineering; and Biosignal Processing* A hard-working desk reference providing all the essential material needed by biomedical and clinical engineers on a day-to-day basis * Fundamentals, key techniques,

  9. Powering biomedical devices

    CERN Document Server

    Romero, Edwar

    2013-01-01

    From exoskeletons to neural implants, biomedical devices are no less than life-changing. Compact and constant power sources are necessary to keep these devices running efficiently. Edwar Romero's Powering Biomedical Devices reviews the background, current technologies, and possible future developments of these power sources, examining not only the types of biomedical power sources available (macro, mini, MEMS, and nano), but also what they power (such as prostheses, insulin pumps, and muscular and neural stimulators), and how they work (covering batteries, biofluids, kinetic and ther

  10. Handbook of photonics for biomedical engineering

    CERN Document Server

    Kim, Donghyun; Somekh, Michael

    2017-01-01

    Nanophotonics has emerged rapidly into technological mainstream with the advent and maturity of nanotechnology available in photonics and enabled many new exciting applications in the area of biomedical science and engineering that were unimagined even a few years ago with conventional photonic engineering techniques. Handbook of Nanophotonics in Biomedical Engineering is intended to be a reliable resource to a wealth of information on nanophotonics that can inspire readers by detailing emerging and established possibilities of nanophotonics in biomedical science and engineering applications. This comprehensive reference presents not only the basics of nanophotonics but also explores recent experimental and clinical methods used in biomedical and bioengineering research. Each peer-reviewed chapter of this book discusses fundamental aspects and materials/fabrication issues of nanophotonics, as well as applications in interfaces, cell, tissue, animal studies, and clinical engineering. The organization provides ...

  11. Review of Biomedical Image Processing

    Directory of Open Access Journals (Sweden)

    Ciaccio Edward J

    2011-11-01

    Full Text Available Abstract This article is a review of the book: 'Biomedical Image Processing', by Thomas M. Deserno, which is published by Springer-Verlag. Salient information that will be useful to decide whether the book is relevant to topics of interest to the reader, and whether it might be suitable as a course textbook, are presented in the review. This includes information about the book details, a summary, the suitability of the text in course and research work, the framework of the book, its specific content, and conclusions.

  12. NDE in biomedical engineering

    International Nuclear Information System (INIS)

    Bhagwat, Aditya; Kumar, Pradeep

    2015-01-01

    Biomedical Engineering (BME) is an interdisciplinary field, marking the conjunction of Medical and Engineering disciplines. It combines the design and problem solving skills of engineering with medical and biological sciences to advance health care treatment, including diagnosis, monitoring, and therapy

  13. Biomedical signal analysis

    CERN Document Server

    Rangayyan, Rangaraj M

    2015-01-01

    The book will help assist a reader in the development of techniques for analysis of biomedical signals and computer aided diagnoses with a pedagogical examination of basic and advanced topics accompanied by over 350 figures and illustrations. Wide range of filtering techniques presented to address various applications. 800 mathematical expressions and equations. Practical questions, problems and laboratory exercises. Includes fractals and chaos theory with biomedical applications.

  14. Magnetic nanoparticles for biomedical applications

    International Nuclear Information System (INIS)

    Krustev, P.; Ruskov, T.

    2007-01-01

    In this paper we describe different biomedical application using magnetic nanoparticles. Over the past decade, a number of biomedical applications have begun to emerge for magnetic nanoparticles of differing sizes, shapes, and compositions. Areas under investigation include targeted drug delivery, ultra-sensitive disease detection, gene therapy, high throughput genetic screening, biochemical sensing, and rapid toxicity cleansing. Magnetic nanoparticles exhibit ferromagnetic or superparamagnetic behavior, magnetizing strongly under an applied field. In the second case (superparamagnetic nanoparticles) there is no permanent magnetism once the field is removed. The superparamagnetic nanoparticles are highly attractive as in vivo probes or in vitro tools to extract information on biochemical systems. The optical properties of magnetic metal nanoparticles are spectacular and, therefore, have promoted a great deal of excitement during the last few decades. Many applications as MRI imaging and hyperthermia rely on the use of iron oxide particles. Moreover magnetic nanoparticles conjugated with antibodies are also applied to hyperthermia and have enabled tumor specific contrast enhancement in MRI. Other promising biomedical applications are connected with tumor cells treated with magnetic nanoparticles with X-ray ionizing radiation, which employs magnetic nanoparticles as a complementary radiate source inside the tumor. (authors)

  15. Biomedical signal and image processing.

    Science.gov (United States)

    Cerutti, Sergio; Baselli, Giuseppe; Bianchi, Anna; Caiani, Enrico; Contini, Davide; Cubeddu, Rinaldo; Dercole, Fabio; Rienzo, Luca; Liberati, Diego; Mainardi, Luca; Ravazzani, Paolo; Rinaldi, Sergio; Signorini, Maria; Torricelli, Alessandro

    2011-01-01

    Generally, physiological modeling and biomedical signal processing constitute two important paradigms of biomedical engineering (BME): their fundamental concepts are taught starting from undergraduate studies and are more completely dealt with in the last years of graduate curricula, as well as in Ph.D. courses. Traditionally, these two cultural aspects were separated, with the first one more oriented to physiological issues and how to model them and the second one more dedicated to the development of processing tools or algorithms to enhance useful information from clinical data. A practical consequence was that those who did models did not do signal processing and vice versa. However, in recent years,the need for closer integration between signal processing and modeling of the relevant biological systems emerged very clearly [1], [2]. This is not only true for training purposes(i.e., to properly prepare the new professional members of BME) but also for the development of newly conceived research projects in which the integration between biomedical signal and image processing (BSIP) and modeling plays a crucial role. Just to give simple examples, topics such as brain–computer machine or interfaces,neuroengineering, nonlinear dynamical analysis of the cardiovascular (CV) system,integration of sensory-motor characteristics aimed at the building of advanced prostheses and rehabilitation tools, and wearable devices for vital sign monitoring and others do require an intelligent fusion of modeling and signal processing competences that are certainly peculiar of our discipline of BME.

  16. Archives of Medical and Biomedical Research: Submissions

    African Journals Online (AJOL)

    Author Guidelines. INFORMATION FOR CONTRIBUTORS This information can also be accessed at http://www.iambr.info/AMBR/author_guidelines.html Articles to Archives of Medical and Biomedical Research are submitted under the condition that the work described has not been published or is not being considered for ...

  17. CONAN : Text Mining in the Biomedical Domain

    NARCIS (Netherlands)

    Malik, R.

    2006-01-01

    This thesis is about Text Mining. Extracting important information from literature. In the last years, the number of biomedical articles and journals is growing exponentially. Scientists might not find the information they want because of the large number of publications. Therefore a system was

  18. Data sharing platforms for de-identified data from human clinical trials.

    Science.gov (United States)

    Huser, Vojtech; Shmueli-Blumberg, Dikla

    2018-04-01

    Data sharing of de-identified individual participant data is being adopted by an increasing number of sponsors of human clinical trials. In addition to standardizing data syntax for shared trial data, semantic integration of various data elements is the focus of several initiatives that define research common data elements. This perspective article, in the first part, compares several data sharing platforms for de-identified clinical research data in terms of their size, policies and supported features. In the second part, we use a case study approach to describe in greater detail one data sharing platform (Data Share from National Institute of Drug Abuse). We present data on the past use of the platform, data formats offered, data de-identification approaches and its use of research common data elements. We conclude with a summary of current and expected future trends that facilitate secondary research use of data from completed human clinical trials.

  19. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

    2011-08-11

    Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  20. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

    Advances in Biomedical Engineering, Volume 6, is a collection of papers that discusses the role of integrated electronics in medical systems and the usage of biological mathematical models in biological systems. Other papers deal with the health care systems, the problems and methods of approach toward rehabilitation, as well as the future of biomedical engineering. One paper discusses the use of system identification as it applies to biological systems to estimate the values of a number of parameters (for example, resistance, diffusion coefficients) by indirect means. More particularly, the i

  1. Biomedical enhancements as justice.

    Science.gov (United States)

    Nam, Jeesoo

    2015-02-01

    Biomedical enhancements, the applications of medical technology to make better those who are neither ill nor deficient, have made great strides in the past few decades. Using Amartya Sen's capability approach as my framework, I argue in this article that far from being simply permissible, we have a prima facie moral obligation to use these new developments for the end goal of promoting social justice. In terms of both range and magnitude, the use of biomedical enhancements will mark a radical advance in how we compensate the most disadvantaged members of society. © 2013 John Wiley & Sons Ltd.

  2. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

    Advances in Biomedical Engineering, Volume 5, is a collection of papers that deals with application of the principles and practices of engineering to basic and applied biomedical research, development, and the delivery of health care. The papers also describe breakthroughs in health improvements, as well as basic research that have been accomplished through clinical applications. One paper examines engineering principles and practices that can be applied in developing therapeutic systems by a controlled delivery system in drug dosage. Another paper examines the physiological and materials vari

  3. 78 FR 60290 - Availability of Masked and De-identified Non-Summary Safety and Efficacy Data; Reopening of...

    Science.gov (United States)

    2013-10-01

    ..., 2013, on the following topics: (1) What factors should be considered in masking study data (e.g., data...] Availability of Masked and De-identified Non-Summary Safety and Efficacy Data; Reopening of Comment Period... of Masked and De- identified Non-Summary Safety and Efficacy Data; Request for Comments,'' which...

  4. Stemcell Information: SKIP000697 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Southern blot analysis Yes ... Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Research W...hitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical... Research Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical R...esearch Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.stemc

  5. Stemcell Information: SKIP000979 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available ot analysis Yes ... Yes qRT-PCR Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Resea...rch Whitehead Institute for Biomedical Research Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.stemcr.

  6. Stemcell Information: SKIP000983 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available RT-PCR Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Researc...h Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical... Research Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.st

  7. Stemcell Information: SKIP000975 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Rese...arch Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Rudolf Jaenisch... Rudolf Jaenisch Information Only Whitehead Institute for Biomedical Research Whi...tehead Institute for Biomedical Research ... 24936472 10.1016/j.stemcr.2014.03.014 Genetic and chemical cor

  8. Stemcell Information: SKIP000694 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available outhern blot analysis Yes ... Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Research Whi...tehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical... Research Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical Res...earch Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.stemcr.

  9. Stemcell Information: SKIP000698 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lf Jaenisch Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedica...l Research Whitehead Institute for Biomedical Research R...udolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical

  10. Stemcell Information: SKIP000696 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available outhern blot analysis Yes ... Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Research Whi...tehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical... Research Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical Res...earch Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.stemcr.

  11. Stemcell Information: SKIP000699 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lf Jaenisch Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedica...l Research Whitehead Institute for Biomedical Research R...udolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical

  12. Stemcell Information: SKIP000977 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available qRT-PCR Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research ...Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.stemcr.2014.03.014 Genetic a

  13. Stemcell Information: SKIP000976 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Rese...arch Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Rudolf Jaenisch... Rudolf Jaenisch Information Only Whitehead Institute for Biomedical Research Whi...tehead Institute for Biomedical Research ... 24936472 10.1016/j.stemcr.2014.03.014 Genetic and chemical cor

  14. Stemcell Information: SKIP000981 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available RT-PCR Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Researc...h Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical... Research Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.st

  15. Stemcell Information: SKIP000980 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available es ... Yes qRT-PCR Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical... Research Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.stemcr.2014.03.014 G

  16. Stemcell Information: SKIP000695 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available outhern blot analysis Yes ... Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Research Whi...tehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical... Research Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical Res...earch Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.stemcr.

  17. Stemcell Information: SKIP000700 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available lf Jaenisch Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedica...l Research Whitehead Institute for Biomedical Research R...udolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical

  18. Stemcell Information: SKIP000978 [SKIP Stemcell Database[Archive

    Lifescience Database Archive (English)

    Full Text Available qRT-PCR Rudolf Jaenisch Rudolf Jaenisch Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research Whitehead Institute for Biomedical Research ...Rudolf Jaenisch Rudolf Jaenisch Information Only Whitehead Institute for Biomedical... Research Whitehead Institute for Biomedical Research ... 24936472 10.1016/j.stemcr.2014.03.014 Genetic a

  19. Biomedical Engineering in Modern Society

    Science.gov (United States)

    Attinger, E. O.

    1971-01-01

    Considers definition of biomedical engineering (BME) and how biomedical engineers should be trained. State of the art descriptions of BME and BME education are followed by a brief look at the future of BME. (TS)

  20. Biomedical Image Registration

    DEFF Research Database (Denmark)

    This book constitutes the refereed proceedings of the 8th International Workshop on Biomedical Image Registration, WBIR 2018, held in Leiden, The Netherlands, in June 2018. The 11 full and poster papers included in this volume were carefully reviewed and selected from 17 submitted papers. The pap...

  1. Careers in biomedical engineering.

    Science.gov (United States)

    Madrid, R E; Rotger, V I; Herrera, M C

    2010-01-01

    Although biomedical engineering was started in Argentina about 35 years ago, it has had a sustained growth for the last 25 years in human resources, with the emergence of new undergraduate and postgraduate careers, as well as in research, knowledge, technological development, and health care.

  2. Anatomy for Biomedical Engineers

    Science.gov (United States)

    Carmichael, Stephen W.; Robb, Richard A.

    2008-01-01

    There is a perceived need for anatomy instruction for graduate students enrolled in a biomedical engineering program. This appeared especially important for students interested in and using medical images. These students typically did not have a strong background in biology. The authors arranged for students to dissect regions of the body that…

  3. Biomedical research applications

    International Nuclear Information System (INIS)

    Anon.

    1982-01-01

    The biomedical research Panel believes that the Calutron facility at Oak Ridge is a national and international resource of immense scientific value and of fundamental importance to continued biomedical research. This resource is essential to the development of new isotope uses in biology and medicine. It should therefore be nurtured by adequate support and operated in a way that optimizes its services to the scientific and technological community. The Panel sees a continuing need for a reliable supply of a wide variety of enriched stable isotopes. The past and present utilization of stable isotopes in biomedical research is documented in Appendix 7. Future requirements for stable isotopes are impossible to document, however, because of the unpredictability of research itself. Nonetheless we expect the demand for isotopes to increase in parallel with the continuing expansion of biomedical research as a whole. There are a number of promising research projects at the present time, and these are expected to lead to an increase in production requirements. The Panel also believes that a high degree of priority should be given to replacing the supplies of the 65 isotopes (out of the 224 previously available enriched isotopes) no longer available from ORNL

  4. Double-compression method for biomedical images

    Science.gov (United States)

    Antonenko, Yevhenii A.; Mustetsov, Timofey N.; Hamdi, Rami R.; Małecka-Massalska, Teresa; Orshubekov, Nurbek; DzierŻak, RóŻa; Uvaysova, Svetlana

    2017-08-01

    This paper describes a double compression method (DCM) of biomedical images. A comparison of image compression factors in size JPEG, PNG and developed DCM was carried out. The main purpose of the DCM - compression of medical images while maintaining the key points that carry diagnostic information. To estimate the minimum compression factor an analysis of the coding of random noise image is presented.

  5. Status of Research in Biomedical Engineering 1968.

    Science.gov (United States)

    National Inst. of General Medical Sciences (NIH), Bethesda, MD.

    This status report is divided into eight sections. The first four represent the classical engineering or building aspects of bioengineering and deal with biomedical instrumentation, prosthetics, man-machine systems and computer and information systems. The next three sections are related to the scientific, intellectual and academic influence of…

  6. Should biomedical research be like Airbnb?

    Directory of Open Access Journals (Sweden)

    Vivien R Bonazzi

    2017-04-01

    Full Text Available The thesis presented here is that biomedical research is based on the trusted exchange of services. That exchange would be conducted more efficiently if the trusted software platforms to exchange those services, if they exist, were more integrated. While simpler and narrower in scope than the services governing biomedical research, comparison to existing internet-based platforms, like Airbnb, can be informative. We illustrate how the analogy to internet-based platforms works and does not work and introduce The Commons, under active development at the National Institutes of Health (NIH and elsewhere, as an example of the move towards platforms for research.

  7. Should biomedical research be like Airbnb?

    Science.gov (United States)

    Bonazzi, Vivien R; Bourne, Philip E

    2017-04-01

    The thesis presented here is that biomedical research is based on the trusted exchange of services. That exchange would be conducted more efficiently if the trusted software platforms to exchange those services, if they exist, were more integrated. While simpler and narrower in scope than the services governing biomedical research, comparison to existing internet-based platforms, like Airbnb, can be informative. We illustrate how the analogy to internet-based platforms works and does not work and introduce The Commons, under active development at the National Institutes of Health (NIH) and elsewhere, as an example of the move towards platforms for research.

  8. Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.

    Science.gov (United States)

    Amith, Muhammad; He, Zhe; Bian, Jiang; Lossio-Ventura, Juan Antonio; Tao, Cui

    2018-04-01

    With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natural language processing, as well as decision support for health information systems and biomedical research. Biomedical ontologies and controlled terminologies are intended to assure interoperability. Nevertheless, the quality of biomedical ontologies has hindered their applicability and subsequent adoption in real-world applications. Ontology evaluation is an integral part of ontology development and maintenance. In the biomedicine domain, ontology evaluation is often conducted by third parties as a quality assurance (or auditing) effort that focuses on identifying modeling errors and inconsistencies. In this work, we first organized four categorical schemes of ontology evaluation methods in the existing literature to create an integrated taxonomy. Further, to understand the ontology evaluation practice in the biomedicine domain, we reviewed a sample of 200 ontologies from the National Center for Biomedical Ontology (NCBO) BioPortal-the largest repository for biomedical ontologies-and observed that only 15 of these ontologies have documented evaluation in their corresponding inception papers. We then surveyed the recent quality assurance approaches for biomedical ontologies and their use. We also mapped these quality assurance approaches to the ontology evaluation criteria. It is our anticipation that ontology evaluation and quality assurance approaches will be more widely adopted in the development life cycle of biomedical ontologies. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Finding and accessing diagrams in biomedical publications.

    Science.gov (United States)

    Kuhn, Tobias; Luong, ThaiBinh; Krauthammer, Michael

    2012-01-01

    Complex relationships in biomedical publications are often communicated by diagrams such as bar and line charts, which are a very effective way of summarizing and communicating multi-faceted data sets. Given the ever-increasing amount of published data, we argue that the precise retrieval of such diagrams is of great value for answering specific and otherwise hard-to-meet information needs. To this end, we demonstrate the use of advanced image processing and classification for identifying bar and line charts by the shape and relative location of the different image elements that make up the charts. With recall and precisions of close to 90% for the detection of relevant figures, we discuss the use of this technology in an existing biomedical image search engine, and outline how it enables new forms of literature queries over biomedical relationships that are represented in these charts.

  10. Biomedical signals, imaging, and informatics

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

    Known as the bible of biomedical engineering, The Biomedical Engineering Handbook, Fourth Edition, sets the standard against which all other references of this nature are measured. As such, it has served as a major resource for both skilled professionals and novices to biomedical engineering.Biomedical Signals, Imaging, and Informatics, the third volume of the handbook, presents material from respected scientists with diverse backgrounds in biosignal processing, medical imaging, infrared imaging, and medical informatics.More than three dozen specific topics are examined, including biomedical s

  11. Optical Polarizationin Biomedical Applications

    CERN Document Server

    Tuchin, Valery V; Zimnyakov, Dmitry A

    2006-01-01

    Optical Polarization in Biomedical Applications introduces key developments in optical polarization methods for quantitative studies of tissues, while presenting the theory of polarization transfer in a random medium as a basis for the quantitative description of polarized light interaction with tissues. This theory uses the modified transfer equation for Stokes parameters and predicts the polarization structure of multiple scattered optical fields. The backscattering polarization matrices (Jones matrix and Mueller matrix) important for noninvasive medical diagnostic are introduced. The text also describes a number of diagnostic techniques such as CW polarization imaging and spectroscopy, polarization microscopy and cytometry. As a new tool for medical diagnosis, optical coherent polarization tomography is analyzed. The monograph also covers a range of biomedical applications, among them cataract and glaucoma diagnostics, glucose sensing, and the detection of bacteria.

  12. BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines.

    Science.gov (United States)

    Jácome, Alberto G; Fdez-Riverola, Florentino; Lourenço, Anália

    2016-07-01

    meaningful to that particular scope of research. Conversely, indirect concept associations, i.e. concepts related by other intermediary concepts, can be useful to integrate information from different studies and look into non-trivial relations. The BIOMedical Search Engine Framework supports the development of domain-specific search engines. The key strengths of the framework are modularity and extensibilityin terms of software design, the use of open-source consolidated Web technologies, and the ability to integrate any number of biomedical text mining tools and information resources. Currently, the Smart Drug Search keeps over 1,186,000 documents, containing more than 11,854,000 annotations for 77,200 different concepts. The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  13. Nigerian Journal of Health and Biomedical Sciences: Editorial Policies

    African Journals Online (AJOL)

    Biomedical Engineering Biotechnology in relation to Medicine Clinical Sciences Dental Sciences Environment and Health Health Economics and Management Health Information Management Hygiene and Health Education Legal Aspects of Healthcare Medical Education Nursing Sciences Pharmaceutical Sciences

  14. Biomedical applications of batteries

    Energy Technology Data Exchange (ETDEWEB)

    Latham, Roger [Faculty of Health and Life Sciences, De Montfort University, The Gateway, Leicester, LE1 9BH (United Kingdom); Linford, Roger [The Research Office, De Montfort University, The Gateway, Leicester, LE1 9BH (United Kingdom); Schlindwein, Walkiria [School of Pharmacy, De Montfort University, The Gateway, Leicester, LE1 9BH (United Kingdom)

    2004-08-31

    An overview is presented of the many ways in which batteries and battery materials are used in medicine and in biomedical studies. These include the use of batteries as power sources for motorised wheelchairs, surgical tools, cardiac pacemakers and defibrillators, dynamic prostheses, sensors and monitors for physiological parameters, neurostimulators, devices for pain relief, and iontophoretic, electroporative and related devices for drug administration. The various types of battery and fuel cell used for this wide range of applications will be considered, together with the potential harmful side effects, including accidental ingestion of batteries and the explosive nature of some of the early cardiac pacemaker battery systems.

  15. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1973-01-01

    Advances in Biomedical Engineering, Volume 2, is a collection of papers that discusses the basic sciences, the applied sciences of engineering, the medical sciences, and the delivery of health services. One paper discusses the models of adrenal cortical control, including the secretion and metabolism of cortisol (the controlled process), as well as the initiation and modulation of secretion of ACTH (the controller). Another paper discusses hospital computer systems-application problems, objective evaluation of technology, and multiple pathways for future hospital computer applications. The pos

  16. Statistics in biomedical research

    Directory of Open Access Journals (Sweden)

    González-Manteiga, Wenceslao

    2007-06-01

    Full Text Available The discipline of biostatistics is nowadays a fundamental scientific component of biomedical, public health and health services research. Traditional and emerging areas of application include clinical trials research, observational studies, physiology, imaging, and genomics. The present article reviews the current situation of biostatistics, considering the statistical methods traditionally used in biomedical research, as well as the ongoing development of new methods in response to the new problems arising in medicine. Clearly, the successful application of statistics in biomedical research requires appropriate training of biostatisticians. This training should aim to give due consideration to emerging new areas of statistics, while at the same time retaining full coverage of the fundamentals of statistical theory and methodology. In addition, it is important that students of biostatistics receive formal training in relevant biomedical disciplines, such as epidemiology, clinical trials, molecular biology, genetics, and neuroscience.La Bioestadística es hoy en día una componente científica fundamental de la investigación en Biomedicina, salud pública y servicios de salud. Las áreas tradicionales y emergentes de aplicación incluyen ensayos clínicos, estudios observacionales, fisología, imágenes, y genómica. Este artículo repasa la situación actual de la Bioestadística, considerando los métodos estadísticos usados tradicionalmente en investigación biomédica, así como los recientes desarrollos de nuevos métodos, para dar respuesta a los nuevos problemas que surgen en Medicina. Obviamente, la aplicación fructífera de la estadística en investigación biomédica exige una formación adecuada de los bioestadísticos, formación que debería tener en cuenta las áreas emergentes en estadística, cubriendo al mismo tiempo los fundamentos de la teoría estadística y su metodología. Es importante, además, que los estudiantes de

  17. Biomedical signals and systems

    CERN Document Server

    Tranquillo, Joseph V

    2013-01-01

    Biomedical Signals and Systems is meant to accompany a one-semester undergraduate signals and systems course. It may also serve as a quick-start for graduate students or faculty interested in how signals and systems techniques can be applied to living systems. The biological nature of the examples allows for systems thinking to be applied to electrical, mechanical, fluid, chemical, thermal and even optical systems. Each chapter focuses on a topic from classic signals and systems theory: System block diagrams, mathematical models, transforms, stability, feedback, system response, control, time

  18. Biomedical photonics handbook

    CERN Document Server

    Vo-Dinh, Tuan

    2003-01-01

    1.Biomedical Photonics: A Revolution at the Interface of Science and Technology, T. Vo-DinhPHOTONICS AND TISSUE OPTICS2.Optical Properties of Tissues, J. Mobley and T. Vo-Dinh3.Light-Tissue Interactions, V.V. Tuchin 4.Theoretical Models and Algorithms in Optical Diffusion Tomography, S.J. Norton and T. Vo-DinhPHOTONIC DEVICES5.Laser Light in Biomedicine and the Life Sciences: From the Present to the Future, V.S. Letokhov6.Basic Instrumentation in Photonics, T. Vo-Dinh7.Optical Fibers and Waveguides for Medical Applications, I. Gannot and

  19. Research evaluation support services in biomedical libraries.

    Science.gov (United States)

    Gutzman, Karen Elizabeth; Bales, Michael E; Belter, Christopher W; Chambers, Thane; Chan, Liza; Holmes, Kristi L; Lu, Ya-Ling; Palmer, Lisa A; Reznik-Zellen, Rebecca C; Sarli, Cathy C; Suiter, Amy M; Wheeler, Terrie R

    2018-01-01

    The paper provides a review of current practices related to evaluation support services reported by seven biomedical and research libraries. A group of seven libraries from the United States and Canada described their experiences with establishing evaluation support services at their libraries. A questionnaire was distributed among the libraries to elicit information as to program development, service and staffing models, campus partnerships, training, products such as tools and reports, and resources used for evaluation support services. The libraries also reported interesting projects, lessons learned, and future plans. The seven libraries profiled in this paper report a variety of service models in providing evaluation support services to meet the needs of campus stakeholders. The service models range from research center cores, partnerships with research groups, and library programs with staff dedicated to evaluation support services. A variety of products and services were described such as an automated tool to develop rank-based metrics, consultation on appropriate metrics to use for evaluation, customized publication and citation reports, resource guides, classes and training, and others. Implementing these services has allowed the libraries to expand their roles on campus and to contribute more directly to the research missions of their institutions. Libraries can leverage a variety of evaluation support services as an opportunity to successfully meet an array of challenges confronting the biomedical research community, including robust efforts to report and demonstrate tangible and meaningful outcomes of biomedical research and clinical care. These services represent a transformative direction that can be emulated by other biomedical and research libraries.

  20. Towards precision medicine; a new biomedical cosmology.

    Science.gov (United States)

    Vegter, M W

    2018-02-10

    Precision Medicine has become a common label for data-intensive and patient-driven biomedical research. Its intended future is reflected in endeavours such as the Precision Medicine Initiative in the USA. This article addresses the question whether it is possible to discern a new 'medical cosmology' in Precision Medicine, a concept that was developed by Nicholas Jewson to describe comprehensive transformations involving various dimensions of biomedical knowledge and practice, such as vocabularies, the roles of patients and physicians and the conceptualisation of disease. Subsequently, I will elaborate my assessment of the features of Precision Medicine with the help of Michel Foucault, by exploring how precision medicine involves a transformation along three axes: the axis of biomedical knowledge, of biomedical power and of the patient as a self. Patients are encouraged to become the managers of their own health status, while the medical domain is reframed as a data-sharing community, characterised by changing power relationships between providers and patients, producers and consumers. While the emerging Precision Medicine cosmology may surpass existing knowledge frameworks; it obscures previous traditions and reduces research-subjects to mere data. This in turn, means that the individual is both subjected to the neoliberal demand to share personal information, and at the same time has acquired the positive 'right' to become a member of the data-sharing community. The subject has to constantly negotiate the meaning of his or her data, which can either enable self-expression, or function as a commanding Superego.

  1. Facilitating biomedical researchers' interrogation of electronic health record data: Ideas from outside of biomedical informatics.

    Science.gov (United States)

    Hruby, Gregory W; Matsoukas, Konstantina; Cimino, James J; Weng, Chunhua

    2016-04-01

    Electronic health records (EHR) are a vital data resource for research uses, including cohort identification, phenotyping, pharmacovigilance, and public health surveillance. To realize the promise of EHR data for accelerating clinical research, it is imperative to enable efficient and autonomous EHR data interrogation by end users such as biomedical researchers. This paper surveys state-of-art approaches and key methodological considerations to this purpose. We adapted a previously published conceptual framework for interactive information retrieval, which defines three entities: user, channel, and source, by elaborating on channels for query formulation in the context of facilitating end users to interrogate EHR data. We show the current progress in biomedical informatics mainly lies in support for query execution and information modeling, primarily due to emphases on infrastructure development for data integration and data access via self-service query tools, but has neglected user support needed during iteratively query formulation processes, which can be costly and error-prone. In contrast, the information science literature has offered elaborate theories and methods for user modeling and query formulation support. The two bodies of literature are complementary, implying opportunities for cross-disciplinary idea exchange. On this basis, we outline the directions for future informatics research to improve our understanding of user needs and requirements for facilitating autonomous interrogation of EHR data by biomedical researchers. We suggest that cross-disciplinary translational research between biomedical informatics and information science can benefit our research in facilitating efficient data access in life sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Citizen Science for Mining the Biomedical Literature

    Directory of Open Access Journals (Sweden)

    Ginger Tsueng

    2016-12-01

    Full Text Available Biomedical literature represents one of the largest and fastest growing collections of unstructured biomedical knowledge. Finding critical information buried in the literature can be challenging. To extract information from free-flowing text, researchers need to: 1. identify the entities in the text (named entity recognition, 2. apply a standardized vocabulary to these entities (normalization, and 3. identify how entities in the text are related to one another (relationship extraction. Researchers have primarily approached these information extraction tasks through manual expert curation and computational methods. We have previously demonstrated that named entity recognition (NER tasks can be crowdsourced to a group of non-experts via the paid microtask platform, Amazon Mechanical Turk (AMT, and can dramatically reduce the cost and increase the throughput of biocuration efforts. However, given the size of the biomedical literature, even information extraction via paid microtask platforms is not scalable. With our web-based application Mark2Cure (http://mark2cure.org, we demonstrate that NER tasks also can be performed by volunteer citizen scientists with high accuracy. We apply metrics from the Zooniverse Matrices of Citizen Science Success and provide the results here to serve as a basis of comparison for other citizen science projects. Further, we discuss design considerations, issues, and the application of analytics for successfully moving a crowdsourcing workflow from a paid microtask platform to a citizen science platform. To our knowledge, this study is the first application of citizen science to a natural language processing task.

  3. [Biomedical engineering today : An overview from the viewpoint of the German Biomedical Engineering Society].

    Science.gov (United States)

    Schlötelburg, C; Becks, T; Stieglitz, T

    2010-08-01

    Biomedical engineering is characterized by the interdisciplinary co-operation of technology, science, and ways of thinking, probably more than any other technological area. The close interaction of engineering and information sciences with medicine and biology results in innovative products and methods, but also requires high standards for the interdisciplinary transfer of ideas into products for patients' benefits. This article describes the situation of biomedical engineering in Germany. It displays characteristics of the medical device industry and ranks it with respect to the international market. The research landscape is described as well as up-to-date research topics and trends. The national funding situation of research in biomedical engineering is reviewed and existing innovation barriers are discussed.

  4. MOLIERE: Automatic Biomedical Hypothesis Generation System.

    Science.gov (United States)

    Sybrandt, Justin; Shtutman, Michael; Safro, Ilya

    2017-08-01

    Hypothesis generation is becoming a crucial time-saving technique which allows biomedical researchers to quickly discover implicit connections between important concepts. Typically, these systems operate on domain-specific fractions of public medical data. MOLIERE, in contrast, utilizes information from over 24.5 million documents. At the heart of our approach lies a multi-modal and multi-relational network of biomedical objects extracted from several heterogeneous datasets from the National Center for Biotechnology Information (NCBI). These objects include but are not limited to scientific papers, keywords, genes, proteins, diseases, and diagnoses. We model hypotheses using Latent Dirichlet Allocation applied on abstracts found near shortest paths discovered within this network, and demonstrate the effectiveness of MOLIERE by performing hypothesis generation on historical data. Our network, implementation, and resulting data are all publicly available for the broad scientific community.

  5. Lessons Learned from Development of De-identification System for Biomedical Research in a Korean Tertiary Hospital.

    Science.gov (United States)

    Shin, Soo-Yong; Lyu, Yongman; Shin, Yongdon; Choi, Hyo Joung; Park, Jihyun; Kim, Woo-Sung; Lee, Jae Ho

    2013-06-01

    The Korean government has enacted two laws, namely, the Personal Information Protection Act and the Bioethics and Safety Act to prevent the unauthorized use of medical information. To protect patients' privacy by complying with governmental regulations and improve the convenience of research, Asan Medical Center has been developing a de-identification system for biomedical research. We reviewed Korean regulations to define the scope of the de-identification methods and well-known previous biomedical research platforms to extract the functionalities of the systems. Based on these review results, we implemented necessary programs based on the Asan Medical Center Information System framework which was built using the Microsoft. NET Framework and C#. The developed de-identification system comprises three main components: a de-identification tool, a search tool, and a chart review tool. The de-identification tool can substitute a randomly assigned research ID for a hospital patient ID, remove the identifiers in the structured format, and mask them in the unstructured format, i.e., texts. This tool achieved 98.14% precision and 97.39% recall for 6,520 clinical notes. The search tool can find the number of patients which satisfies given search criteria. The chart review tool can provide de-identified patient's clinical data for review purposes. We found that a clinical data warehouse was essential for successful implementation of the de-identification system, and this system should be tightly linked to an electronic Institutional Review Board system for easy operation of honest brokers. Additionally, we found that a secure cloud environment could be adopted to protect patients' privacy more thoroughly.

  6. Finding and Accessing Diagrams in Biomedical Publications

    OpenAIRE

    Kuhn, Tobias; Luong, ThaiBinh; Krauthammer, Michael

    2012-01-01

    Complex relationships in biomedical publications are often communicated by diagrams such as bar and line charts, which are a very effective way of summarizing and communicating multi-faceted data sets. Given the ever-increasing amount of published data, we argue that the precise retrieval of such diagrams is of great value for answering specific and otherwise hard-to-meet information needs. To this end, we demonstrate the use of advanced image processing and classification for identifying bar...

  7. Biomedical ontologies: toward scientific debate.

    Science.gov (United States)

    Maojo, V; Crespo, J; García-Remesal, M; de la Iglesia, D; Perez-Rey, D; Kulikowski, C

    2011-01-01

    Biomedical ontologies have been very successful in structuring knowledge for many different applications, receiving widespread praise for their utility and potential. Yet, the role of computational ontologies in scientific research, as opposed to knowledge management applications, has not been extensively discussed. We aim to stimulate further discussion on the advantages and challenges presented by biomedical ontologies from a scientific perspective. We review various aspects of biomedical ontologies going beyond their practical successes, and focus on some key scientific questions in two ways. First, we analyze and discuss current approaches to improve biomedical ontologies that are based largely on classical, Aristotelian ontological models of reality. Second, we raise various open questions about biomedical ontologies that require further research, analyzing in more detail those related to visual reasoning and spatial ontologies. We outline significant scientific issues that biomedical ontologies should consider, beyond current efforts of building practical consensus between them. For spatial ontologies, we suggest an approach for building "morphospatial" taxonomies, as an example that could stimulate research on fundamental open issues for biomedical ontologies. Analysis of a large number of problems with biomedical ontologies suggests that the field is very much open to alternative interpretations of current work, and in need of scientific debate and discussion that can lead to new ideas and research directions.

  8. Professional Identification for Biomedical Engineers

    Science.gov (United States)

    Long, Francis M.

    1973-01-01

    Discusses four methods of professional identification in biomedical engineering including registration, certification, accreditation, and possible membership qualification of the societies. Indicates that the destiny of the biomedical engineer may be under the control of a new profession, neither the medical nor the engineering. (CC)

  9. Egyptian Journal of Biomedical Sciences

    African Journals Online (AJOL)

    The Egyptian Journal of Biomedical Sciences publishes in all aspects of biomedical research sciences. Both basic and clinical research papers are welcomed. Vol 23 (2007). DOWNLOAD FULL TEXT Open Access DOWNLOAD FULL TEXT Subscription or Fee Access. Table of Contents. Articles. Phytochemical And ...

  10. African Journal of Biomedical Research

    African Journals Online (AJOL)

    The African Journal of biomedical Research was founded in 1998 as a joint project ... of the journal led to the formation of a group (Biomedical Communications Group, ... analysis of multidrug resistant aerobic gram-negative clinical isolates from a ... Dental formula and dental abnormalities observed in the Eidolon helvum ...

  11. Biomedical databases: protecting privacy and promoting research.

    Science.gov (United States)

    Wylie, Jean E; Mineau, Geraldine P

    2003-03-01

    When combined with medical information, large electronic databases of information that identify individuals provide superlative resources for genetic, epidemiology and other biomedical research. Such research resources increasingly need to balance the protection of privacy and confidentiality with the promotion of research. Models that do not allow the use of such individual-identifying information constrain research; models that involve commercial interests raise concerns about what type of access is acceptable. Researchers, individuals representing the public interest and those developing regulatory guidelines must be involved in an ongoing dialogue to identify practical models.

  12. Biomedical Science Technologists in Lagos Universities: Meeting ...

    African Journals Online (AJOL)

    Biomedical Science Technologists in Lagos Universities: Meeting Modern Standards ... like to see in biomedical science in Nigeria; 5) their knowledge of ten state-of-the-arts ... KEY WORDS: biomedical science, state-of-the-arts, technical staff ...

  13. Journal of Biomedical Investigation: Editorial Policies

    African Journals Online (AJOL)

    Journal of Biomedical Investigation: Editorial Policies. Journal Home ... The focus of the Journal of Biomedical Research is to promote interdisciplinary research across all Biomedical Sciences. It publishes ... Business editor – Sam Meludu.

  14. A Literature Survey on Wireless Power Transfer for Biomedical Devices

    Directory of Open Access Journals (Sweden)

    Reem Shadid

    2018-01-01

    Full Text Available This paper provides a review and survey of research on power transfer for biomedical applications based on inductive coupling. There is interest in wireless power transfer (WPT for implantable and wearable biomedical devices, for example, heart pacemaker or implantable electrocardiogram (ECG recorders. This paper concentrates on the applications based on near-field power transfer methods, summarizes the main design features in the recent literature, and provides some information about the system model and coil optimization.

  15. Action GRID: assessing the impact of Nanotechnology on biomedical informatics.

    Science.gov (United States)

    Lopez-Alonso, Victoria; Hermosilla-Gimeno, Isabel; Lopez-Campos, Guillermo; Maojo, Victor; Martin-Sanchez, Fernando J

    2008-11-06

    Recent advances in Nanotechnology are slowly extending their influence in biomedical research and clinical practice (nanomedicine). The authors have recently been granted with an European Commission research project, Action-GRID. This initiative will review current developments in nanomedicine, and analyze the area of nanoinformatics. Its main outcome will be the identification of needs and the discussion of future challenges and priorities for Biomedical Informatics in terms of information processing in nanomedicine and regenerative medicine.

  16. Multiscale computer modeling in biomechanics and biomedical engineering

    CERN Document Server

    2013-01-01

    This book reviews the state-of-the-art in multiscale computer modeling, in terms of both accomplishments and challenges. The information in the book is particularly useful for biomedical engineers, medical physicists and researchers in systems biology, mathematical biology, micro-biomechanics and biomaterials who are interested in how to bridge between traditional biomedical engineering work at the organ and tissue scales, and the newer arenas of cellular and molecular bioengineering.

  17. Customization of biomedical terminologies.

    Science.gov (United States)

    Homo, Julien; Dupuch, Laëtitia; Benbrahim, Allel; Grabar, Natalia; Dupuch, Marie

    2012-01-01

    Within the biomedical area over one hundred terminologies exist and are merged in the Unified Medical Language System Metathesaurus, which gives over 1 million concepts. When such huge terminological resources are available, the users must deal with them and specifically they must deal with irrelevant parts of these terminologies. We propose to exploit seed terms and semantic distance algorithms in order to customize the terminologies and to limit within them a semantically homogeneous space. An evaluation performed by a medical expert indicates that the proposed approach is relevant for the customization of terminologies and that the extracted terms are mostly relevant to the seeds. It also indicates that different algorithms provide with similar or identical results within a given terminology. The difference is due to the terminologies exploited. A special attention must be paid to the definition of optimal association between the semantic similarity algorithms and the thresholds specific to a given terminology.

  18. Biomedical applications of nanotechnology.

    Science.gov (United States)

    Ramos, Ana P; Cruz, Marcos A E; Tovani, Camila B; Ciancaglini, Pietro

    2017-04-01

    The ability to investigate substances at the molecular level has boosted the search for materials with outstanding properties for use in medicine. The application of these novel materials has generated the new research field of nanobiotechnology, which plays a central role in disease diagnosis, drug design and delivery, and implants. In this review, we provide an overview of the use of metallic and metal oxide nanoparticles, carbon-nanotubes, liposomes, and nanopatterned flat surfaces for specific biomedical applications. The chemical and physical properties of the surface of these materials allow their use in diagnosis, biosensing and bioimaging devices, drug delivery systems, and bone substitute implants. The toxicology of these particles is also discussed in the light of a new field referred to as nanotoxicology that studies the surface effects emerging from nanostructured materials.

  19. Review of spectral imaging technology in biomedical engineering: achievements and challenges.

    Science.gov (United States)

    Li, Qingli; He, Xiaofu; Wang, Yiting; Liu, Hongying; Xu, Dongrong; Guo, Fangmin

    2013-10-01

    Spectral imaging is a technology that integrates conventional imaging and spectroscopy to get both spatial and spectral information from an object. Although this technology was originally developed for remote sensing, it has been extended to the biomedical engineering field as a powerful analytical tool for biological and biomedical research. This review introduces the basics of spectral imaging, imaging methods, current equipment, and recent advances in biomedical applications. The performance and analytical capabilities of spectral imaging systems for biological and biomedical imaging are discussed. In particular, the current achievements and limitations of this technology in biomedical engineering are presented. The benefits and development trends of biomedical spectral imaging are highlighted to provide the reader with an insight into the current technological advances and its potential for biomedical research.

  20. Biomedical semantics in the Semantic Web.

    Science.gov (United States)

    Splendiani, Andrea; Burger, Albert; Paschke, Adrian; Romano, Paolo; Marshall, M Scott

    2011-03-07

    The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences?We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20th.

  1. Ethical behaviour of authors in biomedical journalism.

    Science.gov (United States)

    Bevan, Joan C

    2002-03-01

    Biomedical journals communicate new information that changes health-care decisions. If authors ignore the fundamental values of honesty and trust, that information becomes flawed, and society or patients may be harmed. By describing two cases of unethical behaviour by authors, and using them as a focus to review acceptable ethics in publication, this article aims to educate readers who have not considered the ethical implications in writing manuscripts for biomedical journals. Two cases of unethical behaviour by authors occurred when the results of new drug trials were reported. They were discovered after publication in a biomedical journal, and in the review process after the submission of a manuscript for publication respectively. In the first case, duplicate publication was identified because the same control data were used, but not acknowledged, in three publications by the same investigators. In the second, ghost writing by a pharmaceutical company writer was suspected because of the atypical presentation of a senior author's work. The editor consulted with the authors of both reports. In the first case, the authors concurred about the duplication, and the editors of the three journals wrote editorials to record the duplicate publications. The second case of ghost writing was unconfirmed by the authors, but the submission was withdrawn, and the article was later published in another journal. These cases draw attention to recently recognized types of scientific misconduct that influence the perception of scientific work. Duplicate publication and ghost writing not only deceive the reader, but may also conceal flawed study design and conflict of interest.

  2. Compound image segmentation of published biomedical figures.

    Science.gov (United States)

    Li, Pengyuan; Jiang, Xiangying; Kambhamettu, Chandra; Shatkay, Hagit

    2018-04-01

    Images convey essential information in biomedical publications. As such, there is a growing interest within the bio-curation and the bio-databases communities, to store images within publications as evidence for biomedical processes and for experimental results. However, many of the images in biomedical publications are compound images consisting of multiple panels, where each individual panel potentially conveys a different type of information. Segmenting such images into constituent panels is an essential first step toward utilizing images. In this article, we develop a new compound image segmentation system, FigSplit, which is based on Connected Component Analysis. To overcome shortcomings typically manifested by existing methods, we develop a quality assessment step for evaluating and modifying segmentations. Two methods are proposed to re-segment the images if the initial segmentation is inaccurate. Experimental results show the effectiveness of our method compared with other methods. The system is publicly available for use at: https://www.eecis.udel.edu/~compbio/FigSplit. The code is available upon request. shatkay@udel.edu. Supplementary data are available online at Bioinformatics.

  3. Finding biomedical categories in Medline®

    Directory of Open Access Journals (Sweden)

    Yeganova Lana

    2012-10-01

    Full Text Available Abstract Background There are several humanly defined ontologies relevant to Medline. However, Medline is a fast growing collection of biomedical documents which creates difficulties in updating and expanding these humanly defined ontologies. Automatically identifying meaningful categories of entities in a large text corpus is useful for information extraction, construction of machine learning features, and development of semantic representations. In this paper we describe and compare two methods for automatically learning meaningful biomedical categories in Medline. The first approach is a simple statistical method that uses part-of-speech and frequency information to extract a list of frequent nouns from Medline. The second method implements an alignment-based technique to learn frequent generic patterns that indicate a hyponymy/hypernymy relationship between a pair of noun phrases. We then apply these patterns to Medline to collect frequent hypernyms as potential biomedical categories. Results We study and compare these two alternative sets of terms to identify semantic categories in Medline. We find that both approaches produce reasonable terms as potential categories. We also find that there is a significant agreement between the two sets of terms. The overlap between the two methods improves our confidence regarding categories predicted by these independent methods. Conclusions This study is an initial attempt to extract categories that are discussed in Medline. Rather than imposing external ontologies on Medline, our methods allow categories to emerge from the text.

  4. Biomedical engineering frontier research and converging technologies

    CERN Document Server

    Jun, Ho-Wook; Shin, Jennifer; Lee, SangHoon

    2016-01-01

    This book provides readers with an integrative overview of the latest research and developments in the broad field of biomedical engineering. Each of the chapters offers a timely review written by leading biomedical engineers and aims at showing how the convergence of scientific and engineering fields with medicine has created a new basis for practically solving problems concerning human health, wellbeing and disease. While some of the latest frontiers of biomedicine, such as neuroscience and regenerative medicine, are becoming increasingly dependent on new ideas and tools from other disciplines, the paradigm shift caused by technological innovations in the fields of information science, nanotechnology, and robotics is opening new opportunities in healthcare, besides dramatically changing the ways we actually practice science. At the same time, a new generation of engineers, fluent in many different scientific “languages,” is creating entirely new fields of research that approach the “old” questions f...

  5. Frontiers of biomedical text mining: current progress

    Science.gov (United States)

    Zweigenbaum, Pierre; Demner-Fushman, Dina; Yu, Hong; Cohen, Kevin B.

    2008-01-01

    It is now almost 15 years since the publication of the first paper on text mining in the genomics domain, and decades since the first paper on text mining in the medical domain. Enormous progress has been made in the areas of information retrieval, evaluation methodologies and resource construction. Some problems, such as abbreviation-handling, can essentially be considered solved problems, and others, such as identification of gene mentions in text, seem likely to be solved soon. However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research. In this article we review the current state of the art in biomedical text mining or ‘BioNLP’ in general, focusing primarily on papers published within the past year. PMID:17977867

  6. De-identifying Swedish clinical text - refinement of a gold standard and experiments with Conditional random fields

    Directory of Open Access Journals (Sweden)

    Dalianis Hercules

    2010-04-01

    Full Text Available Abstract Background In order to perform research on the information contained in Electronic Patient Records (EPRs, access to the data itself is needed. This is often very difficult due to confidentiality regulations. The data sets need to be fully de-identified before they can be distributed to researchers. De-identification is a difficult task where the definitions of annotation classes are not self-evident. Results We present work on the creation of two refined variants of a manually annotated Gold standard for de-identification, one created automatically, and one created through discussions among the annotators. The data is a subset from the Stockholm EPR Corpus, a data set available within our research group. These are used for the training and evaluation of an automatic system based on the Conditional Random Fields algorithm. Evaluating with four-fold cross-validation on sets of around 4-6 000 annotation instances, we obtained very promising results for both Gold Standards: F-score around 0.80 for a number of experiments, with higher results for certain annotation classes. Moreover, 49 false positives that were verified true positives were found by the system but missed by the annotators. Conclusions Our intention is to make this Gold standard, The Stockholm EPR PHI Corpus, available to other research groups in the future. Despite being slightly more time-consuming we believe the manual consensus gold standard is the most valuable for further research. We also propose a set of annotation classes to be used for similar de-identification tasks.

  7. Handbook on advanced design and manufacturing technologies for biomedical devices

    CERN Document Server

    2013-01-01

    The last decades have seen remarkable advances in computer-aided design, engineering and manufacturing technologies, multi-variable simulation tools, medical imaging, biomimetic design, rapid prototyping, micro and nanomanufacturing methods and information management resources, all of which provide new horizons for the Biomedical Engineering fields and the Medical Device Industry. Handbook on Advanced Design and Manufacturing Technologies for Biomedical Devices covers such topics in depth, with an applied perspective and providing several case studies that help to analyze and understand the key factors of the different stages linked to the development of a novel biomedical device, from the conceptual and design steps, to the prototyping and industrialization phases. Main research challenges and future potentials are also discussed, taking into account relevant social demands and a growing market already exceeding billions of dollars. In time, advanced biomedical devices will decisively change methods and resu...

  8. Biomedical data integration in computational drug design and bioinformatics.

    Science.gov (United States)

    Seoane, Jose A; Aguiar-Pulido, Vanessa; Munteanu, Cristian R; Rivero, Daniel; Rabunal, Juan R; Dorado, Julian; Pazos, Alejandro

    2013-03-01

    In recent years, in the post genomic era, more and more data is being generated by biological high throughput technologies, such as proteomics and transcriptomics. This omics data can be very useful, but the real challenge is to analyze all this data, as a whole, after integrating it. Biomedical data integration enables making queries to different, heterogeneous and distributed biomedical data sources. Data integration solutions can be very useful not only in the context of drug design, but also in biomedical information retrieval, clinical diagnosis, system biology, etc. In this review, we analyze the most common approaches to biomedical data integration, such as federated databases, data warehousing, multi-agent systems and semantic technology, as well as the solutions developed using these approaches in the past few years.

  9. Terahertz Imaging for Biomedical Applications Pattern Recognition and Tomographic Reconstruction

    CERN Document Server

    Yin, Xiaoxia; Abbott, Derek

    2012-01-01

    Terahertz Imaging for Biomedical Applications: Pattern Recognition and Tomographic Reconstruction presents the necessary algorithms needed to assist screening, diagnosis, and treatment, and these algorithms will play a critical role in the accurate detection of abnormalities present in biomedical imaging. Terahertz biomedical imaging has become an area of interest due to its ability to simultaneously acquire both image and spectral information. Terahertz imaging systems are being commercialized with an increasing number of trials performed in a biomedical setting. Terahertz tomographic imaging and detection technology contributes to the ability to identify opaque objects with clear boundaries,and would be useful to both in vivo and ex vivo environments. This book also: Introduces terahertz radiation techniques and provides a number of topical examples of signal and image processing, as well as machine learning Presents the most recent developments in an emerging field, terahertz radiation Utilizes new methods...

  10. Figure text extraction in biomedical literature.

    Directory of Open Access Journals (Sweden)

    Daehyun Kim

    2011-01-01

    Full Text Available Figures are ubiquitous in biomedical full-text articles, and they represent important biomedical knowledge. However, the sheer volume of biomedical publications has made it necessary to develop computational approaches for accessing figures. Therefore, we are developing the Biomedical Figure Search engine (http://figuresearch.askHERMES.org to allow bioscientists to access figures efficiently. Since text frequently appears in figures, automatically extracting such text may assist the task of mining information from figures. Little research, however, has been conducted exploring text extraction from biomedical figures.We first evaluated an off-the-shelf Optical Character Recognition (OCR tool on its ability to extract text from figures appearing in biomedical full-text articles. We then developed a Figure Text Extraction Tool (FigTExT to improve the performance of the OCR tool for figure text extraction through the use of three innovative components: image preprocessing, character recognition, and text correction. We first developed image preprocessing to enhance image quality and to improve text localization. Then we adapted the off-the-shelf OCR tool on the improved text localization for character recognition. Finally, we developed and evaluated a novel text correction framework by taking advantage of figure-specific lexicons.The evaluation on 382 figures (9,643 figure texts in total randomly selected from PubMed Central full-text articles shows that FigTExT performed with 84% precision, 98% recall, and 90% F1-score for text localization and with 62.5% precision, 51.0% recall and 56.2% F1-score for figure text extraction. When limiting figure texts to those judged by domain experts to be important content, FigTExT performed with 87.3% precision, 68.8% recall, and 77% F1-score. FigTExT significantly improved the performance of the off-the-shelf OCR tool we used, which on its own performed with 36.6% precision, 19.3% recall, and 25.3% F1-score for

  11. Smart nanomaterials for biomedics.

    Science.gov (United States)

    Choi, Soonmo; Tripathi, Anuj; Singh, Deepti

    2014-10-01

    Nanotechnology has become important in various disciplines of technology and science. It has proven to be a potential candidate for various applications ranging from biosensors to the delivery of genes and therapeutic agents to tissue engineering. Scaffolds for every application can be tailor made to have the appropriate physicochemical properties that will influence the in vivo system in the desired way. For highly sensitive and precise detection of specific signals or pathogenic markers, or for sensing the levels of particular analytes, fabricating target-specific nanomaterials can be very useful. Multi-functional nano-devices can be fabricated using different approaches to achieve multi-directional patterning in a scaffold with the ability to alter topographical cues at scale of less than or equal to 100 nm. Smart nanomaterials are made to understand the surrounding environment and act accordingly by either protecting the drug in hostile conditions or releasing the "payload" at the intended intracellular target site. All of this is achieved by exploiting polymers for their functional groups or incorporating conducting materials into a natural biopolymer to obtain a "smart material" that can be used for detection of circulating tumor cells, detection of differences in the body analytes, or repair of damaged tissue by acting as a cell culture scaffold. Nanotechnology has changed the nature of diagnosis and treatment in the biomedical field, and this review aims to bring together the most recent advances in smart nanomaterials.

  12. Zirconia in biomedical applications.

    Science.gov (United States)

    Chen, Yen-Wei; Moussi, Joelle; Drury, Jeanie L; Wataha, John C

    2016-10-01

    The use of zirconia in medicine and dentistry has rapidly expanded over the past decade, driven by its advantageous physical, biological, esthetic, and corrosion properties. Zirconia orthopedic hip replacements have shown superior wear-resistance over other systems; however, risk of catastrophic fracture remains a concern. In dentistry, zirconia has been widely adopted for endosseous implants, implant abutments, and all-ceramic crowns. Because of an increasing demand for esthetically pleasing dental restorations, zirconia-based ceramic restorations have become one of the dominant restorative choices. Areas covered: This review provides an updated overview of the applications of zirconia in medicine and dentistry with a focus on dental applications. The MEDLINE electronic database (via PubMed) was searched, and relevant original and review articles from 2010 to 2016 were included. Expert commentary: Recent data suggest that zirconia performs favorably in both orthopedic and dental applications, but quality long-term clinical data remain scarce. Concerns about the effects of wear, crystalline degradation, crack propagation, and catastrophic fracture are still debated. The future of zirconia in biomedical applications will depend on the generation of these data to resolve concerns.

  13. 78 FR 33421 - Availability of Masked and De-identified Non-Summary Safety and Efficacy Data; Request for Comments

    Science.gov (United States)

    2013-06-04

    ... available de-identified and masked clinical and preclinical data derived from marketing applications could.... These data have a tremendous potential to help address critical challenges and provide new opportunities... follow up may have utility in guiding dose and treatment strategies when designing registration trials...

  14. Functionalized carbon nanotubes: biomedical applications

    Science.gov (United States)

    Vardharajula, Sandhya; Ali, Sk Z; Tiwari, Pooja M; Eroğlu, Erdal; Vig, Komal; Dennis, Vida A; Singh, Shree R

    2012-01-01

    Carbon nanotubes (CNTs) are emerging as novel nanomaterials for various biomedical applications. CNTs can be used to deliver a variety of therapeutic agents, including biomolecules, to the target disease sites. In addition, their unparalleled optical and electrical properties make them excellent candidates for bioimaging and other biomedical applications. However, the high cytotoxicity of CNTs limits their use in humans and many biological systems. The biocompatibility and low cytotoxicity of CNTs are attributed to size, dose, duration, testing systems, and surface functionalization. The functionalization of CNTs improves their solubility and biocompatibility and alters their cellular interaction pathways, resulting in much-reduced cytotoxic effects. Functionalized CNTs are promising novel materials for a variety of biomedical applications. These potential applications are particularly enhanced by their ability to penetrate biological membranes with relatively low cytotoxicity. This review is directed towards the overview of CNTs and their functionalization for biomedical applications with minimal cytotoxicity. PMID:23091380

  15. Molecular Biomedical Imaging Laboratory (MBIL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Molecular Biomedical Imaging Laboratory (MBIL) is adjacent-a nd has access-to the Department of Radiology and Imaging Sciences clinical imaging facilities. MBIL...

  16. New Directions for Biomedical Engineering

    Science.gov (United States)

    Plonsey, Robert

    1973-01-01

    Discusses the definition of "biomedical engineering" and the development of educational programs in the field. Includes detailed descriptions of the roles of bioengineers, medical engineers, and chemical engineers. (CC)

  17. Summer Biomedical Engineering Institute 1972

    Science.gov (United States)

    Deloatch, E. M.

    1973-01-01

    The five problems studied for biomedical applications of NASA technology are reported. The studies reported are: design modification of electrophoretic equipment, operating room environment control, hematological viscometry, handling system for iridium, and indirect blood pressure measuring device.

  18. Hydroxyapatite coatings for biomedical applications

    CERN Document Server

    Zhang, Sam

    2013-01-01

    Hydroxyapatite coatings are of great importance in the biological and biomedical coatings fields, especially in the current era of nanotechnology and bioapplications. With a bonelike structure that promotes osseointegration, hydroxyapatite coating can be applied to otherwise bioinactive implants to make their surface bioactive, thus achieving faster healing and recovery. In addition to applications in orthopedic and dental implants, this coating can also be used in drug delivery. Hydroxyapatite Coatings for Biomedical Applications explores developments in the processing and property characteri

  19. John Glenn Biomedical Engineering Consortium

    Science.gov (United States)

    Nall, Marsha

    2004-01-01

    The John Glenn Biomedical Engineering Consortium is an inter-institutional research and technology development, beginning with ten projects in FY02 that are aimed at applying GRC expertise in fluid physics and sensor development with local biomedical expertise to mitigate the risks of space flight on the health, safety, and performance of astronauts. It is anticipated that several new technologies will be developed that are applicable to both medical needs in space and on earth.

  20. RPCs in biomedical applications

    Science.gov (United States)

    Belli, G.; De Vecchi, C.; Giroletti, E.; Guida, R.; Musitelli, G.; Nardò, R.; Necchi, M. M.; Pagano, D.; Ratti, S. P.; Sani, G.; Vicini, A.; Vitulo, P.; Viviani, C.

    2006-08-01

    We are studying possible applications of Resistive Plate Chambers (RPCs) in the biomedical domain such as Positron Emission Tomography (PET). The use of RPCs in PET can provide several improvements on the usual scintillation-based detectors. The most striking features are the extremely good spatial and time resolutions. They can be as low as 50 μm and 25 ps respectively, to be compared to the much higher intrinsic limits in bulk detectors. Much efforts have been made to investigate suitable materials to make RPCs sensitive to 511 keV photons. For this reason, we are studying different types of coating employing high Z materials with proper electrical resistivity. Later investigations explored the possibility of coating glass electrodes by mean of serigraphy techniques, employing oxide based mixtures with a high density of high Z materials; the efficiency is strongly dependent on its thickness and it reaches a maximum for a characteristic value that is a function of the compound (usually a few hundred microns). The most promising mixtures seem to be PbO, Bi 2O 3 and Tl 2O. Preliminary gamma efficiency measurements for a Multigap RPC prototype (MRPC) are presented as well as simulations using GEANT4-based framework. The MRPC has 5 gas gaps; their spacings are kept by 0.3 mm diameter nylon fishing line, electrodes are made of thin glasses (1 mm for the outer electrodes, 0.15-0.4 mm for the inner ones). The detector is enclosed in a metallic gas-tight box, filled with a C 2H 2F 4 92.5%, SF 6 2.5%, C 4H 10 5% mixture. Different gas mixtures are being studied increasing the SF6 percentage and results of efficiency as a function of the new mixtures will be presented.

  1. Analyzing rare diseases terms in biomedical terminologies

    Directory of Open Access Journals (Sweden)

    Erika Pasceri

    2012-03-01

    Full Text Available Rare disease patients too often face common problems, including the lack of access to correct diagnosis, lack of quality information on the disease, lack of scientific knowledge of the disease, inequities and difficulties in access to treatment and care. These things could be changed by implementing a comprehensive approach to rare diseases, increasing international cooperation in scientific research, by gaining and sharing scientific knowledge about and by developing tools for extracting and sharing knowledge. A significant aspect to analyze is the organization of knowledge in the biomedical field for the proper management and recovery of health information. For these purposes, the sources needed have been acquired from the Office of Rare Diseases Research, the National Organization of Rare Disorders and Orphanet, organizations that provide information to patients and physicians and facilitate the exchange of information among different actors involved in this field. The present paper shows the representation of rare diseases terms in biomedical terminologies such as MeSH, ICD-10, SNOMED CT and OMIM, leveraging the fact that these terminologies are integrated in the UMLS. At the first level, it was analyzed the overlap among sources and at a second level, the presence of rare diseases terms in target sources included in UMLS, working at the term and concept level. We found that MeSH has the best representation of rare diseases terms.

  2. BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature.

    Directory of Open Access Journals (Sweden)

    Sunwon Lee

    Full Text Available As the volume of publications rapidly increases, searching for relevant information from the literature becomes more challenging. To complement standard search engines such as PubMed, it is desirable to have an advanced search tool that directly returns relevant biomedical entities such as targets, drugs, and mutations rather than a long list of articles. Some existing tools submit a query to PubMed and process retrieved abstracts to extract information at query time, resulting in a slow response time and limited coverage of only a fraction of the PubMed corpus. Other tools preprocess the PubMed corpus to speed up the response time; however, they are not constantly updated, and thus produce outdated results. Further, most existing tools cannot process sophisticated queries such as searches for mutations that co-occur with query terms in the literature. To address these problems, we introduce BEST, a biomedical entity search tool. BEST returns, as a result, a list of 10 different types of biomedical entities including genes, diseases, drugs, targets, transcription factors, miRNAs, and mutations that are relevant to a user's query. To the best of our knowledge, BEST is the only system that processes free text queries and returns up-to-date results in real time including mutation information in the results. BEST is freely accessible at http://best.korea.ac.kr.

  3. [Mass media communication of biomedical advances].

    Science.gov (United States)

    P Salas, Sofía; Beca I, Juan Pablo

    2008-10-01

    The public dissemination of advances in biomedical research and clinical medicine generates several difficulties and problems. Mass media have the responsibility to report accurately and in a comprehensive way, and physicians and researchers must provide this information in a timely manner and without bias. After reviewing the literature related to this subject and discussing some examples of inadequate information in the Chilean context, the authors suggest the following recommendations: journalists should compare and evaluate the information appropriately before its publication, researchers and journalists should work together, reports should inform clearly about the state of the research and every academic institution should avoid reporting publicly preliminary experiences. If these recommendations are followed, the general public, physicians, researchers and health care institutions will be benefited.

  4. The biomedical discourse relation bank

    Directory of Open Access Journals (Sweden)

    Joshi Aravind

    2011-05-01

    Full Text Available Abstract Background Identification of discourse relations, such as causal and contrastive relations, between situations mentioned in text is an important task for biomedical text-mining. A biomedical text corpus annotated with discourse relations would be very useful for developing and evaluating methods for biomedical discourse processing. However, little effort has been made to develop such an annotated resource. Results We have developed the Biomedical Discourse Relation Bank (BioDRB, in which we have annotated explicit and implicit discourse relations in 24 open-access full-text biomedical articles from the GENIA corpus. Guidelines for the annotation were adapted from the Penn Discourse TreeBank (PDTB, which has discourse relations annotated over open-domain news articles. We introduced new conventions and modifications to the sense classification. We report reliable inter-annotator agreement of over 80% for all sub-tasks. Experiments for identifying the sense of explicit discourse connectives show the connective itself as a highly reliable indicator for coarse sense classification (accuracy 90.9% and F1 score 0.89. These results are comparable to results obtained with the same classifier on the PDTB data. With more refined sense classification, there is degradation in performance (accuracy 69.2% and F1 score 0.28, mainly due to sparsity in the data. The size of the corpus was found to be sufficient for identifying the sense of explicit connectives, with classifier performance stabilizing at about 1900 training instances. Finally, the classifier performs poorly when trained on PDTB and tested on BioDRB (accuracy 54.5% and F1 score 0.57. Conclusion Our work shows that discourse relations can be reliably annotated in biomedical text. Coarse sense disambiguation of explicit connectives can be done with high reliability by using just the connective as a feature, but more refined sense classification requires either richer features or more

  5. Image BOSS: a biomedical object storage system

    Science.gov (United States)

    Stacy, Mahlon C.; Augustine, Kurt E.; Robb, Richard A.

    1997-05-01

    Researchers using biomedical images have data management needs which are oriented perpendicular to clinical PACS. The image BOSS system is designed to permit researchers to organize and select images based on research topic, image metadata, and a thumbnail of the image. Image information is captured from existing images in a Unix based filesystem, stored in an object oriented database, and presented to the user in a familiar laboratory notebook metaphor. In addition, the ImageBOSS is designed to provide an extensible infrastructure for future content-based queries directly on the images.

  6. All India Seminar on Biomedical Engineering 2012

    CERN Document Server

    Bhatele, Mukta

    2013-01-01

    This book is a collection of articles presented by researchers and practitioners, including engineers, biologists, health professionals and informatics/computer scientists, interested in both theoretical advances and applications of information systems, artificial intelligence, signal processing, electronics and other engineering tools in areas related to biology and medicine in the All India Seminar on Biomedical Engineering 2012 (AISOBE 2012), organized by The Institution of Engineers (India), Jabalpur Local Centre, Jabalpur, India during November 3-4, 2012. The content of the book is useful to doctors, engineers, researchers and academicians as well as industry professionals.

  7. [Master course in biomedical engineering].

    Science.gov (United States)

    Jobbágy, Akos; Benyó, Zoltán; Monos, Emil

    2009-11-22

    The Bologna Declaration aims at harmonizing the European higher education structure. In accordance with the Declaration, biomedical engineering will be offered as a master (MSc) course also in Hungary, from year 2009. Since 1995 biomedical engineering course has been held in cooperation of three universities: Semmelweis University, Budapest Veterinary University, and Budapest University of Technology and Economics. One of the latter's faculties, Faculty of Electrical Engineering and Informatics, has been responsible for the course. Students could start their biomedical engineering studies - usually in parallel with their first degree course - after they collected at least 180 ECTS credits. Consequently, the biomedical engineering course could have been considered as a master course even before the Bologna Declaration. Students had to collect 130 ECTS credits during the six-semester course. This is equivalent to four-semester full-time studies, because during the first three semesters the curriculum required to gain only one third of the usual ECTS credits. The paper gives a survey on the new biomedical engineering master course, briefly summing up also the subjects in the curriculum.

  8. Biomedical informatics: we are what we publish.

    Science.gov (United States)

    Elkin, P L; Brown, S H; Wright, G

    2013-01-01

    This article is part of a For-Discussion-Section of Methods of Information in Medicine on "Biomedical Informatics: We are what we publish". It is introduced by an editorial and followed by a commentary paper with invited comments. In subsequent issues the discussion may continue through letters to the editor. Informatics experts have attempted to define the field via consensus projects which has led to consensus statements by both AMIA. and by IMIA. We add to the output of this process the results of a study of the Pubmed publications with abstracts from the field of Biomedical Informatics. We took the terms from the AMIA consensus document and the terms from the IMIA definitions of the field of Biomedical Informatics and combined them through human review to create the Health Informatics Ontology. We built a terminology server using the Intelligent Natural Language Processor (iNLP). Then we downloaded the entire set of articles in Medline identified by searching the literature by "Medical Informatics" OR "Bioinformatics". The articles were parsed by the joint AMIA / IMIA terminology and then again using SNOMED CT and for the Bioinformatics they were also parsed using HGNC Ontology. We identified 153,580 articles using "Medical Informatics" and 20,573 articles using "Bioinformatics". This resulted in 168,298 unique articles and an overlap of 5,855 articles. Of these 62,244 articles (37%) had titles and abstracts that contained at least one concept from the Health Informatics Ontology. SNOMED CT indexing showed that the field interacts with most all clinical fields of medicine. Further defining the field by what we publish can add value to the consensus driven processes that have been the mainstay of the efforts to date. Next steps should be to extract terms from the literature that are uncovered and create class hierarchies and relationships for this content. We should also examine the high occurring of MeSH terms as markers to define Biomedical Informatics

  9. Using aggregated, de-identified electronic health record data for multivariate pharmacosurveillance: a case study of azathioprine.

    Science.gov (United States)

    Patel, Vishal N; Kaelber, David C

    2014-12-01

    To demonstrate the use of aggregated and de-identified electronic health record (EHR) data for multivariate post-marketing pharmacosurveillance in a case study of azathioprine (AZA). Using aggregated, standardized, normalized, and de-identified, population-level data from the Explore platform (Explorys, Inc.) we searched over 10 million individuals, of which 14,580 were prescribed AZA based on RxNorm drug orders. Based on logical observation identifiers names and codes (LOINC) and vital sign data, we examined the following side effects: anemia, cell lysis, fever, hepatotoxicity, hypertension, nephrotoxicity, neutropenia, and neutrophilia. Patients prescribed AZA were compared to patients prescribed one of 11 other anti-rheumatologic drugs to determine the relative risk of side effect pairs. Compared to AZA case report trends, hepatotoxicity (marked by elevated transaminases or elevated bilirubin) did not occur as an isolated event more frequently in patients prescribed AZA than other anti-rheumatic agents. While neutropenia occurred in 24% of patients (RR 1.15, 95% CI 1.07-1.23), neutrophilia was also frequent (45%) and increased in patients prescribed AZA (RR 1.28, 95% CI 1.22-1.34). After constructing a pairwise side effect network, neutropenia had no dependencies. A reduced risk of neutropenia was found in patients with co-existing elevations in total bilirubin or liver transaminases, supporting classic clinical knowledge that agranulocytosis is a largely unpredictable phenomenon. Rounding errors propagated in the statistically de-identified datasets for cohorts as small as 40 patients only contributed marginally to the calculated risk. Our work demonstrates that aggregated, standardized, normalized and de-identified population level EHR data can provide both sufficient insight and statistical power to detect potential patterns of medication side effect associations, serving as a multivariate and generalizable approach to post-marketing drug surveillance

  10. Innovations in Biomedical Engineering 2016

    CERN Document Server

    Tkacz, Ewaryst; Paszenda, Zbigniew; Piętka, Ewa

    2017-01-01

    This book presents the proceedings of the “Innovations in Biomedical Engineering IBE’2016” Conference held on October 16–18, 2016 in Poland, discussing recent research on innovations in biomedical engineering. The past decade has seen the dynamic development of more and more sophisticated technologies, including biotechnologies, and more general technologies applied in the area of life sciences. As such the book covers the broadest possible spectrum of subjects related to biomedical engineering innovations. Divided into four parts, it presents state-of-the-art achievements in: • engineering of biomaterials, • modelling and simulations in biomechanics, • informatics in medicine • signal analysis The book helps bridge the gap between technological and methodological engineering achievements on the one hand and clinical requirements in the three major areas diagnosis, therapy and rehabilitation on the other.

  11. Advances in biomedical dosimetry

    International Nuclear Information System (INIS)

    1981-01-01

    Full text: Radiation dosimetry, the accurate determination of the absorbed dose within an irradiated body or a piece of material, is a prerequisite for all applications of ionizing radiation. This has been known since the very first radiation applications in medicine and biology, and increasing efforts are being made by radiation researchers to develop more reliable, effective and safe instruments, and to further improve dosimetric accuracy for all types of radiation used. Development of new techniques and instrumentation was particularly fast in the field of both medical diagnostic and therapeutic radiology. Thus, in Paris in October the IAEA held the latest symposium in its continuing series on dosimetry in medicine and biology. The last one was held in Vienna in 1975. High-quality dosimetry is obviously of great importance for human health, whether the objectives lie in the prevention and control of risks associated with the nuclear industry, in medical uses of radioactive substances or X-ray beams for diagnostic purposes, or in the application of photon, electron or neutron beams in radiotherapy. The symposium dealt with the following subjects: General aspects of dosimetry; Special physical and biomedical aspects; Determination of absorbed dose; Standardization and calibration of dosimetric systems; and Development of dosimetric systems. The forty or so papers presented and the discussions that followed them brought out a certain number of dominant themes, among which three deserve particular mention. - The recent generalization of the International System of Units having prompted a fundamental reassessment of the dosimetric quantities to be considered in calibrating measuring instruments, various proposals were advanced by the representatives of national metrology laboratories to replace the quantity 'exposure' (SI unit = coulomb/kg) by 'Kerma' or 'absorbed dose' (unit joule/kg, the special name of which is 'gray'), this latter being closer to the practical

  12. Biomedical applications of magnetic particles

    CERN Document Server

    Mefford, Thompson

    2018-01-01

    Magnetic particles are increasingly being used in a wide variety of biomedical applications. Written by a team of internationally respected experts, this book provides an up-to-date authoritative reference for scientists and engineers. The first section presents the fundamentals of the field by explaining the theory of magnetism, describing techniques to synthesize magnetic particles, and detailing methods to characterize magnetic particles. The second section describes biomedical applications, including chemical sensors and cellular actuators, and diagnostic applications such as drug delivery, hyperthermia cancer treatment, and magnetic resonance imaging contrast.

  13. Exploring and linking biomedical resources through multidimensional semantic spaces.

    Science.gov (United States)

    Berlanga, Rafael; Jiménez-Ruiz, Ernesto; Nebot, Victoria

    2012-01-25

    The semantic integration of biomedical resources is still a challenging issue which is required for effective information processing and data analysis. The availability of comprehensive knowledge resources such as biomedical ontologies and integrated thesauri greatly facilitates this integration effort by means of semantic annotation, which allows disparate data formats and contents to be expressed under a common semantic space. In this paper, we propose a multidimensional representation for such a semantic space, where dimensions regard the different perspectives in biomedical research (e.g., population, disease, anatomy and protein/genes). This paper presents a novel method for building multidimensional semantic spaces from semantically annotated biomedical data collections. This method consists of two main processes: knowledge and data normalization. The former one arranges the concepts provided by a reference knowledge resource (e.g., biomedical ontologies and thesauri) into a set of hierarchical dimensions for analysis purposes. The latter one reduces the annotation set associated to each collection item into a set of points of the multidimensional space. Additionally, we have developed a visual tool, called 3D-Browser, which implements OLAP-like operators over the generated multidimensional space. The method and the tool have been tested and evaluated in the context of the Health-e-Child (HeC) project. Automatic semantic annotation was applied to tag three collections of abstracts taken from PubMed, one for each target disease of the project, the Uniprot database, and the HeC patient record database. We adopted the UMLS Meta-thesaurus 2010AA as the reference knowledge resource. Current knowledge resources and semantic-aware technology make possible the integration of biomedical resources. Such an integration is performed through semantic annotation of the intended biomedical data resources. This paper shows how these annotations can be exploited for

  14. Archives: Journal of Medical and Biomedical Sciences

    African Journals Online (AJOL)

    Items 1 - 20 of 20 ... Archives: Journal of Medical and Biomedical Sciences. Journal Home > Archives: Journal of Medical and Biomedical Sciences. Log in or Register to get access to full text downloads.

  15. Biomedical Engineering | Classification | College of Engineering & Applied

    Science.gov (United States)

    Engineering Concentration on Ergonomics M.S. Program in Computer Science Interdisciplinary Concentration on Energy Doctoral Programs in Engineering Non-Degree Candidate Departments Biomedical Engineering Biomedical Engineering Industry Advisory Council Civil & Environmental Engineering Civil &

  16. Archives: Journal of Medicine and Biomedical Research

    African Journals Online (AJOL)

    Items 1 - 19 of 19 ... Archives: Journal of Medicine and Biomedical Research. Journal Home > Archives: Journal of Medicine and Biomedical Research. Log in or Register to get access to full text downloads.

  17. Science gateways for biomedical big data analysis

    NARCIS (Netherlands)

    Shahand, S.

    2015-01-01

    Biomedical researchers are facing data deluge challenges such as dealing with large volume of complex heterogeneous data and complex and computationally demanding data processing methods. Such scale and complexity of biomedical research requires multi-disciplinary collaboration between scientists

  18. Integrated Biomaterials for Biomedical Technology

    CERN Document Server

    Ramalingam, Murugan; Ramakrishna, Seeram; Kobayashi, Hisatoshi

    2012-01-01

    This cutting edge book provides all the important aspects dealing with the basic science involved in materials in biomedical technology, especially structure and properties, techniques and technological innovations in material processing and characterizations, as well as the applications. The volume consists of 12 chapters written by acknowledged experts of the biomaterials field and covers a wide range of topics and applications.

  19. Biomedical Engineering Education in Perspective

    Science.gov (United States)

    Gowen, Richard J.

    1973-01-01

    Discusses recent developments in the health care industry and their impact on the future of biomedical engineering education. Indicates that a more thorough understanding of the complex functions of the living organism can be acquired through the application of engineering techniques to problems of life sciences. (CC)

  20. Statistics in three biomedical journals

    Czech Academy of Sciences Publication Activity Database

    Pilčík, Tomáš

    2003-01-01

    Roč. 52, č. 1 (2003), s. 39-43 ISSN 0862-8408 R&D Projects: GA ČR GA310/03/1381 Grant - others:Howard Hughes Medical Institute(US) HHMI55000323 Institutional research plan: CEZ:AV0Z5052915 Keywords : statistics * usage * biomedical journals Subject RIV: EC - Immunology Impact factor: 0.939, year: 2003

  1. Bayes' theorem: A paradigm research tool in biomedical sciences ...

    African Journals Online (AJOL)

    One of the most interesting applications of the results of probability theory involves estimating unknown probability and making decisions on the basis of new (sample) information. Biomedical scientists often use the Bayesian decision theory for the purposes of computing diagnostic values such as sensitivity and specificity ...

  2. Enrolment and Retention of African Women in Biomedical Research ...

    African Journals Online (AJOL)

    Relevant biomedical research literatures on Human Research Participants from Scirus, Pubmed and Medline computerized search were critically evaluated and highlighted. Information was also obtained from research ethics training as well as texts and journals in the medical libraries of the research ethics departments of ...

  3. Biomedical Engineering: A Compendium of Research Training Programs.

    Science.gov (United States)

    National Inst. of General Medical Sciences (NIH), Bethesda, MD.

    This document was prepared to provide a comprehensive view of the programs in biomedical engineering in existence in 1969. These programs are supported by the National Institute of General Medical Sciences and are located at 18 universities. This compendium provides information as to the intent and content of these programs from data provided by…

  4. Crowdsourcing biomedical research: leveraging communities as innovation engines.

    Science.gov (United States)

    Saez-Rodriguez, Julio; Costello, James C; Friend, Stephen H; Kellen, Michael R; Mangravite, Lara; Meyer, Pablo; Norman, Thea; Stolovitzky, Gustavo

    2016-07-15

    The generation of large-scale biomedical data is creating unprecedented opportunities for basic and translational science. Typically, the data producers perform initial analyses, but it is very likely that the most informative methods may reside with other groups. Crowdsourcing the analysis of complex and massive data has emerged as a framework to find robust methodologies. When the crowdsourcing is done in the form of collaborative scientific competitions, known as Challenges, the validation of the methods is inherently addressed. Challenges also encourage open innovation, create collaborative communities to solve diverse and important biomedical problems, and foster the creation and dissemination of well-curated data repositories.

  5. Magnetic Helical Micro- and Nanorobots: Toward Their Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Famin Qiu

    2015-03-01

    Full Text Available Magnetic helical micro- and nanorobots can perform 3D navigation in various liquids with a sub-micrometer precision under low-strength rotating magnetic fields (<10 mT. Since magnetic fields with low strengths are harmless to cells and tissues, magnetic helical micro/nanorobots are promising tools for biomedical applications, such as minimally invasive surgery, cell manipulation and analysis, and targeted therapy. This review provides general information on magnetic helical micro/nanorobots, including their fabrication, motion control, and further functionalization for biomedical applications.

  6. New roles & responsibilities of hospital biomedical engineering.

    Science.gov (United States)

    Frisch, P H; Stone, B; Booth, P; Lui, W

    2014-01-01

    Over the last decade the changing healthcare environment has required hospitals and specifically Biomedical Engineering to critically evaluate, optimize and adapt their operations. The focus is now on new technologies, changes to the environment of care, support requirements and financial constraints. Memorial Sloan Kettering Cancer Center (MSKCC), an NIH-designated comprehensive cancer center, has been transitioning to an increasing outpatient care environment. This transition is driving an increase in-patient acuity coupled with the need for added urgency of support and response time. New technologies, regulatory requirements and financial constraints have impacted operating budgets and in some cases, resulted in a reduction in staffing. Specific initiatives, such as the Joint Commission's National Patient Safety Goals, requirements for an electronic medical record, meaningful use and ICD10 have caused institutions to reevaluate their operations and processes including requiring Biomedical Engineering to manage new technologies, integrations and changes in the electromagnetic environment, while optimizing operational workflow and resource utilization. This paper addresses the new and expanding responsibilities and approach of Biomedical Engineering organizations, specifically at MSKCC. It is suggested that our experience may be a template for other organizations facing similar problems. Increasing support is necessary for Medical Software - Medical Device Data Systems in the evolving wireless environment, including RTLS and RFID. It will be necessary to evaluate the potential impact on the growing electromagnetic environment, on connectivity resulting in the need for dynamic and interactive testing and the growing demand to establish new and needed operational synergies with Information Technology operations and other operational groups within the institution, such as nursing, facilities management, central supply, and the user departments.

  7. Research evaluation support services in biomedical libraries

    Directory of Open Access Journals (Sweden)

    Karen Elizabeth Gutzman

    2018-01-01

    Conclusions: Libraries can leverage a variety of evaluation support services as an opportunity to successfully meet an array of challenges confronting the biomedical research community, including robust efforts to report and demonstrate tangible and meaningful outcomes of biomedical research and clinical care. These services represent a transformative direction that can be emulated by other biomedical and research libraries.

  8. Text Mining in Biomedical Domain with Emphasis on Document Clustering.

    Science.gov (United States)

    Renganathan, Vinaitheerthan

    2017-07-01

    With the exponential increase in the number of articles published every year in the biomedical domain, there is a need to build automated systems to extract unknown information from the articles published. Text mining techniques enable the extraction of unknown knowledge from unstructured documents. This paper reviews text mining processes in detail and the software tools available to carry out text mining. It also reviews the roles and applications of text mining in the biomedical domain. Text mining processes, such as search and retrieval of documents, pre-processing of documents, natural language processing, methods for text clustering, and methods for text classification are described in detail. Text mining techniques can facilitate the mining of vast amounts of knowledge on a given topic from published biomedical research articles and draw meaningful conclusions that are not possible otherwise.

  9. XCEDE: an extensible schema for biomedical data.

    Science.gov (United States)

    Gadde, Syam; Aucoin, Nicole; Grethe, Jeffrey S; Keator, David B; Marcus, Daniel S; Pieper, Steve

    2012-01-01

    The XCEDE (XML-based Clinical and Experimental Data Exchange) XML schema, developed by members of the BIRN (Biomedical Informatics Research Network), provides an extensive metadata hierarchy for storing, describing and documenting the data generated by scientific studies. Currently at version 2.0, the XCEDE schema serves as a specification for the exchange of scientific data between databases, analysis tools, and web services. It provides a structured metadata hierarchy, storing information relevant to various aspects of an experiment (project, subject, protocol, etc.). Each hierarchy level also provides for the storage of data provenance information allowing for a traceable record of processing and/or changes to the underlying data. The schema is extensible to support the needs of various data modalities and to express types of data not originally envisioned by the developers. The latest version of the XCEDE schema and manual are available from http://www.xcede.org/ .

  10. Biomedical informatics discovering knowledge in big data

    CERN Document Server

    Holzinger, Andreas

    2014-01-01

    This book provides a broad overview of the topic Bioinformatics (medical informatics + biological information) with a focus on data, information and knowledge. From data acquisition and storage to visualization, privacy, regulatory, and other practical and theoretical topics, the author touches on several fundamental aspects of the innovative interface between the medical and computational domains that form biomedical informatics. Each chapter starts by providing a useful inventory of definitions and commonly used acronyms for each topic, and throughout the text, the reader finds several real-world examples, methodologies, and ideas that complement the technical and theoretical background. Also at the beginning of each chapter a new section called "key problems", has been added, where the author discusses possible traps and unsolvable or major problems. This new edition includes new sections at the end of each chapter, called "future outlook and research avenues," providing pointers to future challenges.

  11. [Big data, medical language and biomedical terminology systems].

    Science.gov (United States)

    Schulz, Stefan; López-García, Pablo

    2015-08-01

    A variety of rich terminology systems, such as thesauri, classifications, nomenclatures and ontologies support information and knowledge processing in health care and biomedical research. Nevertheless, human language, manifested as individually written texts, persists as the primary carrier of information, in the description of disease courses or treatment episodes in electronic medical records, and in the description of biomedical research in scientific publications. In the context of the discussion about big data in biomedicine, we hypothesize that the abstraction of the individuality of natural language utterances into structured and semantically normalized information facilitates the use of statistical data analytics to distil new knowledge out of textual data from biomedical research and clinical routine. Computerized human language technologies are constantly evolving and are increasingly ready to annotate narratives with codes from biomedical terminology. However, this depends heavily on linguistic and terminological resources. The creation and maintenance of such resources is labor-intensive. Nevertheless, it is sensible to assume that big data methods can be used to support this process. Examples include the learning of hierarchical relationships, the grouping of synonymous terms into concepts and the disambiguation of homonyms. Although clear evidence is still lacking, the combination of natural language technologies, semantic resources, and big data analytics is promising.

  12. Branding the bio/biomedical engineering degree.

    Science.gov (United States)

    Voigt, Herbert F

    2011-01-01

    The future challenges to medical and biological engineering, sometimes referred to as biomedical engineering or simply bioengineering, are many. Some of these are identifiable now and others will emerge from time to time as new technologies are introduced and harnessed. There is a fundamental issue regarding "Branding the bio/biomedical engineering degree" that requires a common understanding of what is meant by a B.S. degree in Biomedical Engineering, Bioengineering, or Biological Engineering. In this paper we address some of the issues involved in branding the Bio/Biomedical Engineering degree, with the aim of clarifying the Bio/Biomedical Engineering brand.

  13. Advanced Methods of Biomedical Signal Processing

    CERN Document Server

    Cerutti, Sergio

    2011-01-01

    This book grew out of the IEEE-EMBS Summer Schools on Biomedical Signal Processing, which have been held annually since 2002 to provide the participants state-of-the-art knowledge on emerging areas in biomedical engineering. Prominent experts in the areas of biomedical signal processing, biomedical data treatment, medicine, signal processing, system biology, and applied physiology introduce novel techniques and algorithms as well as their clinical or physiological applications. The book provides an overview of a compelling group of advanced biomedical signal processing techniques, such as mult

  14. Mathematics and physics of emerging biomedical imaging

    International Nuclear Information System (INIS)

    1996-01-01

    Although the mathematical sciences were used in a general way for image processing, they were of little importance in biomedical work until the development in the 1970s of computed tomography (CT) for the imaging of x-rays and isotope emission tomography. In the 1980s, MRI eclipsed the other modalities in many ways as the most informative medical imaging methodology. Besides these well-established techniques, computer-based mathematical methods are being explored in applications to other well-known methods, such as ultrasound and electroencephalography, as well as new techniques of optical imaging, impedance tomography, and magnetic source imaging. It is worth pointing out that, while the final images of many of these techniques bear many similarities to each other, the technologies involved in each are completely different and the parameters represented in the images are very different in character as well as in medical usefulness. In each case, rather different mathematical or statistical models are used, with different equations. One common thread is the paradigm of reconstruction from indirect measurements--this is the unifying theme of this report. The imaging methods used in biomedical applications that this report discusses include: (1) x-ray projection imaging; (2) x-ray computed tomography (CT); (3) magnetic resonance imaging (MRI) and magnetic resonance spectroscopy; (4) single photon emission computed tomography (SPECT); (5) positron emission tomography (PET); (6) ultrasonics; (7) electrical source imaging (ESI); (8) electrical impedance tomography (EIT); (9) magnetic source imaging (MSI); and (10) medical optical imaging

  15. Contamination control training for biomedical facilities

    International Nuclear Information System (INIS)

    Trinoskey, P.A.

    1994-10-01

    In 1991, a contamination control course was developed for the Biology and Biotechnology Research Program (BBRP) at the Lawrence Livermore National Laboratory (LLNL). This course was based on the developer's experience in Radiation Safety at the University of Utah and University of Kansas Medical Center. This course has been well received at LLNL because it addresses issues that are important to individuals handling small quantities of radioactive materials. This group of users is often overlooked. They are typically very well educated and are expected to ''know'' what they should do. Many of these individuals are not initially comfortable working with radioactive materials. They appreciate the opportunity to be introduced to contamination control techniques and to discuss issues they may have. In addition, the authors benefit by experience that researchers bring from other facilities. The training course will address the specific radiological training requirements for chemists, biologists, and medical researchers who are using small amounts of dispersible radionuclides in tabletop experiments, and will not be exposed to other radiation sources. The training will include: the potential hazards of typical radionuclides, contamination control procedures, and guidance for developing and including site-specific information. The training course will eliminate the need for Radiological Worker II training for bio-medical researchers. The target audience for this training course is bio-medical researchers

  16. New biomedical applications of radiocarbon

    International Nuclear Information System (INIS)

    Davis, J.C.

    1990-12-01

    The potential of accelerator mass spectrometry (AMS) and radiocarbon in biomedical applications is being investigated by Lawrence Livermore National Laboratory (LLNL). A measurement of the dose-response curve for DNA damage caused by a carcinogen in mouse liver cells was an initial experiment. This demonstrated the sensitivity and utility of AMS for detecting radiocarbon tags and led to numerous follow-on experiments. The initial experiment and follow-on experiments are discussed in this report. 12 refs., 4 figs. (SM)

  17. Gold Nanocages for Biomedical Applications**

    OpenAIRE

    Skrabalak, Sara E.; Chen, Jingyi; Au, Leslie; Lu, Xianmao; Li, Xingde; Xia, Younan

    2007-01-01

    Nanostructured materials provide a promising platform for early cancer detection and treatment. Here we highlight recent advances in the synthesis and use of Au nanocages for such biomedical applications. Gold nanocages represent a novel class of nanostructures, which can be prepared via a remarkably simple route based on the galvanic replacement reaction between Ag nanocubes and HAuCl4. The Au nanocages have a tunable surface plasmon resonance peak that extends into the near-infrared, where ...

  18. Biomedical devices and their applications

    CERN Document Server

    2004-01-01

    This volume introduces readers to the basic concepts and recent advances in the field of biomedical devices. The text gives a detailed account of novel developments in drug delivery, protein electrophoresis, estrogen mimicking methods and medical devices. It also provides the necessary theoretical background as well as describing a wide range of practical applications. The level and style make this book accessible not only to scientific and medical researchers but also to graduate students.

  19. [Cluster analysis in biomedical researches].

    Science.gov (United States)

    Akopov, A S; Moskovtsev, A A; Dolenko, S A; Savina, G D

    2013-01-01

    Cluster analysis is one of the most popular methods for the analysis of multi-parameter data. The cluster analysis reveals the internal structure of the data, group the separate observations on the degree of their similarity. The review provides a definition of the basic concepts of cluster analysis, and discusses the most popular clustering algorithms: k-means, hierarchical algorithms, Kohonen networks algorithms. Examples are the use of these algorithms in biomedical research.

  20. Biomedical applications of nanodiamond (Review)

    Science.gov (United States)

    Turcheniuk, K.; Mochalin, Vadym N.

    2017-06-01

    The interest in nanodiamond applications in biology and medicine is on the rise over recent years. This is due to the unique combination of properties that nanodiamond provides. Small size (∼5 nm), low cost, scalable production, negligible toxicity, chemical inertness of diamond core and rich chemistry of nanodiamond surface, as well as bright and robust fluorescence resistant to photobleaching are the distinct parameters that render nanodiamond superior to any other nanomaterial when it comes to biomedical applications. The most exciting recent results have been related to the use of nanodiamonds for drug delivery and diagnostics—two components of a quickly growing area of biomedical research dubbed theranostics. However, nanodiamond offers much more in addition: it can be used to produce biodegradable bone surgery devices, tissue engineering scaffolds, kill drug resistant microbes, help us to fight viruses, and deliver genetic material into cell nucleus. All these exciting opportunities require an in-depth understanding of nanodiamond. This review covers the recent progress as well as general trends in biomedical applications of nanodiamond, and underlines the importance of purification, characterization, and rational modification of this nanomaterial when designing nanodiamond based theranostic platforms.

  1. Superhydrophobic Materials for Biomedical Applications

    Science.gov (United States)

    Colson, Yolonda L.; Grinstaff, Mark W.

    2016-01-01

    Superhydrophobic surfaces are actively studied across a wide range of applications and industries, and are now finding increased use in the biomedical arena as substrates to control protein adsorption, cellular interaction, and bacterial growth, as well as platforms for drug delivery devices and for diagnostic tools. The commonality in the design of these materials is to create a stable or metastable air state at the material surface, which lends itself to a number of unique properties. These activities are catalyzing the development of new materials, applications, and fabrication techniques, as well as collaborations across material science, chemistry, engineering, and medicine given the interdisciplinary nature of this work. The review begins with a discussion of superhydrophobicity, and then explores biomedical applications that are utilizing superhydrophobicity in depth including material selection characteristics, in vitro performance, and in vivo performance. General trends are offered for each application in addition to discussion of conflicting data in the literature, and the review concludes with the authors’ future perspectives on the utility of superhydrophobic surfaces for biomedical applications. PMID:27449946

  2. Resource for the Development of Biomedical Accelerator Mass Spectrometry (AMS)

    Energy Technology Data Exchange (ETDEWEB)

    Turteltaub, K. W. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bench, G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Buchholz, B. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Enright, H. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kulp, K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McCartt, A. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Malfatti, M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ognibene, T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Loots, G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Stewart, B. J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-04-08

    The NIH Research Resource for Biomedical AMS was originally funded at Lawrence Livermore National Laboratory in 1999 to develop and apply the technology of accelerator mass spectrometry (AMS) in broad- based biomedical research. The Resource’s niche is to fill needs for ultra high sensitivity quantitation when isotope-labeled agents are used. The Research Resource’s Technology Research and Development (TR&D) efforts will focus on the needs of the biomedical research community in the context of seven Driving Biomedical Projects (DBPs) that will drive the Center’s technical capabilities through three core TR&Ds. We will expand our present capabilities by developing a fully integrated HPLC AMS to increase our capabilities for metabolic measurements, we will develop methods to understand cellular processes and we will develop and validate methods for the application of AMS in human studies, which is a growing area of demand by collaborators and service users. In addition, we will continue to support new and ongoing collaborative and service projects that require the capabilities of the Resource. The Center will continue to train researchers in the use of the AMS capabilities being developed, and the results of all efforts will be widely disseminated to advance progress in biomedical research. Towards these goals, our specific aims are to:1.) Increase the value and information content of AMS measurements by combining molecular speciation with quantitation of defined macromolecular isolates. Specifically, develop and validate methods for macromolecule labeling, characterization and quantitation.2.) Develop and validate methods and strategies to enable AMS to become more broadly used in human studies. Specifically, demonstrate robust methods for conducting pharmacokinetic/pharmacodynamics studies in humans and model systems.3.) Increase the accessibility of AMS to the Biomedical research community and the throughput of AMS through direct coupling to separatory

  3. Resource for the Development of Biomedical Accelerator Mass Spectrometry (AMS)

    Energy Technology Data Exchange (ETDEWEB)

    Tuerteltaub, K. W. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bench, G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Buchholz, B. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Enright, H. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kulp, K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Loots, G. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McCartt, A. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Malfatti, M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ognibene, T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Stewart, B. J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-03-21

    The NIH Research Resource for Biomedical AMS was originally funded at Lawrence Livermore National Laboratory in 1999 to develop and apply the technology of accelerator mass spectrometry (AMS) in broad- based biomedical research. The Resource’s niche is to fill needs for ultra high sensitivity quantitation when isotope-labeled agents are used. The Research Resource’s Technology Research and Development (TR&D) efforts will focus on the needs of the biomedical research community in the context of seven Driving Biomedical Projects (DBPs) that will drive the Center’s technical capabilities through three core TR&Ds. We will expand our present capabilities by developing a fully integrated HPLC AMS to increase our capabilities for metabolic measurements, we will develop methods to understand cellular processes and we will develop and validate methods for the application of AMS in human studies, which is a growing area of demand by collaborators and service users. In addition, we will continue to support new and ongoing collaborative and service projects that require the capabilities of the Resource. The Center will continue to train researchers in the use of the AMS capabilities being developed, and the results of all efforts will be widely disseminated to advance progress in biomedical research. Towards these goals, our specific aims are to:1.) Increase the value and information content of AMS measurements by combining molecular speciation with quantitation of defined macromolecular isolates. Specifically, develop and validate methods for macromolecule labeling, characterization and quantitation.2.) Develop and validate methods and strategies to enable AMS to become more broadly used in human studies. Specifically, demonstrate robust methods for conducting pharmacokinetic/pharmacodynamics studies in humans and model systems.3.) Increase the accessibility of AMS to the Biomedical research community and the throughput of AMS through direct coupling to separatory

  4. Enhancing biomedical text summarization using semantic relation extraction.

    Directory of Open Access Journals (Sweden)

    Yue Shang

    Full Text Available Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1 We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2 We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3 For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization.

  5. Enhancing biomedical text summarization using semantic relation extraction.

    Science.gov (United States)

    Shang, Yue; Li, Yanpeng; Lin, Hongfei; Yang, Zhihao

    2011-01-01

    Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1) We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2) We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3) For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization.

  6. KaBOB: ontology-based semantic integration of biomedical databases.

    Science.gov (United States)

    Livingston, Kevin M; Bada, Michael; Baumgartner, William A; Hunter, Lawrence E

    2015-04-23

    The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources. We present five processes for semantic data integration that, when applied collectively, solve seven key problems. These processes include making explicit the differences between biomedical concepts and database records, aggregating sets of identifiers denoting the same biomedical concepts across data sources, and using declaratively represented forward-chaining rules to take information that is variably represented in source databases and integrating it into a consistent biomedical representation. We demonstrate these processes and solutions by presenting KaBOB (the Knowledge Base Of Biomedicine), a knowledge base of semantically integrated data from 18 prominent biomedical databases using common representations grounded in Open Biomedical Ontologies. An instance of KaBOB with data about humans and seven major model organisms can be built using on the order of 500 million RDF triples. All source code for building KaBOB is available under an open-source license. KaBOB is an integrated knowledge base of biomedical data representationally based in prominent, actively maintained Open Biomedical Ontologies, thus enabling queries of the underlying data in terms of biomedical concepts (e.g., genes and gene products, interactions and processes) rather than features of source-specific data schemas or file formats. KaBOB resolves many of the issues that routinely plague biomedical researchers intending to work with data from multiple data sources and provides a platform for ongoing data integration and development and for

  7. Data Analysis and Data Mining: Current Issues in Biomedical Informatics

    Science.gov (United States)

    Bellazzi, Riccardo; Diomidous, Marianna; Sarkar, Indra Neil; Takabayashi, Katsuhiko; Ziegler, Andreas; McCray, Alexa T.

    2011-01-01

    Summary Background Medicine and biomedical sciences have become data-intensive fields, which, at the same time, enable the application of data-driven approaches and require sophisticated data analysis and data mining methods. Biomedical informatics provides a proper interdisciplinary context to integrate data and knowledge when processing available information, with the aim of giving effective decision-making support in clinics and translational research. Objectives To reflect on different perspectives related to the role of data analysis and data mining in biomedical informatics. Methods On the occasion of the 50th year of Methods of Information in Medicine a symposium was organized, that reflected on opportunities, challenges and priorities of organizing, representing and analysing data, information and knowledge in biomedicine and health care. The contributions of experts with a variety of backgrounds in the area of biomedical data analysis have been collected as one outcome of this symposium, in order to provide a broad, though coherent, overview of some of the most interesting aspects of the field. Results The paper presents sections on data accumulation and data-driven approaches in medical informatics, data and knowledge integration, statistical issues for the evaluation of data mining models, translational bioinformatics and bioinformatics aspects of genetic epidemiology. Conclusions Biomedical informatics represents a natural framework to properly and effectively apply data analysis and data mining methods in a decision-making context. In the future, it will be necessary to preserve the inclusive nature of the field and to foster an increasing sharing of data and methods between researchers. PMID:22146916

  8. Integrating biomedical and herbal medicine in Ghana

    DEFF Research Database (Denmark)

    Boateng, Millicent Addai; Danso-Appiah, Anthony; Turkson, Bernard Kofi

    2016-01-01

    Background: Over the past decade there has been growing interest in the use of herbal medicine both in developed and developing countries. Given the high proportion of patients using herbal medicine in Ghana, some health facilities have initiated implementation of herbal medicine as a component...... of their healthcare delivery. However, the extent to which herbal medicine has been integrated in Ghanaian health facilities, how integration is implemented and perceived by different stakeholders has not been documented. The study sought to explore these critical issues at the Kumasi South Hospital (KSH) and outline...... the definition, process and goals of integration were lacking, with respondents sharing different views about the purpose and value of integration of herbal medicine within public health facilities. Key informants were supportive of the initiative. Whilst biomedical health workers perceived the system...

  9. Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research.

    Science.gov (United States)

    Purawat, Shweta; Cowart, Charles; Amaro, Rommie E; Altintas, Ilkay

    2016-06-01

    The BBDTC (https://biobigdata.ucsd.edu) is a community-oriented platform to encourage high-quality knowledge dissemination with the aim of growing a well-informed biomedical big data community through collaborative efforts on training and education. The BBDTC collaborative is an e-learning platform that supports the biomedical community to access, develop and deploy open training materials. The BBDTC supports Big Data skill training for biomedical scientists at all levels, and from varied backgrounds. The natural hierarchy of courses allows them to be broken into and handled as modules . Modules can be reused in the context of multiple courses and reshuffled, producing a new and different, dynamic course called a playlist . Users may create playlists to suit their learning requirements and share it with individual users or the wider public. BBDTC leverages the maturity and design of the HUBzero content-management platform for delivering educational content. To facilitate the migration of existing content, the BBDTC supports importing and exporting course material from the edX platform. Migration tools will be extended in the future to support other platforms. Hands-on training software packages, i.e., toolboxes , are supported through Amazon EC2 and Virtualbox virtualization technologies, and they are available as: ( i ) downloadable lightweight Virtualbox Images providing a standardized software tool environment with software packages and test data on their personal machines, and ( ii ) remotely accessible Amazon EC2 Virtual Machines for accessing biomedical big data tools and scalable big data experiments. At the moment, the BBDTC site contains three open Biomedical big data training courses with lecture contents, videos and hands-on training utilizing VM toolboxes, covering diverse topics. The courses have enhanced the hands-on learning environment by providing structured content that users can use at their own pace. A four course biomedical big data series is

  10. For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases.

    Science.gov (United States)

    Liljekvist, Mads Svane; Andresen, Kristoffer; Pommergaard, Hans-Christian; Rosenberg, Jacob

    2015-01-01

    Background. Open access (OA) journals allows access to research papers free of charge to the reader. Traditionally, biomedical researchers use databases like MEDLINE and EMBASE to discover new advances. However, biomedical OA journals might not fulfill such databases' criteria, hindering dissemination. The Directory of Open Access Journals (DOAJ) is a database exclusively listing OA journals. The aim of this study was to investigate DOAJ's coverage of biomedical OA journals compared with the conventional biomedical databases. Methods. Information on all journals listed in four conventional biomedical databases (MEDLINE, PubMed Central, EMBASE and SCOPUS) and DOAJ were gathered. Journals were included if they were (1) actively publishing, (2) full OA, (3) prospectively indexed in one or more database, and (4) of biomedical subject. Impact factor and journal language were also collected. DOAJ was compared with conventional databases regarding the proportion of journals covered, along with their impact factor and publishing language. The proportion of journals with articles indexed by DOAJ was determined. Results. In total, 3,236 biomedical OA journals were included in the study. Of the included journals, 86.7% were listed in DOAJ. Combined, the conventional biomedical databases listed 75.0% of the journals; 18.7% in MEDLINE; 36.5% in PubMed Central; 51.5% in SCOPUS and 50.6% in EMBASE. Of the journals in DOAJ, 88.7% published in English and 20.6% had received impact factor for 2012 compared with 93.5% and 26.0%, respectively, for journals in the conventional biomedical databases. A subset of 51.1% and 48.5% of the journals in DOAJ had articles indexed from 2012 and 2013, respectively. Of journals exclusively listed in DOAJ, one journal had received an impact factor for 2012, and 59.6% of the journals had no content from 2013 indexed in DOAJ. Conclusions. DOAJ is the most complete registry of biomedical OA journals compared with five conventional biomedical databases

  11. Secondary uses and the governance of de-identified data: Lessons from the human genome diversity panel

    Directory of Open Access Journals (Sweden)

    Lee Sandra S-J

    2011-09-01

    Full Text Available Abstract Background Recent changes to regulatory guidance in the US and Europe have complicated oversight of secondary research by rendering most uses of de-identified data exempt from human subjects oversight. To identify the implications of such guidelines for harms to participants and communities, this paper explores the secondary uses of one de-identified DNA sample collection with limited oversight: the Human Genome Diversity Project (HGDP-Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset (CEPH Human Genome Diversity Panel. Methods Using a combination of keyword and cited reference search, we identified English-language scientific articles published between 2002 and 2009 that reported analysis of HGDP Diversity Panel samples and/or data. We then reviewed each article to identify the specific research use to which the samples and/or data was applied. Secondary uses were categorized according to the type and kind of research supported by the collection. Results A wide variety of secondary uses were identified from 148 peer-reviewed articles. While the vast majority of these uses were consistent with the original intent of the collection, a minority of published reports described research whose primary findings could be regarded as controversial, objectionable, or potentially stigmatizing in their interpretation. Conclusions We conclude that potential risks to participants and communities cannot be wholly eliminated by anonymization of individual data and suggest that explicit review of proposed secondary uses, by a Data Access Committee or similar internal oversight body with suitable stakeholder representation, should be a required component of the trustworthy governance of any repository of data or specimens.

  12. The ethics of biomedical big data

    CERN Document Server

    Mittelstadt, Brent Daniel

    2016-01-01

    This book presents cutting edge research on the new ethical challenges posed by biomedical Big Data technologies and practices. ‘Biomedical Big Data’ refers to the analysis of aggregated, very large datasets to improve medical knowledge and clinical care. The book describes the ethical problems posed by aggregation of biomedical datasets and re-use/re-purposing of data, in areas such as privacy, consent, professionalism, power relationships, and ethical governance of Big Data platforms. Approaches and methods are discussed that can be used to address these problems to achieve the appropriate balance between the social goods of biomedical Big Data research and the safety and privacy of individuals. Seventeen original contributions analyse the ethical, social and related policy implications of the analysis and curation of biomedical Big Data, written by leading experts in the areas of biomedical research, medical and technology ethics, privacy, governance and data protection. The book advances our understan...

  13. Text mining patents for biomedical knowledge.

    Science.gov (United States)

    Rodriguez-Esteban, Raul; Bundschus, Markus

    2016-06-01

    Biomedical text mining of scientific knowledge bases, such as Medline, has received much attention in recent years. Given that text mining is able to automatically extract biomedical facts that revolve around entities such as genes, proteins, and drugs, from unstructured text sources, it is seen as a major enabler to foster biomedical research and drug discovery. In contrast to the biomedical literature, research into the mining of biomedical patents has not reached the same level of maturity. Here, we review existing work and highlight the associated technical challenges that emerge from automatically extracting facts from patents. We conclude by outlining potential future directions in this domain that could help drive biomedical research and drug discovery. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Tritium AMS for biomedical applications

    International Nuclear Information System (INIS)

    Roberts, M.L.; Velsko, C.; Turteltaub, K.W.

    1993-08-01

    We are developing 3 H-AMS to measure 3 H activity of mg-sized biological samples. LLNL has already successfully applied 14 C AMS to a variety of problems in the area of biomedical research. Development of 3 H AMS would greatly complement these studies. The ability to perform 3 H AMS measurements at sensitivities equivalent to those obtained for 14 C will allow us to perform experiments using compounds that are not readily available in 14 C-tagged form. A 3 H capability would also allow us to perform unique double-labeling experiments in which we learn the fate, distribution, and metabolism of separate fractions of biological compounds

  15. Luminescent nanodiamonds for biomedical applications.

    Science.gov (United States)

    Say, Jana M; van Vreden, Caryn; Reilly, David J; Brown, Louise J; Rabeau, James R; King, Nicholas J C

    2011-12-01

    In recent years, nanodiamonds have emerged from primarily an industrial and mechanical applications base, to potentially underpinning sophisticated new technologies in biomedical and quantum science. Nanodiamonds are relatively inexpensive, biocompatible, easy to surface functionalise and optically stable. This combination of physical properties are ideally suited to biological applications, including intracellular labelling and tracking, extracellular drug delivery and adsorptive detection of bioactive molecules. Here we describe some of the methods and challenges for processing nanodiamond materials, detection schemes and some of the leading applications currently under investigation.

  16. Thermoresponsive Polymers for Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Theoni K. Georgiou

    2011-08-01

    Full Text Available Thermoresponsive polymers are a class of “smart” materials that have the ability to respond to a change in temperature; a property that makes them useful materials in a wide range of applications and consequently attracts much scientific interest. This review focuses mainly on the studies published over the last 10 years on the synthesis and use of thermoresponsive polymers for biomedical applications including drug delivery, tissue engineering and gene delivery. A summary of the main applications is given following the different studies on thermoresponsive polymers which are categorized based on their 3-dimensional structure; hydrogels, interpenetrating networks, micelles, crosslinked micelles, polymersomes, films and particles.

  17. Biomedical signal and image processing

    CERN Document Server

    Najarian, Kayvan

    2012-01-01

    INTRODUCTION TO DIGITAL SIGNAL AND IMAGE PROCESSINGSignals and Biomedical Signal ProcessingIntroduction and OverviewWhat is a ""Signal""?Analog, Discrete, and Digital SignalsProcessing and Transformation of SignalsSignal Processing for Feature ExtractionSome Characteristics of Digital ImagesSummaryProblemsFourier TransformIntroduction and OverviewOne-Dimensional Continuous Fourier TransformSampling and NYQUIST RateOne-Dimensional Discrete Fourier TransformTwo-Dimensional Discrete Fourier TransformFilter DesignSummaryProblemsImage Filtering, Enhancement, and RestorationIntroduction and Overview

  18. An introduction to biomedical instrumentation

    CERN Document Server

    Dewhurst, D J

    1976-01-01

    An Introduction to Biomedical Instrumentation presents a course of study and applications covering the basic principles of medical and biological instrumentation, as well as the typical features of its design and construction. The book aims to aid not only the cognitive domain of the readers, but also their psychomotor domain as well. Aside from the seminar topics provided, which are divided into 27 chapters, the book complements these topics with practical applications of the discussions. Figures and mathematical formulas are also given. Major topics discussed include the construction, handli

  19. Introduction to biomedical engineering technology

    CERN Document Server

    Street, Laurence J

    2011-01-01

    IntroductionHistory of Medical DevicesThe Role of Biomedical Engineering Technologists in Health CareCharacteristics of Human Anatomy and Physiology That Relate to Medical DevicesSummaryQuestionsDiagnostic Devices: Part OnePhysiological Monitoring SystemsThe HeartSummaryQuestionsDiagnostic Devices: Part TwoCirculatory System and BloodRespiratory SystemNervous SystemSummaryQuestionsDiagnostic Devices: Part ThreeDigestive SystemSensory OrgansReproductionSkin, Bone, Muscle, MiscellaneousChapter SummaryQuestionsDiagnostic ImagingIntroductionX-RaysMagnetic Resonance Imaging ScannersPositron Emissio

  20. Basics of biomedical ultrasound for engineers

    CERN Document Server

    Azhari, Haim

    2010-01-01

    "Basics of Biomedical Ultrasound for Engineers is a structured textbook for university engineering courses in biomedical ultrasound and for researchers in the field. This book offers a tool for building a solid understanding of biomedical ultrasound, and leads the novice through the field in a step-by-step manner. The book begins with the most basic definitions of waves, proceeds to ultrasounds in fluids, and then delves into solid ultrasounds, the most complicated kind of ultrasound. It encompasses a wide range of topics within biomedical ultrasound, from conceptual definitions of waves to the intricacies of focusing devices, transducers, and acoustic fields"--Provided by publisher.

  1. Mathematics and physics of emerging biomedical imaging

    National Research Council Canada - National Science Library

    Committee on the Mathematics and Physics of Emerging Dynamic Biomedical Imaging, National Research Council

    .... Incorporating input from dozens of biomedical researchers who described what they perceived as key open problems of imaging that are amenable to attack by mathematical scientists and physicists...

  2. PhysiomeSpace: digital library service for biomedical data.

    Science.gov (United States)

    Testi, Debora; Quadrani, Paolo; Viceconti, Marco

    2010-06-28

    Every research laboratory has a wealth of biomedical data locked up, which, if shared with other experts, could dramatically improve biomedical and healthcare research. With the PhysiomeSpace service, it is now possible with a few clicks to share with selected users biomedical data in an easy, controlled and safe way. The digital library service is managed using a client-server approach. The client application is used to import, fuse and enrich the data information according to the PhysiomeSpace resource ontology and upload/download the data to the library. The server services are hosted on the Biomed Town community portal, where through a web interface, the user can complete the metadata curation and share and/or publish the data resources. A search service capitalizes on the domain ontology and on the enrichment of metadata for each resource, providing a powerful discovery environment. Once the users have found the data resources they are interested in, they can add them to their basket, following a metaphor popular in e-commerce web sites. When all the necessary resources have been selected, the user can download the basket contents into the client application. The digital library service is now in beta and open to the biomedical research community.

  3. Blended learning as an effective pedagogical paradigm for biomedical science

    Directory of Open Access Journals (Sweden)

    Perry Hartfield

    2013-11-01

    Full Text Available Blended learning combines face-to-face class based and online teaching and learning delivery in order to increase flexibility in how, when, and where students study and learn. The development, integration, and promotion of blended learning in frameworks of curriculum design can optimize the opportunities afforded by information and communication technologies and, concomitantly, accommodate a broad range of student learning styles. This study critically reviews the potential benefits of blended learning as a progressive educative paradigm for the teaching of biomedical science and evaluates the opportunities that blended learning offers for the delivery of accessible, flexible and sustainable teaching and learning experiences. A central tenet of biomedical science education at the tertiary level is the development of comprehensive hands-on practical competencies and technical skills (many of which require laboratory-based learning environments, and it is advanced that a blended learning model, which combines face-to-face synchronous teaching and learning activities with asynchronous online teaching and learning activities, effectively creates an authentic, enriching, and student-centred learning environment for biomedical science. Lastly, a blending learning design for introductory biochemistry will be described as an effective example of integrating face-to-face and online teaching, learning and assessment activities within the teaching domain of biomedical science.   DOI: 10.18870/hlrc.v3i4.169

  4. Labor and skills gap analysis of the biomedical research workforce

    Science.gov (United States)

    Mason, Julie L.; Johnston, Elizabeth; Berndt, Sam; Segal, Katie; Lei, Ming; Wiest, Jonathan S.

    2016-01-01

    The United States has experienced an unsustainable increase of the biomedical research workforce over the past 3 decades. This expansion has led to a myriad of consequences, including an imbalance in the number of researchers and available tenure-track faculty positions, extended postdoctoral training periods, increasing age of investigators at first U.S. National Institutes of Health R01 grant, and exodus of talented individuals seeking careers beyond traditional academe. Without accurate data on the biomedical research labor market, challenges will remain in resolving these problems and in advising trainees of viable career options and the skills necessary to be productive in their careers. We analyzed workforce trends, integrating both traditional labor market information and real-time job data. We generated a profile of the current biomedical research workforce, performed labor gap analyses of occupations in the workforce at regional and national levels, and assessed skill transferability between core and complementary occupations. We conclude that although supply into the workforce and the number of job postings for occupations within that workforce have grown over the past decade, supply continues to outstrip demand. Moreover, we identify practical skill sets from real-time job postings to optimally equip trainees for an array of careers to effectively meet future workforce demand.—Mason, J. L., Johnston, E., Berndt, S., Segal, K., Lei, M., Wiest, J. S. Labor and skills gap analysis of the biomedical research workforce. PMID:27075242

  5. Labor and skills gap analysis of the biomedical research workforce.

    Science.gov (United States)

    Mason, Julie L; Johnston, Elizabeth; Berndt, Sam; Segal, Katie; Lei, Ming; Wiest, Jonathan S

    2016-08-01

    The United States has experienced an unsustainable increase of the biomedical research workforce over the past 3 decades. This expansion has led to a myriad of consequences, including an imbalance in the number of researchers and available tenure-track faculty positions, extended postdoctoral training periods, increasing age of investigators at first U.S. National Institutes of Health R01 grant, and exodus of talented individuals seeking careers beyond traditional academe. Without accurate data on the biomedical research labor market, challenges will remain in resolving these problems and in advising trainees of viable career options and the skills necessary to be productive in their careers. We analyzed workforce trends, integrating both traditional labor market information and real-time job data. We generated a profile of the current biomedical research workforce, performed labor gap analyses of occupations in the workforce at regional and national levels, and assessed skill transferability between core and complementary occupations. We conclude that although supply into the workforce and the number of job postings for occupations within that workforce have grown over the past decade, supply continues to outstrip demand. Moreover, we identify practical skill sets from real-time job postings to optimally equip trainees for an array of careers to effectively meet future workforce demand.-Mason, J. L., Johnston, E., Berndt, S., Segal, K., Lei, M., Wiest, J. S. Labor and skills gap analysis of the biomedical research workforce. © FASEB.

  6. Biomedical applications of control engineering

    CERN Document Server

    Hacısalihzade, Selim S

    2013-01-01

    Biomedical Applications of Control Engineering is a lucidly written textbook for graduate control engin­eering and biomedical engineering students as well as for medical prac­ti­tioners who want to get acquainted with quantitative methods. It is based on decades of experience both in control engineering and clinical practice.   The book begins by reviewing basic concepts of system theory and the modeling process. It then goes on to discuss control engineering application areas like ·         Different models for the human operator, ·         Dosage and timing optimization in oral drug administration, ·         Measuring symptoms of and optimal dopaminergic therapy in Parkinson’s disease, ·         Measure­ment and control of blood glucose le­vels both naturally and by means of external controllers in diabetes, and ·         Control of depth of anaesthesia using inhalational anaesthetic agents like sevoflurane using both fuzzy and state feedback controllers....

  7. Reviewing Manuscripts for Biomedical Journals

    Science.gov (United States)

    Garmel, Gus M

    2010-01-01

    Writing for publication is a complex task. For many professionals, producing a well-executed manuscript conveying one's research, ideas, or educational wisdom is challenging. Authors have varying emotions related to the process of writing for scientific publication. Although not studied, a relationship between an author's enjoyment of the writing process and the product's outcome is highly likely. As with any skill, practice generally results in improvements. Literature focused on preparing manuscripts for publication and the art of reviewing submissions exists. Most journals guard their reviewers' anonymity with respect to the manuscript review process. This is meant to protect them from direct or indirect author demands, which may occur during the review process or in the future. It is generally accepted that author identities are masked in the peer-review process. However, the concept of anonymity for reviewers has been debated recently; many editors consider it problematic that reviewers are not held accountable to the public for their decisions. The review process is often arduous and underappreciated, one reason why biomedical journals acknowledge editors and frequently recognize reviewers who donate their time and expertise in the name of science. This article describes essential elements of a submitted manuscript, with the hopes of improving scientific writing. It also discusses the review process within the biomedical literature, the importance of reviewers to the scientific process, responsibilities of reviewers, and qualities of a good review and reviewer. In addition, it includes useful insights to individuals who read and interpret the medical literature. PMID:20740129

  8. Biomedical support of man in space

    Science.gov (United States)

    Pendergast, D. R.; Olszowka, A. J.; Rokitka, M. A.; Farhi, L. E.

    In its broadest sense, biomedical support of man in space must not be limited to assisting spacecraft crew during the mission; such support should also ensure that flight personnel be able to perform properly during landing and after leaving the craft. Man has developed mechanisms that allow him to cope with specific stresses in his normal habitat; there is indisputable evidence that, in some cases, the space environment, by relieving these stresses, has also allowed the adaptive mechanisms to lapse, causing serious problems after re-entry. Inflight biomedical support must therefore include means to simulate some of the normal stresses of the Earth environment. In the area of cardiovascular performance, we have come to rely heavily on complex feedback mechanisms to cope with two stresses, often combined: postural changes, which alter the body axis along which gravitational acceleration acts, and physical exercise, which increases the total load on the system. Unless the appropriate responses are reinforced continuously during flight, crew members may be incapacitated upon return. The first step in the support process must be a study of the way in which changes in g, even of short duration, affect these responses. In particular we should learn more about effects of g on the "on" and "off" dynamics, using a variety of approaches: increased acceleration on one hand at recumbency, immersion, lower body positive pressure, and other means of simulating some of the effects of low g, on the other. Once we understand this, we will have to determine the minimal exposure dose required to maintain the response mechanisms. Finally, we shall have to design stresses that simulate Earth environment and can be imposed in the space vehicle. Some of the information is already at hand; we know that several aspects of the response to exercise are affected by posture. Results from a current series of studies on the kinetics of tilt and on the dynamics of readjustment to exercise in

  9. Biomedical cloud computing with Amazon Web Services.

    Science.gov (United States)

    Fusaro, Vincent A; Patil, Prasad; Gafni, Erik; Wall, Dennis P; Tonellato, Peter J

    2011-08-01

    In this overview to biomedical computing in the cloud, we discussed two primary ways to use the cloud (a single instance or cluster), provided a detailed example using NGS mapping, and highlighted the associated costs. While many users new to the cloud may assume that entry is as straightforward as uploading an application and selecting an instance type and storage options, we illustrated that there is substantial up-front effort required before an application can make full use of the cloud's vast resources. Our intention was to provide a set of best practices and to illustrate how those apply to a typical application pipeline for biomedical informatics, but also general enough for extrapolation to other types of computational problems. Our mapping example was intended to illustrate how to develop a scalable project and not to compare and contrast alignment algorithms for read mapping and genome assembly. Indeed, with a newer aligner such as Bowtie, it is possible to map the entire African genome using one m2.2xlarge instance in 48 hours for a total cost of approximately $48 in computation time. In our example, we were not concerned with data transfer rates, which are heavily influenced by the amount of available bandwidth, connection latency, and network availability. When transferring large amounts of data to the cloud, bandwidth limitations can be a major bottleneck, and in some cases it is more efficient to simply mail a storage device containing the data to AWS (http://aws.amazon.com/importexport/). More information about cloud computing, detailed cost analysis, and security can be found in references.

  10. The rolling evolution of biomedical science as an essential tool in modern clinical practice.

    Science.gov (United States)

    Blann, Andrew

    2016-01-01

    The British Journal of Biomedical Science is committed to publishing high-quality original research that represents a clear advance in the practice of biomedical science, and reviews that summarise recent advances in the field of biomedical science. The overall aim of the Journal is to provide a platform for the dissemination of new and innovative information on the diagnosis and management of disease that is valuable to the practicing laboratory scientist. The Editorial that follows describes the Journal and provides a perspective of its aims and objectives.

  11. Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts

    OpenAIRE

    Tulkens, Stéphan; Šuster, Simon; Daelemans, Walter

    2016-01-01

    In this paper, we report a knowledge-based method for Word Sense Disambiguation in the domains of biomedical and clinical text. We combine word representations created on large corpora with a small number of definitions from the UMLS to create concept representations, which we then compare to representations of the context of ambiguous terms. Using no relational information, we obtain comparable performance to previous approaches on the MSH-WSD dataset, which is a well-known dataset in the bi...

  12. A Relation Extraction Framework for Biomedical Text Using Hybrid Feature Set

    Directory of Open Access Journals (Sweden)

    Abdul Wahab Muzaffar

    2015-01-01

    Full Text Available The information extraction from unstructured text segments is a complex task. Although manual information extraction often produces the best results, it is harder to manage biomedical data extraction manually because of the exponential increase in data size. Thus, there is a need for automatic tools and techniques for information extraction in biomedical text mining. Relation extraction is a significant area under biomedical information extraction that has gained much importance in the last two decades. A lot of work has been done on biomedical relation extraction focusing on rule-based and machine learning techniques. In the last decade, the focus has changed to hybrid approaches showing better results. This research presents a hybrid feature set for classification of relations between biomedical entities. The main contribution of this research is done in the semantic feature set where verb phrases are ranked using Unified Medical Language System (UMLS and a ranking algorithm. Support Vector Machine and Naïve Bayes, the two effective machine learning techniques, are used to classify these relations. Our approach has been validated on the standard biomedical text corpus obtained from MEDLINE 2001. Conclusively, it can be articulated that our framework outperforms all state-of-the-art approaches used for relation extraction on the same corpus.

  13. The BioIntelligence Framework: a new computational platform for biomedical knowledge computing.

    Science.gov (United States)

    Farley, Toni; Kiefer, Jeff; Lee, Preston; Von Hoff, Daniel; Trent, Jeffrey M; Colbourn, Charles; Mousses, Spyro

    2013-01-01

    Breakthroughs in molecular profiling technologies are enabling a new data-intensive approach to biomedical research, with the potential to revolutionize how we study, manage, and treat complex diseases. The next great challenge for clinical applications of these innovations will be to create scalable computational solutions for intelligently linking complex biomedical patient data to clinically actionable knowledge. Traditional database management systems (DBMS) are not well suited to representing complex syntactic and semantic relationships in unstructured biomedical information, introducing barriers to realizing such solutions. We propose a scalable computational framework for addressing this need, which leverages a hypergraph-based data model and query language that may be better suited for representing complex multi-lateral, multi-scalar, and multi-dimensional relationships. We also discuss how this framework can be used to create rapid learning knowledge base systems to intelligently capture and relate complex patient data to biomedical knowledge in order to automate the recovery of clinically actionable information.

  14. Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research.

    Science.gov (United States)

    Purawat, Shweta; Cowart, Charles; Amaro, Rommie E; Altintas, Ilkay

    2017-05-01

    The BBDTC (https://biobigdata.ucsd.edu) is a community-oriented platform to encourage high-quality knowledge dissemination with the aim of growing a well-informed biomedical big data community through collaborative efforts on training and education. The BBDTC is an e-learning platform that empowers the biomedical community to develop, launch and share open training materials. It deploys hands-on software training toolboxes through virtualization technologies such as Amazon EC2 and Virtualbox. The BBDTC facilitates migration of courses across other course management platforms. The framework encourages knowledge sharing and content personalization through the playlist functionality that enables unique learning experiences and accelerates information dissemination to a wider community.

  15. Disclosing discourses: biomedical and hospitality discourses in patient education materials.

    Science.gov (United States)

    Öresland, Stina; Friberg, Febe; Määttä, Sylvia; Öhlen, Joakim

    2015-09-01

    Patient education materials have the potential to strengthen the health literacy of patients. Previous studies indicate that readability and suitability may be improved. The aim of this study was to explore and analyze discourses inherent in patient education materials since analysis of discourses could illuminate values and norms inherent in them. Clinics in Sweden that provided colorectal cancer surgery allowed access to written information and 'welcome letters' sent to patients. The material was analysed by means of discourse analysis, embedded in Derrida's approach of deconstruction. The analysis revealed a biomedical discourse and a hospitality discourse. In the biomedical discourse, the subject position of the personnel was interpreted as the messenger of medical information while that of the patients as the carrier of diagnoses and recipients of biomedical information. In the hospitality discourse, the subject position of the personnel was interpreted as hosts who invite and welcome the patients as guests. The study highlights the need to eliminate paternalism and fosters a critical reflective stance among professionals regarding power and paternalism inherent in health care communication. © 2015 John Wiley & Sons Ltd.

  16. Archives of Medical and Biomedical Research

    African Journals Online (AJOL)

    Archives of Medical and Biomedical Research is the official journal of the International Association of Medical and Biomedical Researchers (IAMBR) and the Society for Free Radical Research Africa (SFRR-Africa). It is an internationally peer reviewed, open access and multidisciplinary journal aimed at publishing original ...

  17. A new educational program on biomedical engineering

    NARCIS (Netherlands)

    van Alste, Jan A.

    2000-01-01

    At the University of Twente together with the Free University of Amsterdam a new educational program on Biomedical Engineering will be developed. The academic program with a five-year duration will start in September 2001. After a general, broad education in Biomedical Engineering in the first three

  18. Sierra Leone Journal of Biomedical Research

    African Journals Online (AJOL)

    The Sierra Leone Journal of Biomedical Research publishes papers in all fields of Medicine and Allied Health Sciences including Basic Medical Sciences, Clinical Sciences, Dental Sciences, Behavioural Sciences, Biomedical Engineering, Molecular Biology, Pharmaceutical Sciences, Biotechnology in relation to Medicine, ...

  19. Publishing priorities of biomedical research funders

    Science.gov (United States)

    Collins, Ellen

    2013-01-01

    Objectives To understand the publishing priorities, especially in relation to open access, of 10 UK biomedical research funders. Design Semistructured interviews. Setting 10 UK biomedical research funders. Participants 12 employees with responsibility for research management at 10 UK biomedical research funders; a purposive sample to represent a range of backgrounds and organisation types. Conclusions Publicly funded and large biomedical research funders are committed to open access publishing and are pleased with recent developments which have stimulated growth in this area. Smaller charitable funders are supportive of the aims of open access, but are concerned about the practical implications for their budgets and their funded researchers. Across the board, biomedical research funders are turning their attention to other priorities for sharing research outputs, including data, protocols and negative results. Further work is required to understand how smaller funders, including charitable funders, can support open access. PMID:24154520

  20. Ultra low-power biomedical signal processing: An analog wavelet filter approach for pacemakers

    OpenAIRE

    Pavlík Haddad, S.A.

    2006-01-01

    The purpose of this thesis is to describe novel signal processing methodologies and analog integrated circuit techniques for low-power biomedical systems. Physiological signals, such as the electrocardiogram (ECG), the electroencephalogram (EEG) and the electromyogram (EMG) are mostly non-stationary. The main difficulty in dealing with biomedical signal processing is that the information of interest is often a combination of features that are well localized temporally (e.g., spikes) and other...

  1. Piezoelectric nanomaterials for biomedical applications

    CERN Document Server

    Menciassi, Arianna

    2012-01-01

    Nanoscale structures and materials have been explored in many biological applications because of their novel and impressive physical and chemical properties. Such properties allow remarkable opportunities to study and interact with complex biological processes. This book analyses the state of the art of piezoelectric nanomaterials and introduces their applications in the biomedical field. Despite their impressive potentials, piezoelectric materials have not yet received significant attention for bio-applications. This book shows that the exploitation of piezoelectric nanoparticles in nanomedicine is possible and realistic, and their impressive physical properties can be useful for several applications, ranging from sensors and transducers for the detection of biomolecules to “sensible” substrates for tissue engineering or cell stimulation.

  2. Magnetite nanoparticles for biomedical applications

    International Nuclear Information System (INIS)

    Sora, Sergiu; Ion, Rodica Mariana

    2010-01-01

    This work aims to establish and to optimize the conditions for chemical synthesis of nanosized magnetic core-shell iron oxide. The core is magnetite and for the shell we used gold in order to obtain different nanoparticles. Iron oxides was synthesized by sonochemical process using ferrous salts, favoring the synthesis at low-temperature, low costs, high material purity and nanostructure control. After synthesis, some investigation techniques as: X-ray diffraction (XRD), atomic force microscopy (AFM), Thermogravimetric analysis (TGA), Fourier-Transform Infrared Spectroscopy (FTIR) and UVVis absorbance spectroscopy, have been used to see the characteristics of the nanoparticles. For in vitro applications, it is important to prevent any aggregation of the nanoparticles, and may also enable efficient excretion and protection of the cells from toxicity. For biomedical applications like magnetic biofunctional material vectors to target tissues, the particles obtained have to be spherical with 10 nm average diameter. Key words: magnetite, nanocomposite, core-shell, sonochemical method

  3. FULERENIC MATERIALS WITH BIOMEDICAL APPLICATIONS

    Directory of Open Access Journals (Sweden)

    Radu Claudiu FIERASCU

    2010-05-01

    Full Text Available Soluble fullerenic derivates are essential for numerous biomedical techniques that exploit the unique structural chemical and physical properties of carbon nanospheres. Their toxicity, demonstrated in vitro and in vivo is important for the characterization and limitation of those applications. The phototoxicity of some fullerene molecules was identified as a future therapeutical instrument. Other studies focused on the decrease of the phototoxicity of hydrosoluble fullerenes follow the use of those compounds as drug delivery systems or their use in environment protection. Starting from the characteristics of those compounds, which can be by themeselves cytotoxic, or could become during irradiation (photosensitizers we have tried to obtain new materials based on fullerenes and diads/triads fullerene/porphyrines or fullerenes/calixarenes.The obtained complexes were characterized by UV Vis and IR spectroscopy.

  4. Biomedical Wireless Ambulatory Crew Monitor

    Science.gov (United States)

    Chmiel, Alan; Humphreys, Brad

    2009-01-01

    A compact, ambulatory biometric data acquisition system has been developed for space and commercial terrestrial use. BioWATCH (Bio medical Wireless and Ambulatory Telemetry for Crew Health) acquires signals from biomedical sensors using acquisition modules attached to a common data and power bus. Several slots allow the user to configure the unit by inserting sensor-specific modules. The data are then sent real-time from the unit over any commercially implemented wireless network including 802.11b/g, WCDMA, 3G. This system has a distributed computing hierarchy and has a common data controller on each sensor module. This allows for the modularity of the device along with the tailored ability to control the cards using a relatively small master processor. The distributed nature of this system affords the modularity, size, and power consumption that betters the current state of the art in medical ambulatory data acquisition. A new company was created to market this technology.

  5. Titanium nanostructures for biomedical applications

    International Nuclear Information System (INIS)

    Kulkarni, M; Gongadze, E; Perutkova, Š; A Iglič; Mazare, A; Schmuki, P; Kralj-Iglič, V; Milošev, I; Mozetič, M

    2015-01-01

    Titanium and titanium alloys exhibit a unique combination of strength and biocompatibility, which enables their use in medical applications and accounts for their extensive use as implant materials in the last 50 years. Currently, a large amount of research is being carried out in order to determine the optimal surface topography for use in bioapplications, and thus the emphasis is on nanotechnology for biomedical applications. It was recently shown that titanium implants with rough surface topography and free energy increase osteoblast adhesion, maturation and subsequent bone formation. Furthermore, the adhesion of different cell lines to the surface of titanium implants is influenced by the surface characteristics of titanium; namely topography, charge distribution and chemistry. The present review article focuses on the specific nanotopography of titanium, i.e. titanium dioxide (TiO 2 ) nanotubes, using a simple electrochemical anodisation method of the metallic substrate and other processes such as the hydrothermal or sol-gel template. One key advantage of using TiO 2 nanotubes in cell interactions is based on the fact that TiO 2 nanotube morphology is correlated with cell adhesion, spreading, growth and differentiation of mesenchymal stem cells, which were shown to be maximally induced on smaller diameter nanotubes (15 nm), but hindered on larger diameter (100 nm) tubes, leading to cell death and apoptosis. Research has supported the significance of nanotopography (TiO 2 nanotube diameter) in cell adhesion and cell growth, and suggests that the mechanics of focal adhesion formation are similar among different cell types. As such, the present review will focus on perhaps the most spectacular and surprising one-dimensional structures and their unique biomedical applications for increased osseointegration, protein interaction and antibacterial properties. (topical review)

  6. Titanium nanostructures for biomedical applications

    Science.gov (United States)

    Kulkarni, M.; Mazare, A.; Gongadze, E.; Perutkova, Š.; Kralj-Iglič, V.; Milošev, I.; Schmuki, P.; Iglič, A.; Mozetič, M.

    2015-02-01

    Titanium and titanium alloys exhibit a unique combination of strength and biocompatibility, which enables their use in medical applications and accounts for their extensive use as implant materials in the last 50 years. Currently, a large amount of research is being carried out in order to determine the optimal surface topography for use in bioapplications, and thus the emphasis is on nanotechnology for biomedical applications. It was recently shown that titanium implants with rough surface topography and free energy increase osteoblast adhesion, maturation and subsequent bone formation. Furthermore, the adhesion of different cell lines to the surface of titanium implants is influenced by the surface characteristics of titanium; namely topography, charge distribution and chemistry. The present review article focuses on the specific nanotopography of titanium, i.e. titanium dioxide (TiO2) nanotubes, using a simple electrochemical anodisation method of the metallic substrate and other processes such as the hydrothermal or sol-gel template. One key advantage of using TiO2 nanotubes in cell interactions is based on the fact that TiO2 nanotube morphology is correlated with cell adhesion, spreading, growth and differentiation of mesenchymal stem cells, which were shown to be maximally induced on smaller diameter nanotubes (15 nm), but hindered on larger diameter (100 nm) tubes, leading to cell death and apoptosis. Research has supported the significance of nanotopography (TiO2 nanotube diameter) in cell adhesion and cell growth, and suggests that the mechanics of focal adhesion formation are similar among different cell types. As such, the present review will focus on perhaps the most spectacular and surprising one-dimensional structures and their unique biomedical applications for increased osseointegration, protein interaction and antibacterial properties.

  7. SOA-BD: Service Oriented Architecture for Biomedical Devices

    Directory of Open Access Journals (Sweden)

    João Marcos Teixeira Lacerda

    2017-05-01

    Full Text Available Introduction: The communication of information systems with biomedical devices has become complex not only due to the existence of several private communication protocols, but also to the immutable way that software is embedded into these devices. In this sense, this paper proposes a service-oriented architecture to access biomedical devices as a way to abstract the mechanisms of writing and reading data from these devices, thus contributing to enable the focus of the development team of biomedical software to be intended for its functional requirements, i.e. business rules relevant to the problem domain. Methods The SOA-BD architecture consists of five main components: A Web Service for transport and conversion of the device data, Communication Protocols to access the devices, Data Parsers to preprocess data, a Device Repository to store data and transmitted information and Error handling, for error handling of these information. For the development of SOA-BD, technologies such as the XML language and the Java programming language were used. Besides, Software Engineering concepts such as Design Patterns were also used. For the validation of this work, data has been collected from vital sign monitors in an Intensive Care Unit using HL7 standards. Results The tests obtained a difference of about only 1 second in terms of response time with the use of SOA-BD. Conclusion SOA-BD achieves important results such as the reduction on the access protocol complexity, the opportunity for treating patients over long distances, allowing easier development of monitoring applications and interoperability with biomedical devices from diverse manufacturers.

  8. Open Biomedical Engineering education in Africa.

    Science.gov (United States)

    Ahluwalia, Arti; Atwine, Daniel; De Maria, Carmelo; Ibingira, Charles; Kipkorir, Emmauel; Kiros, Fasil; Madete, June; Mazzei, Daniele; Molyneux, Elisabeth; Moonga, Kando; Moshi, Mainen; Nzomo, Martin; Oduol, Vitalice; Okuonzi, John

    2015-08-01

    Despite the virtual revolution, the mainstream academic community in most countries remains largely ignorant of the potential of web-based teaching resources and of the expansion of open source software, hardware and rapid prototyping. In the context of Biomedical Engineering (BME), where human safety and wellbeing is paramount, a high level of supervision and quality control is required before open source concepts can be embraced by universities and integrated into the curriculum. In the meantime, students, more than their teachers, have become attuned to continuous streams of digital information, and teaching methods need to adapt rapidly by giving them the skills to filter meaningful information and by supporting collaboration and co-construction of knowledge using open, cloud and crowd based technology. In this paper we present our experience in bringing these concepts to university education in Africa, as a way of enabling rapid development and self-sufficiency in health care. We describe the three summer schools held in sub-Saharan Africa where both students and teachers embraced the philosophy of open BME education with enthusiasm, and discuss the advantages and disadvantages of opening education in this way in the developing and developed world.

  9. Biomedical waste management operating plan. Revision C

    Energy Technology Data Exchange (ETDEWEB)

    1996-02-14

    Recent national incidents involving medical and/or infectious wastes indicated the need for tighter control of medical wastes. Within the last five years, improper management of medical waste resulted in the spread of disease, reuse of needles by drug addicts, and the closing of large sections of public beaches due to medical waste that washed ashore from ocean disposal. Several regulations, both at the federal and state level, govern management (i.e., handling, storage, transport, treatment, and disposal) of solid or liquid waste which may present a threat of infection to humans. This waste, called infectious, biomedical, biohazardous, or biological waste, generally includes non-liquid human tissue and body parts; laboratory waste which contains human disease-causing agents; discarded sharps; human blood, blood products, and other body fluids. The information that follows outlines and summarizes the general requirements of each standard or rule applicable to biohazardous waste management. In addition, it informs employees of risks associated with biohazardous waste management.

  10. Biochemical imaging of tissues by SIMS for biomedical applications

    International Nuclear Information System (INIS)

    Lee, Tae Geol; Park, Ji-Won; Shon, Hyun Kyong; Moon, Dae Won; Choi, Won Woo; Li, Kapsok; Chung, Jin Ho

    2008-01-01

    With the development of optimal surface cleaning techniques by cluster ion beam sputtering, certain applications of SIMS for analyzing cells and tissues have been actively investigated. For this report, we collaborated with bio-medical scientists to study bio-SIMS analyses of skin and cancer tissues for biomedical diagnostics. We pay close attention to the setting up of a routine procedure for preparing tissue specimens and treating the surface before obtaining the bio-SIMS data. Bio-SIMS was used to study two biosystems, skin tissues for understanding the effects of photoaging and colon cancer tissues for insight into the development of new cancer diagnostics for cancer. Time-of-flight SIMS imaging measurements were taken after surface cleaning with cluster ion bombardment by Bi n or C 60 under varying conditions. The imaging capability of bio-SIMS with a spatial resolution of a few microns combined with principal component analysis reveal biologically meaningful information, but the lack of high molecular weight peaks even with cluster ion bombardment was a problem. This, among other problems, shows that discourse with biologists and medical doctors are critical to glean any meaningful information from SIMS mass spectrometric and imaging data. For SIMS to be accepted as a routine, daily analysis tool in biomedical laboratories, various practical sample handling methodology such as surface matrix treatment, including nano-metal particles and metal coating, in addition to cluster sputtering, should be studied

  11. Publications in biomedical and environmental sciences programs, 1980

    International Nuclear Information System (INIS)

    Pfuderer, H.A.; Moody, J.B.

    1981-07-01

    This bibliography contains 690 references to articles in journals, books, and reports published in the subject area of biomedical and environmental sciences during 1980. There are 529 references to articles published in journals and books and 161 references to reports. Staff members in the Biomedical and Environmental Sciences divisions have other publications not included in this bibliography; for example, theses, book reviews, abstracts published in journals or symposia proceedings, pending journal publications and reports such as monthly and bimonthly progress reports, contractor reports, and reports for internal distribution. This document is sorted by the division, and then alphabetically by author. The sorting by divisions separates the references by subject area in a simple way. The divisions represented in the order that they appear in the bibliography are Analytical Chemistry, Biology, Chemical Technology, Information R and D, Health and Safety Research, Energy, Environmental Sciences, and Computer Sciences

  12. Publications in biomedical and environmental sciences programs, 1980

    Energy Technology Data Exchange (ETDEWEB)

    Pfuderer, H.A.; Moody, J.B.

    1981-07-01

    This bibliography contains 690 references to articles in journals, books, and reports published in the subject area of biomedical and environmental sciences during 1980. There are 529 references to articles published in journals and books and 161 references to reports. Staff members in the Biomedical and Environmental Sciences divisions have other publications not included in this bibliography; for example, theses, book reviews, abstracts published in journals or symposia proceedings, pending journal publications and reports such as monthly and bimonthly progress reports, contractor reports, and reports for internal distribution. This document is sorted by the division, and then alphabetically by author. The sorting by divisions separates the references by subject area in a simple way. The divisions represented in the order that they appear in the bibliography are Analytical Chemistry, Biology, Chemical Technology, Information R and D, Health and Safety Research, Energy, Environmental Sciences, and Computer Sciences.

  13. Revisit of Machine Learning Supported Biological and Biomedical Studies.

    Science.gov (United States)

    Yu, Xiang-Tian; Wang, Lu; Zeng, Tao

    2018-01-01

    Generally, machine learning includes many in silico methods to transform the principles underlying natural phenomenon to human understanding information, which aim to save human labor, to assist human judge, and to create human knowledge. It should have wide application potential in biological and biomedical studies, especially in the era of big biological data. To look through the application of machine learning along with biological development, this review provides wide cases to introduce the selection of machine learning methods in different practice scenarios involved in the whole biological and biomedical study cycle and further discusses the machine learning strategies for analyzing omics data in some cutting-edge biological studies. Finally, the notes on new challenges for machine learning due to small-sample high-dimension are summarized from the key points of sample unbalance, white box, and causality.

  14. Biomedical photoacoustics: fundamentals, instrumentation and perspectives on nanomedicine.

    Science.gov (United States)

    Zou, Chunpeng; Wu, Beibei; Dong, Yanyan; Song, Zhangwei; Zhao, Yaping; Ni, Xianwei; Yang, Yan; Liu, Zhe

    Photoacoustic imaging (PAI) is an integrated biomedical imaging modality which combines the advantages of acoustic deep penetration and optical high sensitivity. It can provide functional and structural images with satisfactory resolution and contrast which could provide abundant pathological information for disease-oriented diagnosis. Therefore, it has found vast applications so far and become a powerful tool of precision nanomedicine. However, the investigation of PAI-based imaging nanomaterials is still in its infancy. This perspective article aims to summarize the developments in photoacoustic technologies and instrumentations in the past years, and more importantly, present a bright outlook for advanced PAI-based imaging nanomaterials as well as their emerging biomedical applications in nanomedicine. Current challenges and bottleneck issues have also been discussed and elucidated in this article to bring them to the attention of the readership.

  15. Genome typing of nonhuman primate models: implications for biomedical research.

    Science.gov (United States)

    Haus, Tanja; Ferguson, Betsy; Rogers, Jeffrey; Doxiadis, Gaby; Certa, Ulrich; Rose, Nicola J; Teepe, Robert; Weinbauer, Gerhard F; Roos, Christian

    2014-11-01

    The success of personalized medicine rests on understanding the genetic variation between individuals. Thus, as medical practice evolves and variation among individuals becomes a fundamental aspect of clinical medicine, a thorough consideration of the genetic and genomic information concerning the animals used as models in biomedical research also becomes critical. In particular, nonhuman primates (NHPs) offer great promise as models for many aspects of human health and disease. These are outbred species exhibiting substantial levels of genetic variation; however, understanding of the contribution of this variation to phenotypes is lagging behind in NHP species. Thus, there is a pivotal need to address this gap and define strategies for characterizing both genomic content and variability within primate models of human disease. Here, we discuss the current state of genomics of NHP models and offer guidelines for future work to ensure continued improvement and utility of this line of biomedical research. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Porting Biomedical Applications to Grids

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2008-01-01

    textabstractToday advances in scientific research as well as clinical diagnostics and treatment are inevitably connected with information solutions concerning computation power and information storage. The needs for information technology are enormous and are in many cases the limiting

  17. Enhancing biomedical design with design thinking.

    Science.gov (United States)

    Kemnitzer, Ronald; Dorsa, Ed

    2009-01-01

    The development of biomedical equipment is justifiably focused on making products that "work." However, this approach leaves many of the people affected by these designs (operators, patients, etc.) with little or no representation when it comes to the design of these products. Industrial design is a "user focused" profession which takes into account the needs of diverse groups when making design decisions. The authors propose that biomedical equipment design can be enhanced, made more user and patient "friendly" by adopting the industrial design approach to researching, analyzing, and ultimately designing biomedical products.

  18. Biomedical Optical Imaging Technologies Design and Applications

    CERN Document Server

    2013-01-01

    This book provides an introduction to design of biomedical optical imaging technologies and their applications. The main topics include: fluorescence imaging, confocal imaging, micro-endoscope, polarization imaging, hyperspectral imaging, OCT imaging, multimodal imaging and spectroscopic systems. Each chapter is written by the world leaders of the respective fields, and will cover: principles and limitations of optical imaging technology, system design and practical implementation for one or two specific applications, including design guidelines, system configuration, optical design, component requirements and selection, system optimization and design examples, recent advances and applications in biomedical researches and clinical imaging. This book serves as a reference for students and researchers in optics and biomedical engineering.

  19. Investigating and Annotating the Role of Citation in Biomedical Full-Text Articles.

    Science.gov (United States)

    Yu, Hong; Agarwal, Shashank; Frid, Nadya

    2009-11-01

    Citations are ubiquitous in scientific articles and play important roles for representing the semantic content of a full-text biomedical article. In this work, we manually examined full-text biomedical articles to analyze the semantic content of citations in full-text biomedical articles. After developing a citation relation schema and annotation guideline, our pilot annotation results show an overall agreement of 0.71, and here we report on the research challenges and the lessons we've learned while trying to overcome them. Our work is a first step toward automatic citation classification in full-text biomedical articles, which may contribute to many text mining tasks, including information retrieval, extraction, summarization, and question answering.

  20. Gold Nanocages for Biomedical Applications**

    Science.gov (United States)

    Skrabalak, Sara E.; Chen, Jingyi; Au, Leslie; Lu, Xianmao; Li, Xingde; Xia, Younan

    2008-01-01

    Nanostructured materials provide a promising platform for early cancer detection and treatment. Here we highlight recent advances in the synthesis and use of Au nanocages for such biomedical applications. Gold nanocages represent a novel class of nanostructures, which can be prepared via a remarkably simple route based on the galvanic replacement reaction between Ag nanocubes and HAuCl4. The Au nanocages have a tunable surface plasmon resonance peak that extends into the near-infrared, where the optical attenuation caused by blood and soft tissue is essentially negligible. They are also biocompatible and present a well-established surface for easy functionalization. We have tailored the scattering and absorption cross-sections of Au nanocages for use in optical coherence tomography and photothermal treatment, respectively. Our preliminary studies show greatly improved spectroscopic image contrast for tissue phantoms containing Au nanocages. Our most recent results also demonstrate the photothermal destruction of breast cancer cells in vitro by using immuno-targeted Au nanocages as an effective photo-thermal transducer. These experiments suggest that Au nanocages may be a new class of nanometer-sized agents for cancer diagnosis and therapy. PMID:18648528

  1. Gold Nanocages for Biomedical Applications.

    Science.gov (United States)

    Skrabalak, Sara E; Chen, Jingyi; Au, Leslie; Lu, Xianmao; Li, Xingde; Xia, Younan

    2007-10-17

    Nanostructured materials provide a promising platform for early cancer detection and treatment. Here we highlight recent advances in the synthesis and use of Au nanocages for such biomedical applications. Gold nanocages represent a novel class of nanostructures, which can be prepared via a remarkably simple route based on the galvanic replacement reaction between Ag nanocubes and HAuCl(4). The Au nanocages have a tunable surface plasmon resonance peak that extends into the near-infrared, where the optical attenuation caused by blood and soft tissue is essentially negligible. They are also biocompatible and present a well-established surface for easy functionalization. We have tailored the scattering and absorption cross-sections of Au nanocages for use in optical coherence tomography and photothermal treatment, respectively. Our preliminary studies show greatly improved spectroscopic image contrast for tissue phantoms containing Au nanocages. Our most recent results also demonstrate the photothermal destruction of breast cancer cells in vitro by using immuno-targeted Au nanocages as an effective photo-thermal transducer. These experiments suggest that Au nanocages may be a new class of nanometer-sized agents for cancer diagnosis and therapy.

  2. The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Rubin, Daniel L.; Lewis, Suzanna E.; Mungall, Chris J.; Misra,Sima; Westerfield, Monte; Ashburner, Michael; Sim, Ida; Chute,Christopher G.; Solbrig, Harold; Storey, Margaret-Anne; Smith, Barry; Day-Richter, John; Noy, Natalya F.; Musen, Mark A.

    2006-01-23

    The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are: (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. The Center is working toward these objectives by providing tools to develop ontologies and to annotate experimental data, and by developing resources to integrate and relate existing ontologies as well as by creating repositories of biomedical data that are annotated using those ontologies. The Center is providing training workshops in ontology design, development, and usage, and is also pursuing research in ontology evaluation, quality, and use of ontologies to promote scientific discovery. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease.

  3. TLC/HPTLC in Biomedical Applications

    Science.gov (United States)

    Mohammad, A.; Moheman, A.

    The main objective of this chapter is to encapsulate the applications of thin-layer chromatography (TLC) and high-performance thin-layer chromatography (HPTLC) as used in the analysis of compounds of pharmaceutical importance. The chapter discusses the advantages of using TLC or HPTLC for biomedical applications and summarizes important information on stationary and mobile phases, adopted methodology, sample application, zone detection, and identification and quantification of amino acids and proteins, carbohydrates, lipids, bile acids, drugs, vitamins, and porphyrins in biological matrices such as blood, urine, feces, saliva, cerebrospinal fluid, body tissues, etc. Among the stationary phases, silica gel has been the most preferred layer material in combination of mixed aqueous- organic or multicomponent organic solvent systems as mobile phase. For quantitative determination of analyte in various matrices, densitometry has been more commonly used. According to the literature survey, the interest of chromatographers in using the TLC/HPTLC has been in the following order: drugs > amino acids and proteins > lipids > bile acids > carbohydrates/vitamins > porphyrins.

  4. Relational Databases and Biomedical Big Data.

    Science.gov (United States)

    de Silva, N H Nisansa D

    2017-01-01

    In various biomedical applications that collect, handle, and manipulate data, the amounts of data tend to build up and venture into the range identified as bigdata. In such occurrences, a design decision has to be taken as to what type of database would be used to handle this data. More often than not, the default and classical solution to this in the biomedical domain according to past research is relational databases. While this used to be the norm for a long while, it is evident that there is a trend to move away from relational databases in favor of other types and paradigms of databases. However, it still has paramount importance to understand the interrelation that exists between biomedical big data and relational databases. This chapter will review the pros and cons of using relational databases to store biomedical big data that previous researches have discussed and used.

  5. NIH/NSF accelerate biomedical research innovations

    Science.gov (United States)

    A collaboration between the National Science Foundation and the National Institutes of Health will give NIH-funded researchers training to help them evaluate their scientific discoveries for commercial potential, with the aim of accelerating biomedical in

  6. VII Latin American Congress on Biomedical Engineering

    CERN Document Server

    Bustamante, John; Sierra, Daniel

    2017-01-01

    This volume presents the proceedings of the CLAIB 2016, held in Bucaramanga, Santander, Colombia, 26, 27 & 28 October 2016. The proceedings, presented by the Regional Council of Biomedical Engineering for Latin America (CORAL), offer research findings, experiences and activities between institutions and universities to develop Bioengineering, Biomedical Engineering and related sciences. The conferences of the American Congress of Biomedical Engineering are sponsored by the International Federation for Medical and Biological Engineering (IFMBE), Society for Engineering in Biology and Medicine (EMBS) and the Pan American Health Organization (PAHO), among other organizations and international agencies to bring together scientists, academics and biomedical engineers in Latin America and other continents in an environment conducive to exchange and professional growth.

  7. International Journal of Medicine and Biomedical Research

    African Journals Online (AJOL)

    The International Journal of Medicine and Biomedical Research (IJMBR) is a peer-reviewed ... useful to researchers in all aspects of Clinical and Basic Medical Sciences including Anatomical Sciences, Biochemistry, Dentistry, Genetics, ...

  8. Sierra Leone Journal of Biomedical Research

    African Journals Online (AJOL)

    MHRL

    Sierra Leone Journal of Biomedical Research. (A publication of the College of Medicine and Allied Health Sciences, University of Sierra Leone). ©Sierra Leone Journal .... was used to. She seemed to have had a change of mind after ingesting.

  9. VI Latin American Congress on Biomedical Engineering

    CERN Document Server

    Hadad, Alejandro

    2015-01-01

    This volume presents the proceedings of the CLAIB 2014, held in Paraná, Entre Ríos, Argentina 29, 30 & 31 October 2014. The proceedings, presented by the Regional Council of Biomedical Engineering for Latin America (CORAL) offer research findings, experiences and activities between institutions and universities to develop Bioengineering, Biomedical Engineering and related sciences. The conferences of the American Congress of Biomedical Engineering are sponsored by the International Federation for Medical and Biological Engineering (IFMBE), Society for Engineering in Biology and Medicine (EMBS) and the Pan American Health Organization (PAHO), among other organizations and international agencies and bringing together scientists, academics and biomedical engineers in Latin America and other continents in an environment conducive to exchange and professional growth. The Topics include: - Bioinformatics and Computational Biology - Bioinstrumentation; Sensors, Micro and Nano Technologies - Biomaterials, Tissu...

  10. Distributed System for Spaceflight Biomedical Support

    Data.gov (United States)

    National Aeronautics and Space Administration — Our project investigated whether a software platform could integrate as wide a variety of devices and data types as needed for spaceflight biomedical support. The...

  11. Journal of Medical and Biomedical Sciences

    African Journals Online (AJOL)

    PROMOTING ACCESS TO AFRICAN RESEARCH ... The Journal of Medical and Biomedical Science publishes original, novel, peer-reviewed reports that pertain to medical and allied health sciences; confirmatory reports of previously ...

  12. A Program on Biochemical and Biomedical Engineering.

    Science.gov (United States)

    San, Ka-Yiu; McIntire, Larry V.

    1989-01-01

    Presents an introduction to the Biochemical and Biomedical Engineering program at Rice University. Describes the development of the academic and enhancement programs, including organizational structure and research project titles. (YP)

  13. NICHD Biomedical Mass Spectrometry Core Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The NICHD Biomedical Mass Spectrometry Core Facility was created under the auspices of the Office of the Scientific Director to provide high-end mass-spectrometric...

  14. Computer vision for biomedical image applications. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yanxi [Carnegie Mellon Univ., Pittsburgh, PA (United States). School of Computer Science, The Robotics Institute; Jiang, Tianzi [Chinese Academy of Sciences, Beijing (China). National Lab. of Pattern Recognition, Inst. of Automation; Zhang, Changshui (eds.) [Tsinghua Univ., Beijing, BJ (China). Dept. of Automation

    2005-07-01

    This book constitutes the refereed proceedings of the First International Workshop on Computer Vision for Biomedical Image Applications: Current Techniques and Future Trends, CVBIA 2005, held in Beijing, China, in October 2005 within the scope of ICCV 20. (orig.)

  15. Information

    International Nuclear Information System (INIS)

    Boyard, Pierre.

    1981-01-01

    The fear for nuclear energy and more particularly for radioactive wastes is analyzed in the sociological context. Everybody agree on the information need, information is available but there is a problem for their diffusion. Reactions of the public are analyzed and journalists, scientists and teachers have a role to play [fr

  16. Semiconducting silicon nanowires for biomedical applications

    CERN Document Server

    Coffer, JL

    2014-01-01

    Biomedical applications have benefited greatly from the increasing interest and research into semiconducting silicon nanowires. Semiconducting Silicon Nanowires for Biomedical Applications reviews the fabrication, properties, and applications of this emerging material. The book begins by reviewing the basics, as well as the growth, characterization, biocompatibility, and surface modification, of semiconducting silicon nanowires. It goes on to focus on silicon nanowires for tissue engineering and delivery applications, including cellular binding and internalization, orthopedic tissue scaffol

  17. European virtual campus for biomedical engineering EVICAB.

    Science.gov (United States)

    Malmivuo, Jaakko A; Nousiainen, Juha O; Lindroos, Kari V

    2007-01-01

    European Commission has funded building a curriculum on Biomedical Engineering to the Internet for European universities under the project EVICAB. EVICAB forms a curriculum which will be free access and available free of charge. Therefore, in addition to the European universities, it will be available worldwide. EVICAB will make high quality education available for everyone, not only for the university students, and facilitate the development of the discipline of Biomedical Engineering.

  18. Advanced computational approaches to biomedical engineering

    CERN Document Server

    Saha, Punam K; Basu, Subhadip

    2014-01-01

    There has been rapid growth in biomedical engineering in recent decades, given advancements in medical imaging and physiological modelling and sensing systems, coupled with immense growth in computational and network technology, analytic approaches, visualization and virtual-reality, man-machine interaction and automation. Biomedical engineering involves applying engineering principles to the medical and biological sciences and it comprises several topics including biomedicine, medical imaging, physiological modelling and sensing, instrumentation, real-time systems, automation and control, sig

  19. Biomedical Applications of Enzymes From Marine Actinobacteria.

    Science.gov (United States)

    Kamala, K; Sivaperumal, P

    Marine microbial enzyme technologies have progressed significantly in the last few decades for different applications. Among the various microorganisms, marine actinobacterial enzymes have significant active properties, which could allow them to be biocatalysts with tremendous bioactive metabolites. Moreover, marine actinobacteria have been considered as biofactories, since their enzymes fulfill biomedical and industrial needs. In this chapter, the marine actinobacteria and their enzymes' uses in biological activities and biomedical applications are described. © 2017 Elsevier Inc. All rights reserved.

  20. Biomedical photonics handbook therapeutics and advanced biophotonics

    CERN Document Server

    Vo-Dinh, Tuan

    2014-01-01

    Shaped by Quantum Theory, Technology, and the Genomics RevolutionThe integration of photonics, electronics, biomaterials, and nanotechnology holds great promise for the future of medicine. This topic has recently experienced an explosive growth due to the noninvasive or minimally invasive nature and the cost-effectiveness of photonic modalities in medical diagnostics and therapy. The second edition of the Biomedical Photonics Handbook presents recent fundamental developments as well as important applications of biomedical photonics of interest to scientists, engineers, manufacturers, teachers,

  1. Special Issue: 3D Printing for Biomedical Engineering.

    Science.gov (United States)

    Chua, Chee Kai; Yeong, Wai Yee; An, Jia

    2017-02-28

    Three-dimensional (3D) printing has a long history of applications in biomedical engineering. The development and expansion of traditional biomedical applications are being advanced and enriched by new printing technologies. New biomedical applications such as bioprinting are highly attractive and trendy. This Special Issue aims to provide readers with a glimpse of the recent profile of 3D printing in biomedical research.

  2. An Insufferable Business: Ethics, Nonhuman Animals and Biomedical Experiments

    Directory of Open Access Journals (Sweden)

    Kay Peggs

    2015-07-01

    Full Text Available Each year millions of nonhuman animals suffer in biomedical experiments for human health benefits. Clinical ethics demand that nonhuman animals are used in the development of pharmaceuticals and vaccines. Nonhuman animals are also used for fundamental biomedical research. Biomedical research that uses nonhuman animals is big business but the financial gains are generally occluded. This paper explores how such research generates profits and gains for those associated with the industry. Research establishments, scientists, laboratories, companies that sell nonhuman animal subjects, that supply equipment for the research, and corporations that market the resulting products are among those that benefit financially. Given the complex articulation of ethical codes, enormous corporate profits that are secured and personal returns that are made, the accepted moral legitimacy of such experiments is compromised. In order to address this, within the confines of the moral orthodoxy, more could to be done to ensure transparency and to extricate the vested financial interests from the human health benefits. But such a determination would not address the fundamental issues that should be at the heart of human actions in respect of the nonhuman animals who are used in experiments. The paper concludes with such an address by calling for an end to the denigration of nonhuman animals as experimental subjects who can be used as commodities for profit-maximisation and as tools in experiments for human health benefits, and the implementation of a more inclusive ethic that is informed by universal concern about the suffering of and compassion for all oppressed beings.

  3. An Insufferable Business: Ethics, Nonhuman Animals and Biomedical Experiments.

    Science.gov (United States)

    Peggs, Kay

    2015-07-22

    Each year millions of nonhuman animals suffer in biomedical experiments for human health benefits. Clinical ethics demand that nonhuman animals are used in the development of pharmaceuticals and vaccines. Nonhuman animals are also used for fundamental biomedical research. Biomedical research that uses nonhuman animals is big business but the financial gains are generally occluded. This paper explores how such research generates profits and gains for those associated with the industry. Research establishments, scientists, laboratories, companies that sell nonhuman animal subjects, that supply equipment for the research, and corporations that market the resulting products are among those that benefit financially. Given the complex articulation of ethical codes, enormous corporate profits that are secured and personal returns that are made, the accepted moral legitimacy of such experiments is compromised. In order to address this, within the confines of the moral orthodoxy, more could to be done to ensure transparency and to extricate the vested financial interests from the human health benefits. But such a determination would not address the fundamental issues that should be at the heart of human actions in respect of the nonhuman animals who are used in experiments. The paper concludes with such an address by calling for an end to the denigration of nonhuman animals as experimental subjects who can be used as commodities for profit-maximisation and as tools in experiments for human health benefits, and the implementation of a more inclusive ethic that is informed by universal concern about the suffering of and compassion for all oppressed beings.

  4. Private Data Analytics on Biomedical Sensing Data via Distributed Computation.

    Science.gov (United States)

    Gong, Yanmin; Fang, Yuguang; Guo, Yuanxiong

    2016-01-01

    Advances in biomedical sensors and mobile communication technologies have fostered the rapid growth of mobile health (mHealth) applications in the past years. Users generate a high volume of biomedical data during health monitoring, which can be used by the mHealth server for training predictive models for disease diagnosis and treatment. However, the biomedical sensing data raise serious privacy concerns because they reveal sensitive information such as health status and lifestyles of the sensed subjects. This paper proposes and experimentally studies a scheme that keeps the training samples private while enabling accurate construction of predictive models. We specifically consider logistic regression models which are widely used for predicting dichotomous outcomes in healthcare, and decompose the logistic regression problem into small subproblems over two types of distributed sensing data, i.e., horizontally partitioned data and vertically partitioned data. The subproblems are solved using individual private data, and thus mHealth users can keep their private data locally and only upload (encrypted) intermediate results to the mHealth server for model training. Experimental results based on real datasets show that our scheme is highly efficient and scalable to a large number of mHealth users.

  5. Exploring subdomain variation in biomedical language

    Directory of Open Access Journals (Sweden)

    Séaghdha Diarmuid Ó

    2011-05-01

    Full Text Available Abstract Background Applications of Natural Language Processing (NLP technology to biomedical texts have generated significant interest in recent years. In this paper we identify and investigate the phenomenon of linguistic subdomain variation within the biomedical domain, i.e., the extent to which different subject areas of biomedicine are characterised by different linguistic behaviour. While variation at a coarser domain level such as between newswire and biomedical text is well-studied and known to affect the portability of NLP systems, we are the first to conduct an extensive investigation into more fine-grained levels of variation. Results Using the large OpenPMC text corpus, which spans the many subdomains of biomedicine, we investigate variation across a number of lexical, syntactic, semantic and discourse-related dimensions. These dimensions are chosen for their relevance to the performance of NLP systems. We use clustering techniques to analyse commonalities and distinctions among the subdomains. Conclusions We find that while patterns of inter-subdomain variation differ somewhat from one feature set to another, robust clusters can be identified that correspond to intuitive distinctions such as that between clinical and laboratory subjects. In particular, subdomains relating to genetics and molecular biology, which are the most common sources of material for training and evaluating biomedical NLP tools, are not representative of all biomedical subdomains. We conclude that an awareness of subdomain variation is important when considering the practical use of language processing applications by biomedical researchers.

  6. Writing intelligible English prose for biomedical journals.

    Science.gov (United States)

    Ludbrook, John

    2007-01-01

    1. I present a combination of semi-objective and subjective evidence that the quality of English prose in biomedical scientific writing is deteriorating. 2. I consider seven possible strategies for reversing this apparent trend. These refer to a greater emphasis on good writing by students in schools and by university students, consulting books on science writing, one-on-one mentoring, using 'scientific' measures to reveal lexical poverty, making use of freelance science editors and encouraging the editors of biomedical journals to pay more attention to the problem. 3. I conclude that a fruitful, long-term, strategy would be to encourage more biomedical scientists to embark on a career in science editing. This strategy requires a complementary initiative on the part of biomedical research institutions and universities to employ qualified science editors. 4. An immediately realisable strategy is to encourage postgraduate students in the biomedical sciences to undertake the service courses provided by many universities on writing English prose in general and scientific prose in particular. This strategy would require that heads of departments and supervisors urge their postgraduate students to attend such courses. 5. Two major publishers of biomedical journals, Blackwell Publications and Elsevier Science, now provide lists of commercial editing services on their web sites. I strongly recommend that authors intending to submit manuscripts to their journals (including Blackwell's Clinical and Experimental Pharmacology and Physiology) make use of these services. This recommendation applies especially to those for whom English is a second language.

  7. Sortal anaphora resolution to enhance relation extraction from biomedical literature.

    Science.gov (United States)

    Kilicoglu, Halil; Rosemblat, Graciela; Fiszman, Marcelo; Rindflesch, Thomas C

    2016-04-14

    Entity coreference is common in biomedical literature and it can affect text understanding systems that rely on accurate identification of named entities, such as relation extraction and automatic summarization. Coreference resolution is a foundational yet challenging natural language processing task which, if performed successfully, is likely to enhance such systems significantly. In this paper, we propose a semantically oriented, rule-based method to resolve sortal anaphora, a specific type of coreference that forms the majority of coreference instances in biomedical literature. The method addresses all entity types and relies on linguistic components of SemRep, a broad-coverage biomedical relation extraction system. It has been incorporated into SemRep, extending its core semantic interpretation capability from sentence level to discourse level. We evaluated our sortal anaphora resolution method in several ways. The first evaluation specifically focused on sortal anaphora relations. Our methodology achieved a F1 score of 59.6 on the test portion of a manually annotated corpus of 320 Medline abstracts, a 4-fold improvement over the baseline method. Investigating the impact of sortal anaphora resolution on relation extraction, we found that the overall effect was positive, with 50 % of the changes involving uninformative relations being replaced by more specific and informative ones, while 35 % of the changes had no effect, and only 15 % were negative. We estimate that anaphora resolution results in changes in about 1.5 % of approximately 82 million semantic relations extracted from the entire PubMed. Our results demonstrate that a heavily semantic approach to sortal anaphora resolution is largely effective for biomedical literature. Our evaluation and error analysis highlight some areas for further improvements, such as coordination processing and intra-sentential antecedent selection.

  8. Misconduct Policies in High-Impact Biomedical Journals

    Science.gov (United States)

    Bosch, Xavier; Hernández, Cristina; Pericas, Juan M.; Doti, Pamela; Marušić, Ana

    2012-01-01

    Background It is not clear which research misconduct policies are adopted by biomedical journals. This study assessed the prevalence and content policies of the most influential biomedical journals on misconduct and procedures for handling and responding to allegations of misconduct. Methods We conducted a cross-sectional study of misconduct policies of 399 high-impact biomedical journals in 27 biomedical categories of the Journal Citation Reports in December 2011. Journal websites were reviewed for information relevant to misconduct policies. Results Of 399 journals, 140 (35.1%) provided explicit definitions of misconduct. Falsification was explicitly mentioned by 113 (28.3%) journals, fabrication by 104 (26.1%), plagiarism by 224 (56.1%), duplication by 242 (60.7%) and image manipulation by 154 (38.6%). Procedures for responding to misconduct were described in 179 (44.9%) websites, including retraction, (30.8%) and expression of concern (16.3%). Plagiarism-checking services were used by 112 (28.1%) journals. The prevalences of all types of misconduct policies were higher in journals that endorsed any policy from editors’ associations, Office of Research Integrity or professional societies compared to those that did not state adherence to these policy-producing bodies. Elsevier and Wiley-Blackwell had the most journals included (22.6% and 14.8%, respectively), with Wiley journals having greater a prevalence of misconduct definition and policies on falsification, fabrication and expression of concern and Elsevier of plagiarism-checking services. Conclusions Only a third of top-ranking peer-reviewed journals had publicly-available definitions of misconduct and less than a half described procedures for handling allegations of misconduct. As endorsement of international policies from policy-producing bodies was positively associated with implementation of policies and procedures, journals and their publishers should standardize their policies globally in order to

  9. DTMiner: identification of potential disease targets through biomedical literature mining.

    Science.gov (United States)

    Xu, Dong; Zhang, Meizhuo; Xie, Yanping; Wang, Fan; Chen, Ming; Zhu, Kenny Q; Wei, Jia

    2016-12-01

    Biomedical researchers often search through massive catalogues of literature to look for potential relationships between genes and diseases. Given the rapid growth of biomedical literature, automatic relation extraction, a crucial technology in biomedical literature mining, has shown great potential to support research of gene-related diseases. Existing work in this field has produced datasets that are limited both in scale and accuracy. In this study, we propose a reliable and efficient framework that takes large biomedical literature repositories as inputs, identifies credible relationships between diseases and genes, and presents possible genes related to a given disease and possible diseases related to a given gene. The framework incorporates name entity recognition (NER), which identifies occurrences of genes and diseases in texts, association detection whereby we extract and evaluate features from gene-disease pairs, and ranking algorithms that estimate how closely the pairs are related. The F1-score of the NER phase is 0.87, which is higher than existing studies. The association detection phase takes drastically less time than previous work while maintaining a comparable F1-score of 0.86. The end-to-end result achieves a 0.259 F1-score for the top 50 genes associated with a disease, which performs better than previous work. In addition, we released a web service for public use of the dataset. The implementation of the proposed algorithms is publicly available at http://gdr-web.rwebox.com/public_html/index.php?page=download.php The web service is available at http://gdr-web.rwebox.com/public_html/index.php CONTACT: jenny.wei@astrazeneca.com or kzhu@cs.sjtu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  10. Science communication in the field of fundamental biomedical research (editorial).

    Science.gov (United States)

    Illingworth, Sam; Prokop, Andreas

    2017-10-01

    The aim of this special issue on science communication is to inspire and help scientists who are taking part or want to take part in science communication and engage with the wider public, clinicians, other scientists or policy makers. For this, some articles provide concise and accessible advice to individual scientists, science networks, or learned societies on how to communicate effectively; others share rationales, objectives and aims, experiences, implementation strategies and resources derived from existing long-term science communication initiatives. Although this issue is primarily addressing scientists working in the field of biomedical research, much of it similarly applies to scientists from other disciplines. Furthermore, we hope that this issue will also be used as a helpful resource by academic science communicators and social scientists, as a collection that highlights some of the major communication challenges that the biomedical sciences face, and which provides interesting case studies of initiatives that use a breadth of strategies to address these challenges. In this editorial, we first discuss why we should communicate our science and contemplate some of the different approaches, aspirations and definitions of science communication. We then address the specific challenges that researchers in the biomedical sciences are faced with when engaging with wider audiences. Finally, we explain the rationales and contents of the different articles in this issue and the various science communication initiatives and strategies discussed in each of them, whilst also providing some information on the wide range of further science communication activities in the biomedical sciences that could not all be covered here. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. Misconduct policies in high-impact biomedical journals.

    Directory of Open Access Journals (Sweden)

    Xavier Bosch

    Full Text Available It is not clear which research misconduct policies are adopted by biomedical journals. This study assessed the prevalence and content policies of the most influential biomedical journals on misconduct and procedures for handling and responding to allegations of misconduct.We conducted a cross-sectional study of misconduct policies of 399 high-impact biomedical journals in 27 biomedical categories of the Journal Citation Reports in December 2011. Journal websites were reviewed for information relevant to misconduct policies.Of 399 journals, 140 (35.1% provided explicit definitions of misconduct. Falsification was explicitly mentioned by 113 (28.3% journals, fabrication by 104 (26.1%, plagiarism by 224 (56.1%, duplication by 242 (60.7% and image manipulation by 154 (38.6%. Procedures for responding to misconduct were described in 179 (44.9% websites, including retraction, (30.8% and expression of concern (16.3%. Plagiarism-checking services were used by 112 (28.1% journals. The prevalences of all types of misconduct policies were higher in journals that endorsed any policy from editors' associations, Office of Research Integrity or professional societies compared to those that did not state adherence to these policy-producing bodies. Elsevier and Wiley-Blackwell had the most journals included (22.6% and 14.8%, respectively, with Wiley journals having greater a prevalence of misconduct definition and policies on falsification, fabrication and expression of concern and Elsevier of plagiarism-checking services.Only a third of top-ranking peer-reviewed journals had publicly-available definitions of misconduct and less than a half described procedures for handling allegations of misconduct. As endorsement of international policies from policy-producing bodies was positively associated with implementation of policies and procedures, journals and their publishers should standardize their policies globally in order to increase public trust in the

  12. Biomedical informatics and the convergence of Nano-Bio-Info-Cogno (NBIC) technologies.

    Science.gov (United States)

    Martin-Sanchez, F; Maojo, V

    2009-01-01

    To analyze the role that biomedical informatics could play in the application of the NBIC Converging Technologies in the medical field and raise awareness of these new areas throughout the Biomedical Informatics community. Review of the literature and analysis of the reference documents in this domain from the biomedical informatics perspective. Detailing existing developments showing that partial convergence of technologies have already yielded relevant results in biomedicine (such as bioinformatics or biochips). Input from current projects in which the authors are involved is also used. Information processing is a key issue in enabling the convergence of NBIC technologies. Researchers in biomedical informatics are in a privileged position to participate and actively develop this new scientific direction. The experience of biomedical informaticians in five decades of research in the medical area and their involvement in the completion of the Human and other genome projects will help them participate in a similar role for the development of applications of converging technologies -particularly in nanomedicine. The proposed convergence will bring bridges between traditional disciplines. Particular attention should be placed on the ethical, legal, and social issues raised by the NBIC convergence. These technologies provide new directions for research and education in Biomedical Informatics placing a greater emphasis in multidisciplinary approaches.

  13. Are we studying what matters? Health priorities and NIH-funded biomedical engineering research.

    Science.gov (United States)

    Rubin, Jessica B; Paltiel, A David; Saltzman, W Mark

    2010-07-01

    With the founding of the National Institute of Biomedical Imaging and Bioengineering (NIBIB) in 1999, the National Institutes of Health (NIH) made explicit its dedication to expanding research in biomedical engineering. Ten years later, we sought to examine how closely federal funding for biomedical engineering aligns with U.S. health priorities. Using a publicly accessible database of research projects funded by the NIH in 2008, we identified 641 grants focused on biomedical engineering, 48% of which targeted specific diseases. Overall, we found that these disease-specific NIH-funded biomedical engineering research projects align with national health priorities, as quantified by three commonly utilized measures of disease burden: cause of death, disability-adjusted survival losses, and expenditures. However, we also found some illnesses (e.g., cancer and heart disease) for which the number of research projects funded deviated from our expectations, given their disease burden. Our findings suggest several possibilities for future studies that would serve to further inform the allocation of limited research dollars within the field of biomedical engineering.

  14. Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension.

    Science.gov (United States)

    Yu, Hong; Agarwal, Shashank; Johnston, Mark; Cohen, Aaron

    2009-01-06

    Biomedical scientists need to access figures to validate research facts and to formulate or to test novel research hypotheses. However, figures are difficult to comprehend without associated text (e.g., figure legend and other reference text). We are developing automated systems to extract the relevant explanatory information along with figures extracted from full text articles. Such systems could be very useful in improving figure retrieval and in reducing the workload of biomedical scientists, who otherwise have to retrieve and read the entire full-text journal article to determine which figures are relevant to their research. As a crucial step, we studied the importance of associated text in biomedical figure comprehension. Twenty subjects evaluated three figure-text combinations: figure+legend, figure+legend+title+abstract, and figure+full-text. Using a Likert scale, each subject scored each figure+text according to the extent to which the subject thought he/she understood the meaning of the figure and the confidence in providing the assigned score. Additionally, each subject entered a free text summary for each figure-text. We identified missing information using indicator words present within the text summaries. Both the Likert scores and the missing information were statistically analyzed for differences among the figure-text types. We also evaluated the quality of text summaries with the text-summarization evaluation method the ROUGE score. Our results showed statistically significant differences in figure comprehension when varying levels of text were provided. When the full-text article is not available, presenting just the figure+legend left biomedical researchers lacking 39-68% of the information about a figure as compared to having complete figure comprehension; adding the title and abstract improved the situation, but still left biomedical researchers missing 30% of the information. When the full-text article is available, figure comprehension

  15. ICNBME-2011: International Conference on Nanotechnologies and Biomedical Engineering; German-Moldovan Workshop on Novel Nanomaterials for Electronic, Photonic and Biomedical Applications. Proceedings

    International Nuclear Information System (INIS)

    Tiginyanu, Ion; Sontea, Victor

    2011-01-01

    This book includes articles which cover a vast range of subjects, such as: nano technologies and nano materials, micro- and nano-objects, nanostructured and highly integrated systems, biophysics, biomedical instrumentation and devices, biomaterials, medical imaging, information technologies for health care, tele medicine, etc.

  16. ICNBME-2013: 2. international conference on nanotechnologies and biomedical engineering; German-Moldovan workshop on novel nanomaterials for electronic, photonic and biomedical applications. Proceedings

    International Nuclear Information System (INIS)

    Tiginyanu, Ion; Sontea, Victor

    2013-01-01

    This book includes articles which cover a vast range of subjects, such as: nano technologies and nano materials, micro- and nano-objects, nanostructured and highly integrated systems, biophysics, biomedical instrumentation and devices, biomaterials, medical imaging, information technologies for health care, tele medicine, etc.

  17. A coherent graph-based semantic clustering and summarization approach for biomedical literature and a new summarization evaluation method.

    Science.gov (United States)

    Yoo, Illhoi; Hu, Xiaohua; Song, Il-Yeol

    2007-11-27

    A huge amount of biomedical textual information has been produced and collected in MEDLINE for decades. In order to easily utilize biomedical information in the free text, document clustering and text summarization together are used as a solution for text information overload problem. In this paper, we introduce a coherent graph-based semantic clustering and summarization approach for biomedical literature. Our extensive experimental results show the approach shows 45% cluster quality improvement and 72% clustering reliability improvement, in terms of misclassification index, over Bisecting K-means as a leading document clustering approach. In addition, our approach provides concise but rich text summary in key concepts and sentences. Our coherent biomedical literature clustering and summarization approach that takes advantage of ontology-enriched graphical representations significantly improves the quality of document clusters and understandability of documents through summaries.

  18. Informe

    Directory of Open Access Journals (Sweden)

    Egon Lichetenberger

    1950-10-01

    Full Text Available Informe del doctor Egon Lichetenberger ante el Consejo Directivo de la Facultad, sobre el  curso de especialización en Anatomía Patológica patrocinado por la Kellogg Foundation (Departamento de Patología

  19. Globalizing and crowdsourcing biomedical research.

    Science.gov (United States)

    Afshinnekoo, Ebrahim; Ahsanuddin, Sofia; Mason, Christopher E

    2016-12-01

    Crowdfunding and crowdsourcing of medical research has emerged as a novel paradigm for many biomedical disciplines to rapidly collect, process and interpret data from high-throughput and high-dimensional experiments. The novelty and promise of these approaches have led to fundamental discoveries about RNA mechanisms, microbiome dynamics and even patient interpretation of test results. However, these methods require robust training protocols, uniform sampling methods and experimental rigor in order to be useful for subsequent research efforts. Executed correctly, crowdfunding and crowdsourcing can leverage public resources and engagement to generate support for scientific endeavors that would otherwise be impossible due to funding constraints and or the large number of participants needed for data collection. We conducted a comprehensive literature review of scientific studies that utilized crowdsourcing and crowdfunding to generate data. We also discuss our own experiences conducting citizen-science research initiatives (MetaSUB and PathoMap) in ensuring data robustness, educational outreach and public engagement. We demonstrate the efficacy of crowdsourcing mechanisms for revolutionizing microbiome and metagenomic research to better elucidate the microbial and genetic dynamics of cities around the world (as well as non-urban areas). Crowdsourced studies have been able to create an improved and unprecedented ability to monitor, design and measure changes at the microbial and macroscopic scale. Thus, the use of crowdsourcing strategies has dramatically altered certain genomics research to create global citizen-science initiatives that reveal new discoveries about the world's genetic dynamics. The effectiveness of crowdfunding and crowdsourcing is largely dependent on the study design and methodology. One point of contention for the present discussion is the validity and scientific rigor of data that are generated by non-scientists. Selection bias, limited sample

  20. Nonlinear aspects of acoustic radiation force in biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

    Ostrovsky, Lev, E-mail: Lev.A.Ostrovsky@noaa.gov [NOAA Earth System Research Laboratory, 325 Broadway, Boulder, Colorado 80305 (United States); Tsyuryupa, Sergey; Sarvazyan, Armen, E-mail: armen@artannlabs.com [Artann Laboratories, Inc., 1459 Lower Ferry Rd., West Trenton, New Jersey,08618 (United States)

    2015-10-28

    In the past decade acoustic radiation force (ARF) became a powerful tool in numerous biomedical applications. ARF from a focused ultrasound beam acts as a virtual “finger” for remote probing of internal anatomical structures and obtaining diagnostic information. This presentation deals with generation of shear waves by nonlinear focused beams. Albeit the ARF has intrinsically nonlinear origin, in most cases the primary ultrasonic wave was considered in the linear approximation. In this presentation, we consider the effects of nonlinearly distorted beams on generation of shear waves by such beams.

  1. The HIPAA Security Rule: implications for biomedical devices.

    Science.gov (United States)

    2004-11-01

    The HIPAA Security Rule, with which hospitals must become compliant by April 2005, is broad in scope. Some aspect of this rule will affect virtually every function and department within a healthcare organization. The functions and departments that deal with biomedical technologies face special challenges due to the great diversity of technologies, the variety of data maintained and transmitted, and the risks associated with compromises to data security--combined with the presence of older technology and the absence of integrated expertise. It is essential that hospitals recognize this challenge and initiate steps now to implement appropriate information security management.

  2. Nonlinear aspects of acoustic radiation force in biomedical applications

    International Nuclear Information System (INIS)

    Ostrovsky, Lev; Tsyuryupa, Sergey; Sarvazyan, Armen

    2015-01-01

    In the past decade acoustic radiation force (ARF) became a powerful tool in numerous biomedical applications. ARF from a focused ultrasound beam acts as a virtual “finger” for remote probing of internal anatomical structures and obtaining diagnostic information. This presentation deals with generation of shear waves by nonlinear focused beams. Albeit the ARF has intrinsically nonlinear origin, in most cases the primary ultrasonic wave was considered in the linear approximation. In this presentation, we consider the effects of nonlinearly distorted beams on generation of shear waves by such beams

  3. Visualization and classification in biomedical terahertz pulsed imaging

    International Nuclear Information System (INIS)

    Loeffler, Torsten; Siebert, Karsten; Czasch, Stephanie; Bauer, Tobias; Roskos, Hartmut G

    2002-01-01

    'Visualization' in imaging is the process of extracting useful information from raw data in such a way that meaningful physical contrasts are developed. 'Classification' is the subsequent process of defining parameter ranges which allow us to identify elements of images such as different tissues or different objects. In this paper, we explore techniques for visualization and classification in terahertz pulsed imaging (TPI) for biomedical applications. For archived (formalin-fixed, alcohol-dehydrated and paraffin-mounted) test samples, we investigate both time- and frequency-domain methods based on bright- and dark-field TPI. Successful tissue classification is demonstrated

  4. Nonlinear aspects of acoustic radiation force in biomedical applications

    Science.gov (United States)

    Ostrovsky, Lev; Tsyuryupa, Sergey; Sarvazyan, Armen

    2015-10-01

    In the past decade acoustic radiation force (ARF) became a powerful tool in numerous biomedical applications. ARF from a focused ultrasound beam acts as a virtual "finger" for remote probing of internal anatomical structures and obtaining diagnostic information. This presentation deals with generation of shear waves by nonlinear focused beams. Albeit the ARF has intrinsically nonlinear origin, in most cases the primary ultrasonic wave was considered in the linear approximation. In this presentation, we consider the effects of nonlinearly distorted beams on generation of shear waves by such beams.

  5. Improving ethical and participatory practice for marginalized populations in biomedical HIV prevention trials: lessons from Thailand.

    Directory of Open Access Journals (Sweden)

    Dan Allman

    Full Text Available BACKGROUND: This paper presents findings from a qualitative investigation of ethical and participatory issues related to the conduct of biomedical HIV prevention trials among marginalized populations in Thailand. This research was deemed important to conduct, as several large-scale biomedical HIV prevention trials among marginalized populations had closed prematurely in other countries, and a better understanding of how to prevent similar trial closures from occurring in the future was desired. METHODS: In-depth key informant interviews were held in Bangkok and Chiang Mai, Thailand. Interviews were audio recorded, transcribed, translated and thematically analyzed. The Good Participatory Practice Guidelines for Biomedical HIV Prevention Trials (GPP guided this work. RESULTS: Fourteen interviews were conducted: 10 with policymakers, academic and community-based researchers and trial staff and four with representatives of non-governmental organizations (NGOs. Suggested ways to improve ethical and participatory practice centered on standards of HIV prevention, informed consent, communication and human rights. In particular, the need to overcome language and literacy differences was identified. Key informants felt communication was the basis of ethical understanding and trust within biomedical HIV prevention trial contexts, and thus fundamental to trial participants' ability to exercise free will. DISCUSSION: Biomedical HIV prevention trials present opportunities for inclusive and productive ethical and participatory practice. Key informants suggested that efforts to improve practice could result in better relationships between research stakeholders and research investigative teams and by extension, better, more ethical participatory trials. This research took place in Thailand and its findings apply primarily to Thailand. However, given the universality of many ethical considerations, the results of this study can inform the improvement of ethical

  6. Improving ethical and participatory practice for marginalized populations in biomedical HIV prevention trials: lessons from Thailand.

    Science.gov (United States)

    Allman, Dan; Ditmore, Melissa Hope; Kaplan, Karyn

    2014-01-01

    This paper presents findings from a qualitative investigation of ethical and participatory issues related to the conduct of biomedical HIV prevention trials among marginalized populations in Thailand. This research was deemed important to conduct, as several large-scale biomedical HIV prevention trials among marginalized populations had closed prematurely in other countries, and a better understanding of how to prevent similar trial closures from occurring in the future was desired. In-depth key informant interviews were held in Bangkok and Chiang Mai, Thailand. Interviews were audio recorded, transcribed, translated and thematically analyzed. The Good Participatory Practice Guidelines for Biomedical HIV Prevention Trials (GPP) guided this work. Fourteen interviews were conducted: 10 with policymakers, academic and community-based researchers and trial staff and four with representatives of non-governmental organizations (NGOs). Suggested ways to improve ethical and participatory practice centered on standards of HIV prevention, informed consent, communication and human rights. In particular, the need to overcome language and literacy differences was identified. Key informants felt communication was the basis of ethical understanding and trust within biomedical HIV prevention trial contexts, and thus fundamental to trial participants' ability to exercise free will. Biomedical HIV prevention trials present opportunities for inclusive and productive ethical and participatory practice. Key informants suggested that efforts to improve practice could result in better relationships between research stakeholders and research investigative teams and by extension, better, more ethical participatory trials. This research took place in Thailand and its findings apply primarily to Thailand. However, given the universality of many ethical considerations, the results of this study can inform the improvement of ethical and participatory practice in other parts of the world where

  7. BioCause: Annotating and analysing causality in the biomedical domain.

    Science.gov (United States)

    Mihăilă, Claudiu; Ohta, Tomoko; Pyysalo, Sampo; Ananiadou, Sophia

    2013-01-16

    Biomedical corpora annotated with event-level information represent an important resource for domain-specific information extraction (IE) systems. However, bio-event annotation alone cannot cater for all the needs of biologists. Unlike work on relation and event extraction, most of which focusses on specific events and named entities, we aim to build a comprehensive resource, covering all statements of causal association present in discourse. Causality lies at the heart of biomedical knowledge, such as diagnosis, pathology or systems biology, and, thus, automatic causality recognition can greatly reduce the human workload by suggesting possible causal connections and aiding in the curation of pathway models. A biomedical text corpus annotated with such relations is, hence, crucial for developing and evaluating biomedical text mining. We have defined an annotation scheme for enriching biomedical domain corpora with causality relations. This schema has subsequently been used to annotate 851 causal relations to form BioCause, a collection of 19 open-access full-text biomedical journal articles belonging to the subdomain of infectious diseases. These documents have been pre-annotated with named entity and event information in the context of previous shared tasks. We report an inter-annotator agreement rate of over 60% for triggers and of over 80% for arguments using an exact match constraint. These increase significantly using a relaxed match setting. Moreover, we analyse and describe the causality relations in BioCause from various points of view. This information can then be leveraged for the training of automatic causality detection systems. Augmenting named entity and event annotations with information about causal discourse relations could benefit the development of more sophisticated IE systems. These will further influence the development of multiple tasks, such as enabling textual inference to detect entailments, discovering new facts and providing new

  8. Simbody: multibody dynamics for biomedical research.

    Science.gov (United States)

    Sherman, Michael A; Seth, Ajay; Delp, Scott L

    Multibody software designed for mechanical engineering has been successfully employed in biomedical research for many years. For real time operation some biomedical researchers have also adapted game physics engines. However, these tools were built for other purposes and do not fully address the needs of biomedical researchers using them to analyze the dynamics of biological structures and make clinically meaningful recommendations. We are addressing this problem through the development of an open source, extensible, high performance toolkit including a multibody mechanics library aimed at the needs of biomedical researchers. The resulting code, Simbody, supports research in a variety of fields including neuromuscular, prosthetic, and biomolecular simulation, and related research such as biologically-inspired design and control of humanoid robots and avatars. Simbody is the dynamics engine behind OpenSim, a widely used biomechanics simulation application. This article reviews issues that arise uniquely in biomedical research, and reports on the architecture, theory, and computational methods Simbody uses to address them. By addressing these needs explicitly Simbody provides a better match to the needs of researchers than can be obtained by adaptation of mechanical engineering or gaming codes. Simbody is a community resource, free for any purpose. We encourage wide adoption and invite contributions to the code base at https://simtk.org/home/simbody.

  9. [Biomedical research in Revista de Biologia Tropical].

    Science.gov (United States)

    Gutiérrez, José María

    2002-01-01

    The contributions published in Revista de Biología Tropical in the area of Biomedical Sciences are reviewed in terms of number of contributions and scope of research subjects. Biomedical Sciences, particularly Parasitology and Microbiology, constituted the predominant subject in the Revista during the first decade, reflecting the intense research environment at the School of Microbiology of the University of Costa Rica and at Hospital San Juan de Dios. The relative weight of Biomedicine in the following decades diminished, due to the outstanding increment in publications in Biological Sciences; however, the absolute number of contributions in Biomedical Sciences remained constant throughout the last decades, with around 80 contributions per decade. In spite of the predominance of Parasitology as the main biomedical subject, the last decades have witnessed the emergence of new areas of interest in the Revista, such as Pharmacology of natural products, Toxinology, especially related to snake venoms, and Human Genetics. This retrospective analysis evidences that Biomedical Sciences, particularly those related to Tropical Medicine, were a fundamental component during the first years of Revista de Biología Tropical, and have maintained a significant presence in the scientific output of this journal, the most relevant scientific publication in biological sciences in Central America.

  10. Biomedical engineering education--status and perspectives.

    Science.gov (United States)

    Magjarevic, Ratko; Zequera Diaz, Martha L

    2014-01-01

    Biomedical Engineering programs are present at a large number of universities all over the world with an increasing trend. New generations of biomedical engineers have to face the challenges of health care systems round the world which need a large number of professionals not only to support the present technology in the health care system but to develop new devices and services. Health care stakeholders would like to have innovative solutions directed towards solving problems of the world growing incidence of chronic disease and ageing population. These new solutions have to meet the requirements for continuous monitoring, support or care outside clinical settlements. Presence of these needs can be tracked through data from the Labor Organization in the U.S. showing that biomedical engineering jobs have the largest growth at the engineering labor market with expected 72% growth rate in the period from 2008-2018. In European Union the number of patents (i.e. innovation) is the highest in the category of biomedical technology. Biomedical engineering curricula have to adopt to the new needs and for expectations of the future. In this paper we want to give an overview of engineering professions in related to engineering in medicine and biology and the current status of BME education in some regions, as a base for further discussions.

  11. The importance of Zebrafish in biomedical research.

    Science.gov (United States)

    Tavares, Bárbara; Santos Lopes, Susana

    2013-01-01

    Zebrafish (Danio rerio) is an ideal model organism for the study of vertebrate development. This is due to the large clutches that each couple produces, with up to 200 embryos every 7 days, and to the fact that the embryos and larvae are small, transparent and undergo rapid external development. Using scientific literature research tools available online and the keywords Zebrafish, biomedical research, human disease, and drug screening, we reviewed original studies and reviews indexed in PubMed. In this review we summarized work conducted with this model for the advancement of our knowledge related to several human diseases. We also focused on the biomedical research being performed in Portugal with the zebrafish model. Powerful live imaging and genetic tools are currently available for zebrafish making it a valuable model in biomedical research. The combination of these properties with the optimization of automated systems for drug screening has transformed the zebrafish into "a top model" in biomedical research, drug discovery and toxicity testing. Furthermore, with the optimization of xenografts technology it will be possible to use zebrafish to aide in the choice of the best therapy for each patient. Zebrafish is an excellent model organism in biomedical research, drug development and in clinical therapy.

  12. Industry careers for the biomedical engineer.

    Science.gov (United States)

    Munzner, Robert F

    2004-01-01

    This year's conference theme is "linkages for innovation in biomedicine." Biomedical engineers, especially those transitioning their career from academic study into medical device industry, will play a critical role in converting the fruits of scientific research into the reality of modern medical devices. This special session is organized to help biomedical engineers to achieve their career goals more effectively. Participants will have opportunities to hear from and interact with leading industrial experts on many issues. These may include but not limited to 1) career paths for biomedical engineers (industrial, academic, or federal; technical vs. managerial track; small start-up or large established companies); 2) unique design challenges and regulatory requirements in medical device development; 3) aspects of a successful biomedical engineering job candidate (such as resume, interview, follow-up). Suggestions for other topics are welcome and should be directed to xkong@ieee.org The distinguished panelists include: Xuan Kong, Ph.D., VP of Research, NEUROMetrix Inc, Waltham, MA Robert F. Munzner, Ph.D., Medical Device Consultant, Doctor Device, Herndon, VA Glen McLaughlin, Ph.D., VP of Engineering and CTO, Zonare Medical System Inc., Mountain View, CA Grace Bartoo, Ph.D., RAC, General Manager, Decus Biomedical LLC San Carlos, CA.

  13. Biomedical engineering for health research and development.

    Science.gov (United States)

    Zhang, X-Y

    2015-01-01

    Biomedical engineering is a new area of research in medicine and biology, providing new concepts and designs for the diagnosis, treatment and prevention of various diseases. There are several types of biomedical engineering, such as tissue, genetic, neural and stem cells, as well as chemical and clinical engineering for health care. Many electronic and magnetic methods and equipments are used for the biomedical engineering such as Computed Tomography (CT) scans, Magnetic Resonance Imaging (MRI) scans, Electroencephalography (EEG), Ultrasound and regenerative medicine and stem cell cultures, preparations of artificial cells and organs, such as pancreas, urinary bladders, liver cells, and fibroblasts cells of foreskin and others. The principle of tissue engineering is described with various types of cells used for tissue engineering purposes. The use of several medical devices and bionics are mentioned with scaffold, cells and tissue cultures and various materials are used for biomedical engineering. The use of biomedical engineering methods is very important for the human health, and research and development of diseases. The bioreactors and preparations of artificial cells or tissues and organs are described here.

  14. Wireless RF communication in biomedical applications

    Science.gov (United States)

    Jones, Inke; Ricciardi, Lucas; Hall, Leonard; Hansen, Hedley; Varadan, Vijay; Bertram, Chris; Maddocks, Simon; Enderling, Stefan; Saint, David; Al-Sarawi, Said; Abbott, Derek

    2008-02-01

    This paper focuses on wireless transcutaneous RF communication in biomedical applications. It discusses current technology, restrictions and applications and also illustrates possible future developments. It focuses on the application in biotelemetry where the system consists of a transmitter and a receiver with a transmission link in between. The transmitted information can either be a biopotential or a nonelectric value like arterial pressure, respiration, body temperature or pH value. In this paper the use of radio-frequency (RF) communication and identification for those applications is described. Basically, radio-frequency identification or RFID is a technology that is analogous to the working principle of magnetic barcode systems. Unlike magnetic barcodes, passive RFID can be used in extreme climatic conditions—also the tags do not need to be within close proximity of the reader. Our proposed solution is to exploit an exciting new development in making circuits on polymers without the need for battery power. This solution exploits the principle of a surface acoustic wave (SAW) device on a polymer substrate. The SAW device is a set of interdigitated conducting fingers on the polymer substrate. If an appropriate RF signal is sent to the device, the fingers act as microantennas that pick up the signal, and this energy is then converted into acoustic waves that travel across the surface of the polymer substrate. Being a flexible polymer, the acoustic waves cause stresses that can either contract or stretch the material. In our case we mainly focus on an RF controllable microvalve that could ultimately be used for fertility control.

  15. Wireless RF communication in biomedical applications

    International Nuclear Information System (INIS)

    Jones, Inke; Ricciardi, Lucas; Hall, Leonard; Enderling, Stefan; Saint, David; Al-Sarawi, Said; Abbott, Derek; Hansen, Hedley; Varadan, Vijay; Bertram, Chris; Maddocks, Simon

    2008-01-01

    This paper focuses on wireless transcutaneous RF communication in biomedical applications. It discusses current technology, restrictions and applications and also illustrates possible future developments. It focuses on the application in biotelemetry where the system consists of a transmitter and a receiver with a transmission link in between. The transmitted information can either be a biopotential or a nonelectric value like arterial pressure, respiration, body temperature or pH value. In this paper the use of radio-frequency (RF) communication and identification for those applications is described. Basically, radio-frequency identification or RFID is a technology that is analogous to the working principle of magnetic barcode systems. Unlike magnetic barcodes, passive RFID can be used in extreme climatic conditions—also the tags do not need to be within close proximity of the reader. Our proposed solution is to exploit an exciting new development in making circuits on polymers without the need for battery power. This solution exploits the principle of a surface acoustic wave (SAW) device on a polymer substrate. The SAW device is a set of interdigitated conducting fingers on the polymer substrate. If an appropriate RF signal is sent to the device, the fingers act as microantennas that pick up the signal, and this energy is then converted into acoustic waves that travel across the surface of the polymer substrate. Being a flexible polymer, the acoustic waves cause stresses that can either contract or stretch the material. In our case we mainly focus on an RF controllable microvalve that could ultimately be used for fertility control

  16. Incorporating the Last Four Digits of Social Security Numbers Substantially Improves Linking Patient Data from De-identified Hospital Claims Databases.

    Science.gov (United States)

    Naessens, James M; Visscher, Sue L; Peterson, Stephanie M; Swanson, Kristi M; Johnson, Matthew G; Rahman, Parvez A; Schindler, Joe; Sonneborn, Mark; Fry, Donald E; Pine, Michael

    2015-08-01

    Assess algorithms for linking patients across de-identified databases without compromising confidentiality. Hospital discharges from 11 Mayo Clinic hospitals during January 2008-September 2012 (assessment and validation data). Minnesota death certificates and hospital discharges from 2009 to 2012 for entire state (application data). Cross-sectional assessment of sensitivity and positive predictive value (PPV) for four linking algorithms tested by identifying readmissions and posthospital mortality on the assessment data with application to statewide data. De-identified claims included patient gender, birthdate, and zip code. Assessment records were matched with institutional sources containing unique identifiers and the last four digits of Social Security number (SSNL4). Gender, birthdate, and five-digit zip code identified readmissions with a sensitivity of 98.0 percent and a PPV of 97.7 percent and identified postdischarge mortality with 84.4 percent sensitivity and 98.9 percent PPV. Inclusion of SSNL4 produced nearly perfect identification of readmissions and deaths. When applied statewide, regions bordering states with unavailable hospital discharge data had lower rates. Addition of SSNL4 to administrative data, accompanied by appropriate data use and data release policies, can enable trusted repositories to link data with nearly perfect accuracy without compromising patient confidentiality. States maintaining centralized de-identified databases should add SSNL4 to data specifications. © Health Research and Educational Trust.

  17. Radiation protection in medical and biomedical research

    International Nuclear Information System (INIS)

    Fuente Puch, A.E. de la

    2013-01-01

    The human exposure to ionizing radiation in the context of medical and biomedical research raises specific ethical challenges whose resolution approaches should be based on scientific, legal and procedural matters. Joint Resolution MINSAP CITMA-Regulation 'Basic Standards of Radiation Safety' of 30 November 2001 (hereafter NBS) provides for the first time in Cuba legislation specifically designed to protect patients and healthy people who participate in research programs medical and biomedical and exposed to radiation. The objective of this paper is to demonstrate the need to develop specific requirements for radiation protection in medical and biomedical research, as well as to identify all the institutions involved in this in order to establish the necessary cooperation to ensure the protection of persons participating in the investigation

  18. Networked Biomedical System for Ubiquitous Health Monitoring

    Directory of Open Access Journals (Sweden)

    Arjan Durresi

    2008-01-01

    Full Text Available We propose a distributed system that enables global and ubiquitous health monitoring of patients. The biomedical data will be collected by wearable health diagnostic devices, which will include various types of sensors and will be transmitted towards the corresponding Health Monitoring Centers. The permanent medical data of patients will be kept in the corresponding Home Data Bases, while the measured biomedical data will be sent to the Visitor Health Monitor Center and Visitor Data Base that serves the area of present location of the patient. By combining the measured biomedical data and the permanent medical data, Health Medical Centers will be able to coordinate the needed actions and help the local medical teams to make quickly the best decisions that could be crucial for the patient health, and that can reduce the cost of health service.

  19. Practical radiation shielding for biomedical research

    International Nuclear Information System (INIS)

    Klein, R.C.; Reginatto, M.; Party, E.; Gershey, E.L.

    1990-01-01

    This paper reports on calculations which exist for estimating shielding required for radioactivity; however, they are often not applicable for the radionuclides and activities common in biomedical research. A variety of commercially available Lucite shields are being marketed to the biomedical community. Their advertisements may lead laboratory workers to expect better radiation protection than these shields can provide or to assume erroneously that very weak beta emitters require extensive shielding. The authors have conducted a series of shielding experiments designed to simulate exposures from the amounts of 32 P, 51 Cr and 125 I typically used in biomedical laboratories. For most routine work, ≥0.64 cm of Lucite covered with various thicknesses of lead will reduce whole-body occupational exposure rates of < 1mR/hr at the point of contact

  20. Personalized biomedical devices & systems for healthcare applications

    Science.gov (United States)

    Chen, I.-Ming; Phee, Soo Jay; Luo, Zhiqiang; Lim, Chee Kian

    2011-03-01

    With the advancement in micro- and nanotechnology, electromechanical components and systems are getting smaller and smaller and gradually can be applied to the human as portable, mobile and even wearable devices. Healthcare industry have started to benefit from this technology trend by providing more and more miniature biomedical devices for personalized medical treatments in order to obtain better and more accurate outcome. This article introduces some recent development in non-intrusive and intrusive biomedical devices resulted from the advancement of niche miniature sensors and actuators, namely, wearable biomedical sensors, wearable haptic devices, and ingestible medical capsules. The development of these devices requires carful integration of knowledge and people from many different disciplines like medicine, electronics, mechanics, and design. Furthermore, designing affordable devices and systems to benefit all mankind is a great challenge ahead. The multi-disciplinary nature of the R&D effort in this area provides a new perspective for the future mechanical engineers.

  1. Biomedical engineering and society: policy and ethics.

    Science.gov (United States)

    Flexman, J A; Lazareck, L

    2007-01-01

    Biomedical engineering impacts health care and contributes to fundamental knowledge in medicine and biology. Policy, such as through regulation and research funding, has the potential to dramatically affect biomedical engineering research and commercialization. New developments, in turn, may affect society in new ways. The intersection of biomedical engineering and society and related policy issues must be discussed between scientists and engineers, policy-makers and the public. As a student, there are many ways to become engaged in the issues surrounding science and technology policy. At the University of Washington in Seattle, the Forum on Science Ethics and Policy (FOSEP, www.fosep.org) was started by graduate students and post-doctoral fellows interested in improving the dialogue between scientists, policymakers and the public and has received support from upper-level administration. This is just one example of how students can start thinking about science policy and ethics early in their careers.

  2. Building the biomedical data science workforce.

    Science.gov (United States)

    Dunn, Michelle C; Bourne, Philip E

    2017-07-01

    This article describes efforts at the National Institutes of Health (NIH) from 2013 to 2016 to train a national workforce in biomedical data science. We provide an analysis of the Big Data to Knowledge (BD2K) training program strengths and weaknesses with an eye toward future directions aimed at any funder and potential funding recipient worldwide. The focus is on extramurally funded programs that have a national or international impact rather than the training of NIH staff, which was addressed by the NIH's internal Data Science Workforce Development Center. From its inception, the major goal of BD2K was to narrow the gap between needed and existing biomedical data science skills. As biomedical research increasingly relies on computational, mathematical, and statistical thinking, supporting the training and education of the workforce of tomorrow requires new emphases on analytical skills. From 2013 to 2016, BD2K jump-started training in this area for all levels, from graduate students to senior researchers.

  3. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    Science.gov (United States)

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2015-06-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. 15th International Conference on Biomedical Engineering

    CERN Document Server

    2014-01-01

    This volume presents the proceedings of the 15th ICMBE held from 4th to 7th December 2013, Singapore. Biomedical engineering is applied in most aspects of our healthcare ecosystem. From electronic health records to diagnostic tools to therapeutic, rehabilitative and regenerative treatments, the work of biomedical engineers is evident. Biomedical engineers work at the intersection of engineering, life sciences and healthcare. The engineers would use principles from applied science including mechanical, electrical, chemical and computer engineering together with physical sciences including physics, chemistry and mathematics to apply them to biology and medicine. Applying such concepts to the human body is very much the same concepts that go into building and programming a machine. The goal is to better understand, replace or fix a target system to ultimately improve the quality of healthcare. With this understanding, the conference proceedings offer a single platform for individuals and organisations working i...

  5. Biomedical applications using low temperature plasma technology

    International Nuclear Information System (INIS)

    Dai Xiujuan; Jiang Nan

    2006-01-01

    Low temperature plasma technology and biomedicine are two different subjects, but the combination of the two may play a critical role in modern science and technology. The 21 st century is believed to be a biotechnology century. Plasma technology is becoming a widely used platform for the fabrication of biomaterials and biomedical devices. In this paper some of the technologies used for material surface modification are briefly introduced. Some biomedical applications using plasma technology are described, followed by suggestions as to how a bridge between plasma technology and biomedicine can be built. A pulsed plasma technique that is used for surface functionalization is discussed in detail as an example of this kind of bridge or combination. Finally, it is pointed out that the combination of biomedical and plasma technology will be an important development for revolutionary 21st century technologies that requires different experts from different fields to work together. (authors)

  6. Biomedical sensor design using analog compressed sensing

    Science.gov (United States)

    Balouchestani, Mohammadreza; Krishnan, Sridhar

    2015-05-01

    The main drawback of current healthcare systems is the location-specific nature of the system due to the use of fixed/wired biomedical sensors. Since biomedical sensors are usually driven by a battery, power consumption is the most important factor determining the life of a biomedical sensor. They are also restricted by size, cost, and transmission capacity. Therefore, it is important to reduce the load of sampling by merging the sampling and compression steps to reduce the storage usage, transmission times, and power consumption in order to expand the current healthcare systems to Wireless Healthcare Systems (WHSs). In this work, we present an implementation of a low-power biomedical sensor using analog Compressed Sensing (CS) framework for sparse biomedical signals that addresses both the energy and telemetry bandwidth constraints of wearable and wireless Body-Area Networks (BANs). This architecture enables continuous data acquisition and compression of biomedical signals that are suitable for a variety of diagnostic and treatment purposes. At the transmitter side, an analog-CS framework is applied at the sensing step before Analog to Digital Converter (ADC) in order to generate the compressed version of the input analog bio-signal. At the receiver side, a reconstruction algorithm based on Restricted Isometry Property (RIP) condition is applied in order to reconstruct the original bio-signals form the compressed bio-signals with high probability and enough accuracy. We examine the proposed algorithm with healthy and neuropathy surface Electromyography (sEMG) signals. The proposed algorithm achieves a good level for Average Recognition Rate (ARR) at 93% and reconstruction accuracy at 98.9%. In addition, The proposed architecture reduces total computation time from 32 to 11.5 seconds at sampling-rate=29 % of Nyquist rate, Percentage Residual Difference (PRD)=26 %, Root Mean Squared Error (RMSE)=3 %.

  7. Eli Lilly and Company's bioethics framework for human biomedical research.

    Science.gov (United States)

    Van Campen, Luann E; Therasse, Donald G; Klopfenstein, Mitchell; Levine, Robert J

    2015-11-01

    Current ethics and good clinical practice guidelines address various aspects of pharmaceutical research and development, but do not comprehensively address the bioethical responsibilities of sponsors. To fill this void, in 2010 Eli Lilly and Company developed and implemented a Bioethics Framework for Human Biomedical Research to guide ethical decisions. (See our companion article that describes how the framework was developed and implemented and provides a critique of its usefulness and limitations.) This paper presents the actual framework that serves as a company resource for employee education and bioethics deliberations. The framework consists of four basic ethical principles and 13 essential elements for ethical human biomedical research and resides within the context of our company's mission, vision and values. For each component of the framework, we provide a high-level overview followed by a detailed description with cross-references to relevant well regarded guidance documents. The principles and guidance described should be familiar to those acquainted with research ethics. Therefore the novelty of the framework lies not in the foundational concepts presented as much as the attempt to specify and compile a sponsor's bioethical responsibilities to multiple stakeholders into one resource. When such a framework is employed, it can serve as a bioethical foundation to inform decisions and actions throughout clinical planning, trial design, study implementation and closeout, as well as to inform company positions on bioethical issues. The framework is, therefore, a useful tool for translating ethical aspirations into action - to help ensure pharmaceutical human biomedical research is conducted in a manner that aligns with consensus ethics principles, as well as a sponsor's core values.

  8. Polymer/metal nanocomposites for biomedical applications.

    Science.gov (United States)

    Zare, Yasser; Shabani, Iman

    2016-03-01

    Polymer/metal nanocomposites consisting of polymer as matrix and metal nanoparticles as nanofiller commonly show several attractive advantages such as electrical, mechanical and optical characteristics. Accordingly, many scientific and industrial communities have focused on polymer/metal nanocomposites in order to develop some new products or substitute the available materials. In the current paper, characteristics and applications of polymer/metal nanocomposites for biomedical applications are extensively explained in several categories including strong and stable materials, conductive devices, sensors and biomedical products. Moreover, some perspective utilizations are suggested for future studies. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Developing biomedical devices design, innovation and protection

    CERN Document Server

    Andreoni, Giuseppe; Colombo, Barbara

    2013-01-01

    During the past two decades incredible progress has been achieved in the instruments and devices used in the biomedical field. This progress stems from continuous scientific research that has taken advantage of many findings and advances in technology made available by universities and industry. Innovation is the key word, and in this context legal protection and intellectual property rights (IPR) are of crucial importance. This book provides students and practitioners with the fundamentals for designing biomedical devices and explains basic design principles. Furthermore, as an aid to the dev

  10. Discrete-Time Biomedical Signal Encryption

    Directory of Open Access Journals (Sweden)

    Victor Grigoraş

    2017-12-01

    Full Text Available Chaotic modulation is a strong method of improving communication security. Analog and discrete chaotic systems are presented in actual literature. Due to the expansion of digital communication, discrete-time systems become more efficient and closer to actual technology. The present contribution offers an in-depth analysis of the effects chaos encryption produce on 1D and 2D biomedical signals. The performed simulations show that modulating signals are precisely recovered by the synchronizing receiver if discrete systems are digitally implemented and the coefficients precisely correspond. Channel noise is also applied and its effects on biomedical signal demodulation are highlighted.

  11. Conference on medical physics and biomedical engineering

    International Nuclear Information System (INIS)

    2013-01-01

    Due to the rapid technological development in the world today, the role of physics in modern medicine is of great importance. The frequent use of equipment that produces ionizing radiation further increases the need for radiation protection, complicated equipment requires technical support, the diagnostic and therapeutic methods impose the highest professionals in the field of medical physics. Thus, medical physics and biomedical engineering have become an inseparable part of everyday medical practice. There are a certain number of highly qualified and dedicated professionals in medical physics in Macedonia who committed themselves to work towards resolving medical physics issues. In 2000 they established the first and still only professional Association for Medical Physics and Biomedical Engineering (AMPBE) in Macedonia; a one competent to cope with problems in the fields of medicine, which applies methods of physics and biomedical engineering to medical procedures in order to develop tools essential to the physicians that will ultimately lead to improve the quality of medical practice in general. The First National Conference on Medical Physics and Biomedical Engineering was organized by the AMPBE in 2007. The idea was to gather all the professionals working in medical physics and biomedical engineering in one place in order to present their work and increase the collaboration among them. Other involved professions such as medical doctors, radiation technologists, engineers and professors of physics at the University also took part and contributed to the success of the conference. As a result, the Proceedings were published in Macedonian, with summaries in English. In order to further promote the medical physics amongst the scientific community in Macedonia, our society decided to organize The Second Conference on Medical Physics and Biomedical Engineering in November 2010. Unlike the first, this one was with international participation. This was very suitable

  12. Biomedical engineering education through global engineering teams.

    Science.gov (United States)

    Scheffer, C; Blanckenberg, M; Garth-Davis, B; Eisenberg, M

    2012-01-01

    Most industrial projects require a team of engineers from a variety of disciplines. The team members are often culturally diverse and geographically dispersed. Many students do not acquire sufficient skills from typical university courses to function efficiently in such an environment. The Global Engineering Teams (GET) programme was designed to prepare students such a scenario in industry. This paper discusses five biomedical engineering themed projects completed by GET students. The benefits and success of the programme in educating students in the field of biomedical engineering are discussed.

  13. Optimization and Data Analysis in Biomedical Informatics

    CERN Document Server

    Pardalos, Panos M; Xanthopoulos, Petros

    2012-01-01

    This volume covers some of the topics that are related to the rapidly growing field of biomedical informatics. In June 11-12, 2010 a workshop entitled 'Optimization and Data Analysis in Biomedical Informatics' was organized at The Fields Institute. Following this event invited contributions were gathered based on the talks presented at the workshop, and additional invited chapters were chosen from world's leading experts. In this publication, the authors share their expertise in the form of state-of-the-art research and review chapters, bringing together researchers from different disciplines

  14. Training May Affect Primary Care Staff Access to the Biomedical Electronic Evidence Base. A review of: Doney, Liz, Helen Barlow, and Joe West. “Use of Libraries and Electronic Information Resources by Primary Care Staff: Outcomes from a Survey.” Health Information and Libraries Journal 22.3 (September 2005: 182-188.

    Directory of Open Access Journals (Sweden)

    Marcy L. Brown

    2006-03-01

    Full Text Available Objective – To assess use of existing local libraries, the Internet, and biomedical databases by primary care staff prior to implementation of the Primary Care Knowledge Management Projects. Additionally, to assess the need to train primary care staff to use the Internet and biomedical databases. Design – Cross‐sectional postal questionnaire survey. Setting – Nottingham and Rotherham, two cities in the Trent region of the UK. Subjects – Questionnaires were analyzed from 243 general practitioners, practice nurses, and practice managers in four Nottingham primary care trusts as well as practices in the Rotherham Health Authority area. Methods – Questionnaires and cover letters were sent between May 2001 and February 2002. To encourage response, a postage‐paid envelope was enclosed. A total of 709 questionnaires were sent in Nottingham, and 169 were returned for a response rate of 24%. In Rotherham, 179 questionnaires were sent and 61 returned, for a 34% response rate. Thirteen responses from a May 2001 pilot in Rotherham were also included in the data analysis. Survey questions included a variety of formats, including tick boxes and open‐ended questions. Data was entered into an Access database and analysis was performed using Stata software. Main results – Reported use of libraries was low overall, with only 30% of respondents claiming to have used library facilities. However, there was significant variation among professional groups. Practice nurses (PNs had significantly higher usage of libraries than general practitioners (GPs and practice managers (P Conclusion – Based on the results of this admittedly small study, additional training is needed – and desired – by primary care staff in both Nottingham and Rotherham. Developing and offering training in Internet searching and evaluation as well as use of the biomedical databases is one important way in which libraries can build partnerships with primary care practitioners

  15. Semantic relatedness and similarity of biomedical terms: examining the effects of recency, size, and section of biomedical publications on the performance of word2vec.

    Science.gov (United States)

    Zhu, Yongjun; Yan, Erjia; Wang, Fei

    2017-07-03

    Understanding semantic relatedness and similarity between biomedical terms has a great impact on a variety of applications such as biomedical information retrieval, information extraction, and recommender systems. The objective of this study is to examine word2vec's ability in deriving semantic relatedness and similarity between biomedical terms from large publication data. Specifically, we focus on the effects of recency, size, and section of biomedical publication data on the performance of word2vec. We download abstracts of 18,777,129 articles from PubMed and 766,326 full-text articles from PubMed Central (PMC). The datasets are preprocessed and grouped into subsets by recency, size, and section. Word2vec models are trained on these subtests. Cosine similarities between biomedical terms obtained from the word2vec models are compared against reference standards. Performance of models trained on different subsets are compared to examine recency, size, and section effects. Models trained on recent datasets did not boost the performance. Models trained on larger datasets identified more pairs of biomedical terms than models trained on smaller datasets in relatedness task (from 368 at the 10% level to 494 at the 100% level) and similarity task (from 374 at the 10% level to 491 at the 100% level). The model trained on abstracts produced results that have higher correlations with the reference standards than the one trained on article bodies (i.e., 0.65 vs. 0.62 in the similarity task and 0.66 vs. 0.59 in the relatedness task). However, the latter identified more pairs of biomedical terms than the former (i.e., 344 vs. 498 in the similarity task and 339 vs. 503 in the relatedness task). Increasing the size of dataset does not always enhance the performance. Increasing the size of datasets can result in the identification of more relations of biomedical terms even though it does not guarantee better precision. As summaries of research articles, compared with article

  16. Discovering gene annotations in biomedical text databases

    Directory of Open Access Journals (Sweden)

    Ozsoyoglu Gultekin

    2008-03-01

    Full Text Available Abstract Background Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. Results In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. Conclusion GEANN is useful for two distinct purposes: (i automating the annotation of genomic entities with Gene Ontology concepts, and (ii providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate

  17. SparkText: Biomedical Text Mining on Big Data Framework

    Science.gov (United States)

    He, Karen Y.; Wang, Kai

    2016-01-01

    Background Many new biomedical research articles are published every day, accumulating rich information, such as genetic variants, genes, diseases, and treatments. Rapid yet accurate text mining on large-scale scientific literature can discover novel knowledge to better understand human diseases and to improve the quality of disease diagnosis, prevention, and treatment. Results In this study, we designed and developed an efficient text mining framework called SparkText on a Big Data infrastructure, which is composed of Apache Spark data streaming and machine learning methods, combined with a Cassandra NoSQL database. To demonstrate its performance for classifying cancer types, we extracted information (e.g., breast, prostate, and lung cancers) from tens of thousands of articles downloaded from PubMed, and then employed Naïve Bayes, Support Vector Machine (SVM), and Logistic Regression to build prediction models to mine the articles. The accuracy of predicting a cancer type by SVM using the 29,437 full-text articles was 93.81%. While competing text-mining tools took more than 11 hours, SparkText mined the dataset in approximately 6 minutes. Conclusions This study demonstrates the potential for mining large-scale scientific articles on a Big Data infrastructure, with real-time update from new articles published daily. SparkText can be extended to other areas of biomedical research. PMID:27685652

  18. Drug knowledge bases and their applications in biomedical informatics research.

    Science.gov (United States)

    Zhu, Yongjun; Elemento, Olivier; Pathak, Jyotishman; Wang, Fei

    2018-01-03

    Recent advances in biomedical research have generated a large volume of drug-related data. To effectively handle this flood of data, many initiatives have been taken to help researchers make good use of them. As the results of these initiatives, many drug knowledge bases have been constructed. They range from simple ones with specific focuses to comprehensive ones that contain information on almost every aspect of a drug. These curated drug knowledge bases have made significant contributions to the development of efficient and effective health information technologies for better health-care service delivery. Understanding and comparing existing drug knowledge bases and how they are applied in various biomedical studies will help us recognize the state of the art and design better knowledge bases in the future. In addition, researchers can get insights on novel applications of the drug knowledge bases through a review of successful use cases. In this study, we provide a review of existing popular drug knowledge bases and their applications in drug-related studies. We discuss challenges in constructing and using drug knowledge bases as well as future research directions toward a better ecosystem of drug knowledge bases. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  19. Grapefruit and its biomedical, antigenotoxic and chemopreventive properties.

    Science.gov (United States)

    Cristóbal-Luna, José Melesio; Álvarez-González, Isela; Madrigal-Bujaidar, Eduardo; Chamorro-Cevallos, Germán

    2018-02-01

    Grapefruit (Citrus paradisi Mcfad) is a perenifolium tree 5-6 m high with a fruit of about 15 cm in diameter, protected by the peel we can find about 11-14 segments (carpels), each of which is surrounded by a membrane and each containing the juice sacs, as well as the seeds. The fruit is made up of numerous compounds, and is known to have nutritive value because of the presence of various vitamins and minerals, among other chemicals. The fruit is also used in the field of gastronomy. Information has been accumulated regarding the participation of the fruit structures in a variety of biomedical, antigenotoxic and chemopreventive effects, surely related with the presence of the numerous chemicals that have been determined to constitute the fruit. Such studies have been carried out in different in vitro and in vivo experimental models, and in a few human assays. The information published so far has shown interesting results, therefore, the aims of the present review are to initially examine the main characteristics of the fruit, followed by systematization of the acquired knowledge concerning the biomedical, antigenotoxic and chemopreventive effects produced by the three main structures of the fruit: peel, seed, and pulp. Copyright © 2018 Elsevier Ltd. All rights reserved.

  20. SparkText: Biomedical Text Mining on Big Data Framework.

    Directory of Open Access Journals (Sweden)

    Zhan Ye

    Full Text Available Many new biomedical research articles are published every day, accumulating rich information, such as genetic variants, genes, diseases, and treatments. Rapid yet accurate text mining on large-scale scientific literature can discover novel knowledge to better understand human diseases and to improve the quality of disease diagnosis, prevention, and treatment.In this study, we designed and developed an efficient text mining framework called SparkText on a Big Data infrastructure, which is composed of Apache Spark data streaming and machine learning methods, combined with a Cassandra NoSQL database. To demonstrate its performance for classifying cancer types, we extracted information (e.g., breast, prostate, and lung cancers from tens of thousands of articles downloaded from PubMed, and then employed Naïve Bayes, Support Vector Machine (SVM, and Logistic Regression to build prediction models to mine the articles. The accuracy of predicting a cancer type by SVM using the 29,437 full-text articles was 93.81%. While competing text-mining tools took more than 11 hours, SparkText mined the dataset in approximately 6 minutes.This study demonstrates the potential for mining large-scale scientific articles on a Big Data infrastructure, with real-time update from new articles published daily. SparkText can be extended to other areas of biomedical research.

  1. SparkText: Biomedical Text Mining on Big Data Framework.

    Science.gov (United States)

    Ye, Zhan; Tafti, Ahmad P; He, Karen Y; Wang, Kai; He, Max M

    Many new biomedical research articles are published every day, accumulating rich information, such as genetic variants, genes, diseases, and treatments. Rapid yet accurate text mining on large-scale scientific literature can discover novel knowledge to better understand human diseases and to improve the quality of disease diagnosis, prevention, and treatment. In this study, we designed and developed an efficient text mining framework called SparkText on a Big Data infrastructure, which is composed of Apache Spark data streaming and machine learning methods, combined with a Cassandra NoSQL database. To demonstrate its performance for classifying cancer types, we extracted information (e.g., breast, prostate, and lung cancers) from tens of thousands of articles downloaded from PubMed, and then employed Naïve Bayes, Support Vector Machine (SVM), and Logistic Regression to build prediction models to mine the articles. The accuracy of predicting a cancer type by SVM using the 29,437 full-text articles was 93.81%. While competing text-mining tools took more than 11 hours, SparkText mined the dataset in approximately 6 minutes. This study demonstrates the potential for mining large-scale scientific articles on a Big Data infrastructure, with real-time update from new articles published daily. SparkText can be extended to other areas of biomedical research.

  2. International Symposium on Biomedical Engineering and Medical Physics

    CERN Document Server

    Katashev, Alexei; Lancere, Linda

    2013-01-01

    This volume presents the proceedings of the International Symposium on Biomedical Engineering and Medical Physics and is dedicated to the 150 anniversary of the Riga Technical University, Latvia. The content includes various hot topics in biomedical engineering and medical physics.

  3. Time-Resolved Microfluorescence In Biomedical Diagnosis

    Science.gov (United States)

    Schneckenburger, Herbert

    1985-02-01

    A measuring system combining subnanosecond laser-induced fluorescence with microscopic signal detection was installed and used for diverse projects in the biomedical and environmental field. These projects are ranging from tumor diagnosis and enzymatic analysis to measurements of the activity of methanogenic bacteria which effect biogas production and waste water cleaning. The advantages of this method and its practical applicability are discussed.

  4. Time Resolved Microfluorescence In Biomedical Diagnosis

    Science.gov (United States)

    Schneckenburger, Herbert

    1985-12-01

    A measuring system combining subnanosecond laser-induced fluorescence with microscopic signal detection was installed and used for diverse projects in the biomedical and environmental fields. These projects range from tumor diagnosis and enzymatic analysis to measurements of the activity of methanogenic bacteria, which affect biogas production and waste water cleaning. The advantages of this method and its practical applicability are discussed.

  5. Biomedical engineering at UCT - challenges and opportunities.

    Science.gov (United States)

    Douglas, Tania S

    2012-03-02

    The biomedical engineering programme at the University of Cape Town has the potential to address some of South Africa's unique public health challenges and to contribute to growth of the local medical device industry, directly and indirectly, through research activities and postgraduate education. Full realisation of this potential requires engagement with the clinical practice environment and with industry.

  6. Welcome to Biomedical Research and Therapy

    OpenAIRE

    Phuc Van Pham

    2014-01-01

    On behalf of the Laboratory of Stem Cell Research and Application (SCL) and the Biomedical Research and Therapy' editorial team, we would like to extend a warm welcome to you. [Biomed Res Ther 2014; 1(1.000): 1-1

  7. Multiplicative calculus in biomedical image analysis

    NARCIS (Netherlands)

    Florack, L.M.J.; Assen, van H.C.

    2011-01-01

    We advocate the use of an alternative calculus in biomedical image analysis, known as multiplicative (a.k.a. non-Newtonian) calculus. It provides a natural framework in problems in which positive images or positive definite matrix fields and positivity preserving operators are of interest. Indeed,

  8. Love troubles : human attachment and biomedical enhancements

    NARCIS (Netherlands)

    Nyholm, S.

    ABSTRACT In fascinating recent work, Julian Savulescu and his various co-authors argue that human love is one of the things we can improve upon using biomedical enhancements. Is that so? This article first notes that Savulescu and his co-authors mainly treat love as a means to various other goods.

  9. Usage of cell nomenclature in biomedical literature

    KAUST Repository

    Kafkas, Senay; Sarntivijai, Sirarat; Hoehndorf, Robert

    2017-01-01

    large scale for understanding the level of uptake of cell nomenclature in literature by scientists. In this study, we analyse the usage of cell nomenclature, both in Vivo, and in Vitro in biomedical literature by using text mining methods and present our

  10. Biomedical composites materials, manufacturing and engineering

    CERN Document Server

    Davim, J Paulo

    2013-01-01

    Composite materials are engineered materials, made from two or more constituents with significantly different physical or chemical properties which remain separate on a macroscopic level within the finished structure. Due to their special mechanical and physical properties they have the potential to replace conventional materials in various fields such as the biomedical industry.

  11. Electrosprayed calcium phosphate coatings for biomedical purposes.

    NARCIS (Netherlands)

    Leeuwenburgh, S.C.G.

    2006-01-01

    In this thesis, the suitability of the Electrostatic Spray Deposition (ESD) technique was studied for biomedical purposes, i.e., deposition of calcium phosphate (CaP) coatings onto titanium substrates. Using ESD, which is a simple and cheap deposition method for inorganic and organic coatings, it

  12. Biomedical Engineering Education: A Conservative Approach

    Science.gov (United States)

    Niemi, Eugene E., Jr.

    1973-01-01

    Describes the demand for graduates from biomedical engineering programs as being not yet fully able to absorb the supply. Suggests small schools interested in entering the field consider offering their programs at the undergraduate level via a minor or an option. Examples of such options and student projects are included. (CC)

  13. Sierra Leone Journal of Biomedical Research: Submissions

    African Journals Online (AJOL)

    AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced Search · USING ... Sierra Leone Journal of Biomedical Research (SLJBR) publishes papers in all ... An original article should give sufficient detail of experimental procedures for .... For references cited in a paper which has been accepted for publication but not ...

  14. Thermoforming of film-based biomedical microdevices

    NARCIS (Netherlands)

    Truckenmüller, R.K.; Giselbrecht, Stefan; Rivron, N.C.; Gottwald, Eric; Saile, Volker; van den Berg, Albert; Wessling, Matthias; van Blitterswijk, Clemens

    2011-01-01

    For roughly ten years now, a new class of polymer micromoulding processes comes more and more into the focus both of the microtechnology and the biomedical engineering community. These processes can be subsumed under the term "microthermoforming". In microthermoforming, thin polymer films are heated

  15. Biomedical Visual Computing: Case Studies and Challenges

    KAUST Repository

    Johnson, Christopher

    2012-01-01

    Advances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it\\'s also fundamental to understanding models of complex phenomena. © 2012 IEEE.

  16. Journal of Medicine and Biomedical Research

    African Journals Online (AJOL)

    The Journal of Medicine and Biomedical Research is published by the College of Medical Sciences, University of Benin to encourage research into primary health care. The journal will publish original research articles, reviews, editorials, commentaries, case reports and letters to the editor. Articles are welcome in all ...

  17. Nigerian Journal of Health and Biomedical Sciences

    African Journals Online (AJOL)

    The Nigerian Journal of Health and Biomedical Sciences is a multidisciplinary and peer-reviewed journal. This journal was established to meet the challenges of health care delivery in the 21st century in Nigeria and other countries with similar setting in the ever-changing world of science and technology. The health care ...

  18. Biomedical Visual Computing: Case Studies and Challenges

    KAUST Repository

    Johnson, Christopher

    2012-01-01

    Advances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it's also fundamental to understanding models of complex phenomena. © 2012 IEEE.

  19. Biomedical image retrieval using microscopic configuration with ...

    Indian Academy of Sciences (India)

    G DEEP

    2018-03-10

    Mar 10, 2018 ... The selection of feature descriptors affects the image .... Example of obtaining LBP for 3 9 3 neighbourhoods (adopted from Ojala et al [9]). 20 Page 2 of 13 ...... Directional binary wavelet patterns for biomedical image indexing ...

  20. Electromembrane extraction for pharmaceutical and biomedical analysis

    DEFF Research Database (Denmark)

    Huang, Chuixiu; Seip, Knut Fredrik; Gjelstad, Astrid

    2015-01-01

    . The present paper discusses recent development of EME. The paper focuses on the principles of EME, and discusses how to optimize operational parameters. In addition, pharmaceutical and biomedical applications of EME are reviewed, with emphasis on basic drugs, acidic drugs, amino acids, and peptides. Finally...

  1. Europium enabled luminescent nanoparticles for biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

    Syamchand, S.S., E-mail: syamchand.ss@gmail.com; Sony, G., E-mail: emailtosony@gmail.com

    2015-09-15

    Lanthanide based nanoparticles are receiving great attention ought to their excellent luminescent and magnetic properties and find challenging biomedical applications. Among the luminescent lanthanide NPs, europium based NPs (Eu-NPs) are better candidates for immunoassay and imaging applications. The Eu-NPs have an edge over quantum dots (QDs) by means of their stable luminescence, long fluorescence lifetime, sharp emission peaks with narrow band width, lack of blinking and biocompatibility. This review surveys the synthesis and properties of a variety of Eu-NPs consolidated from different research articles, for their applications in medicine and biology. The exquisite luminescent properties of Eu-NPs are explored for developing biomedical applications such as immunoassay and bioimaging including multimodal imaging. The biomedical applications of Eu-NPs are mostly diagnostic in nature and mainly focus on various key analytes present in biological systems. The luminescent properties of europium enabled NPs are influenced by a number of factors such as the site symmetry, the metal nanoparticles, metal ions, quantum dots, surfactants, morphology of Eu-NPs, crystal defect, phenomena like antenna effect and physical parameters like temperature. Through this review we explore and assimilate all the factors which affect the luminescence in Eu-NPs and coil a new thread of parameters that control the luminescence in Eu-NPs, which would provide further insight in developing Eu-based nanoprobes for future biomedical prospects. - Highlights: • The review describes 14 major factors that influence the luminescence properties of europium enabled luminescent nanoparticles (Eu-NPs). • Surveys different types of europium containing nanoparticles that have been reported for their biomedical applications. • Eu-NPs are conveniently divided into four different categories, based on the type of the substrates involved. The four categories are (1) virgin Eu-substrate based NPs; (2

  2. Europium enabled luminescent nanoparticles for biomedical applications

    International Nuclear Information System (INIS)

    Syamchand, S.S.; Sony, G.

    2015-01-01

    Lanthanide based nanoparticles are receiving great attention ought to their excellent luminescent and magnetic properties and find challenging biomedical applications. Among the luminescent lanthanide NPs, europium based NPs (Eu-NPs) are better candidates for immunoassay and imaging applications. The Eu-NPs have an edge over quantum dots (QDs) by means of their stable luminescence, long fluorescence lifetime, sharp emission peaks with narrow band width, lack of blinking and biocompatibility. This review surveys the synthesis and properties of a variety of Eu-NPs consolidated from different research articles, for their applications in medicine and biology. The exquisite luminescent properties of Eu-NPs are explored for developing biomedical applications such as immunoassay and bioimaging including multimodal imaging. The biomedical applications of Eu-NPs are mostly diagnostic in nature and mainly focus on various key analytes present in biological systems. The luminescent properties of europium enabled NPs are influenced by a number of factors such as the site symmetry, the metal nanoparticles, metal ions, quantum dots, surfactants, morphology of Eu-NPs, crystal defect, phenomena like antenna effect and physical parameters like temperature. Through this review we explore and assimilate all the factors which affect the luminescence in Eu-NPs and coil a new thread of parameters that control the luminescence in Eu-NPs, which would provide further insight in developing Eu-based nanoprobes for future biomedical prospects. - Highlights: • The review describes 14 major factors that influence the luminescence properties of europium enabled luminescent nanoparticles (Eu-NPs). • Surveys different types of europium containing nanoparticles that have been reported for their biomedical applications. • Eu-NPs are conveniently divided into four different categories, based on the type of the substrates involved. The four categories are (1) virgin Eu-substrate based NPs; (2

  3. Semiconductor quantum dots: synthesis and water-solubilization for biomedical applications.

    Science.gov (United States)

    Yu, William W

    2008-10-01

    Quantum dots (QDs) are generally nanosized inorganic particles. They have distinctive size-dependent optical properties due to their very small size (mostly semiconductor QDs (mainly metal-chalcogenide compounds) and forming biocompatible structures for biomedical applications are discussed in this paper. This information may facilitate the research to create new materials/technologies for future clinical applications.

  4. An overview of biomedical literature search on the World Wide Web in the third millennium.

    Science.gov (United States)

    Kumar, Prince; Goel, Roshni; Jain, Chandni; Kumar, Ashish; Parashar, Abhishek; Gond, Ajay Ratan

    2012-06-01

    Complete access to the existing pool of biomedical literature and the ability to "hit" upon the exact information of the relevant specialty are becoming essential elements of academic and clinical expertise. With the rapid expansion of the literature database, it is almost impossible to keep up to date with every innovation. Using the Internet, however, most people can freely access this literature at any time, from almost anywhere. This paper highlights the use of the Internet in obtaining valuable biomedical research information, which is mostly available from journals, databases, textbooks and e-journals in the form of web pages, text materials, images, and so on. The authors present an overview of web-based resources for biomedical researchers, providing information about Internet search engines (e.g., Google), web-based bibliographic databases (e.g., PubMed, IndMed) and how to use them, and other online biomedical resources that can assist clinicians in reaching well-informed clinical decisions.

  5. Biomedical Informatics Research and Education at the EuroMISE Center

    Czech Academy of Sciences Publication Activity Database

    Zvárová, Jana

    2006-01-01

    Roč. 45, Suppl. (2006), s. 166-173 ISSN 0026-1270 Grant - others:Evropské sociální fondy CZ04307/42011/0013 Institutional research plan: CEZ:AV0Z10300504 Keywords : biomedical informatics * research * education * healthcare * information society Subject RIV: BJ - Thermodynamics Impact factor: 1.684, year: 2006

  6. Special Issue: 3D Printing for Biomedical Engineering

    Directory of Open Access Journals (Sweden)

    Chee Kai Chua

    2017-02-01

    Full Text Available Three-dimensional (3D printing has a long history of applications in biomedical engineering. The development and expansion of traditional biomedical applications are being advanced and enriched by new printing technologies. New biomedical applications such as bioprinting are highly attractive and trendy. This Special Issue aims to provide readers with a glimpse of the recent profile of 3D printing in biomedical research.

  7. Building a biomedical ontology recommender web service

    Directory of Open Access Journals (Sweden)

    Jonquet Clement

    2010-06-01

    Full Text Available Abstract Background Researchers in biomedical informatics use ontologies and terminologies to annotate their data in order to facilitate data integration and translational discoveries. As the use of ontologies for annotation of biomedical datasets has risen, a common challenge is to identify ontologies that are best suited to annotating specific datasets. The number and variety of biomedical ontologies is large, and it is cumbersome for a researcher to figure out which ontology to use. Methods We present the Biomedical Ontology Recommender web service. The system uses textual metadata or a set of keywords describing a domain of interest and suggests appropriate ontologies for annotating or representing the data. The service makes a decision based on three criteria. The first one is coverage, or the ontologies that provide most terms covering the input text. The second is connectivity, or the ontologies that are most often mapped to by other ontologies. The final criterion is size, or the number of concepts in the ontologies. The service scores the ontologies as a function of scores of the annotations created using the National Center for Biomedical Ontology (NCBO Annotator web service. We used all the ontologies from the UMLS Metathesaurus and the NCBO BioPortal. Results We compare and contrast our Recommender by an exhaustive functional comparison to previously published efforts. We evaluate and discuss the results of several recommendation heuristics in the context of three real world use cases. The best recommendations heuristics, rated ‘very relevant’ by expert evaluators, are the ones based on coverage and connectivity criteria. The Recommender service (alpha version is available to the community and is embedded into BioPortal.

  8. Biomedical technology prosperity game{trademark}

    Energy Technology Data Exchange (ETDEWEB)

    Berman, M.; Boyack, K.W.; Wesenberg, D.L.

    1996-07-01

    Prosperity Games{trademark} are an outgrowth and adaptation of move/countermove and seminar War Games. Prosperity Games{trademark} are simulations that explore complex issues in a variety of areas including economics, politics, sociology, environment, education and research. These issues can be examined from a variety of perspectives ranging from a global, macroeconomic and geopolitical viewpoint down to the details of customer/supplier/market interactions in specific industries. All Prosperity Games{trademark} are unique in that both the game format and the player contributions vary from game to game. This report documents the Biomedical Technology Prosperity Game{trademark} conducted under the sponsorship of Sandia National Laboratories, the Defense Advanced Research Projects Agency, and the Koop Foundation, Inc. Players were drawn from all stakeholders involved in biomedical technologies including patients, hospitals, doctors, insurance companies, legislators, suppliers/manufacturers, regulators, funding organizations, universities/laboratories, and the legal profession. The primary objectives of this game were to: (1) Identify advanced/critical technology issues that affect the cost and quality of health care. (2) Explore the development, patenting, manufacturing and licensing of needed technologies that would decrease costs while maintaining or improving quality. (3) Identify policy and regulatory changes that would reduce costs and improve quality and timeliness of health care delivery. (4) Identify and apply existing resources and facilities to develop and implement improved technologies and policies. (5) Begin to develop Biomedical Technology Roadmaps for industry and government cooperation. The deliberations and recommendations of these players provided valuable insights as to the views of this diverse group of decision makers concerning biomedical issues. Significant progress was made in the roadmapping of key areas in the biomedical technology field.

  9. BOSS: context-enhanced search for biomedical objects

    Directory of Open Access Journals (Sweden)

    Choi Jaehoon

    2012-04-01

    Full Text Available Abstract Background There exist many academic search solutions and most of them can be put on either ends of spectrum: general-purpose search and domain-specific "deep" search systems. The general-purpose search systems, such as PubMed, offer flexible query interface, but churn out a list of matching documents that users have to go through the results in order to find the answers to their queries. On the other hand, the "deep" search systems, such as PPI Finder and iHOP, return the precompiled results in a structured way. Their results, however, are often found only within some predefined contexts. In order to alleviate these problems, we introduce a new search engine, BOSS, Biomedical Object Search System. Methods Unlike the conventional search systems, BOSS indexes segments, rather than documents. A segment refers to a Maximal Coherent Semantic Unit (MCSU such as phrase, clause or sentence that is semantically coherent in the given context (e.g., biomedical objects or their relations. For a user query, BOSS finds all matching segments, identifies the objects appearing in those segments, and aggregates the segments for each object. Finally, it returns the ranked list of the objects along with their matching segments. Results The working prototype of BOSS is available at http://boss.korea.ac.kr. The current version of BOSS has indexed abstracts of more than 20 million articles published during last 16 years from 1996 to 2011 across all science disciplines. Conclusion BOSS fills the gap between either ends of the spectrum by allowing users to pose context-free queries and by returning a structured set of results. Furthermore, BOSS exhibits the characteristic of good scalability, just as with conventional document search engines, because it is designed to use a standard document-indexing model with minimal modifications. Considering the features, BOSS notches up the technological level of traditional solutions for search on biomedical information.

  10. Where to search top-K biomedical ontologies?

    Science.gov (United States)

    Oliveira, Daniela; Butt, Anila Sahar; Haller, Armin; Rebholz-Schuhmann, Dietrich; Sahay, Ratnesh

    2018-03-20

    Searching for precise terms and terminological definitions in the biomedical data space is problematic, as researchers find overlapping, closely related and even equivalent concepts in a single or multiple ontologies. Search engines that retrieve ontological resources often suggest an extensive list of search results for a given input term, which leads to the tedious task of selecting the best-fit ontological resource (class or property) for the input term and reduces user confidence in the retrieval engines. A systematic evaluation of these search engines is necessary to understand their strengths and weaknesses in different search requirements. We have implemented seven comparable Information Retrieval ranking algorithms to search through ontologies and compared them against four search engines for ontologies. Free-text queries have been performed, the outcomes have been judged by experts and the ranking algorithms and search engines have been evaluated against the expert-based ground truth (GT). In addition, we propose a probabilistic GT that is developed automatically to provide deeper insights and confidence to the expert-based GT as well as evaluating a broader range of search queries. The main outcome of this work is the identification of key search factors for biomedical ontologies together with search requirements and a set of recommendations that will help biomedical experts and ontology engineers to select the best-suited retrieval mechanism in their search scenarios. We expect that this evaluation will allow researchers and practitioners to apply the current search techniques more reliably and that it will help them to select the right solution for their daily work. The source code (of seven ranking algorithms), ground truths and experimental results are available at https://github.com/danielapoliveira/bioont-search-benchmark.

  11. A semantic graph-based approach to biomedical summarisation.

    Science.gov (United States)

    Plaza, Laura; Díaz, Alberto; Gervás, Pablo

    2011-09-01

    Access to the vast body of research literature that is available in biomedicine and related fields may be improved by automatic summarisation. This paper presents a method for summarising biomedical scientific literature that takes into consideration the characteristics of the domain and the type of documents. To address the problem of identifying salient sentences in biomedical texts, concepts and relations derived from the Unified Medical Language System (UMLS) are arranged to construct a semantic graph that represents the document. A degree-based clustering algorithm is then used to identify different themes or topics within the text. Different heuristics for sentence selection, intended to generate different types of summaries, are tested. A real document case is drawn up to illustrate how the method works. A large-scale evaluation is performed using the recall-oriented understudy for gisting-evaluation (ROUGE) metrics. The results are compared with those achieved by three well-known summarisers (two research prototypes and a commercial application) and two baselines. Our method significantly outperforms all summarisers and baselines. The best of our heuristics achieves an improvement in performance of almost 7.7 percentage units in the ROUGE-1 score over the LexRank summariser (0.7862 versus 0.7302). A qualitative analysis of the summaries also shows that our method succeeds in identifying sentences that cover the main topic of the document and also considers other secondary or "satellite" information that might be relevant to the user. The method proposed is proved to be an efficient approach to biomedical literature summarisation, which confirms that the use of concepts rather than terms can be very useful in automatic summarisation, especially when dealing with highly specialised domains. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Emerging roles for biomedical librarians: a survey of current practice, challenges, and changes.

    Science.gov (United States)

    Crum, Janet A; Cooper, I Diane

    2013-10-01

    This study is intended to (1) identify emerging roles for biomedical librarians and determine how common these roles are in a variety of library settings, (2) identify barriers to taking on new roles, and (3) determine how librarians are developing the capacity to take on new roles. A survey was conducted of librarians in biomedical settings. Most biomedical librarians are taking on new roles. The most common roles selected by survey respondents include analysis and enhancement of user experiences, support for social media, support for systematic reviews, clinical informationist, help for faculty or staff with authorship issues, and implementation of researcher profiling and collaboration tools. Respondents in academic settings are more likely to report new roles than hospital librarians are, but some new roles are common in both settings. Respondents use a variety of methods to free up time for new roles, but predominant methods vary between directors and librarians and between academic and hospital respondents. Lack of time is the biggest barrier that librarians face when trying to adopt new roles. New roles are associated with increased collaboration with individuals and/or groups outside the library. This survey documents the widespread incorporation of new roles in biomedical libraries in the United States, as well as the barriers to adopting these roles and the means by which librarians are making time for them. The results of the survey can be used to inform strategic planning, succession planning, library education, and career development for biomedical librarians.

  13. An exploration of the biomedical optics course construction of undergraduate biomedical engineering program in medical colleges

    Science.gov (United States)

    Guo, Shijun; Lyu, Jie; Zhang, Peiming

    2017-08-01

    In this paper, the teaching goals, teaching contents and teaching methods in biomedical optics course construction are discussed. From the dimension of teaching goals, students should master the principle of optical inspection on the human body, diagnosis and treatment of methodology and instruments, through the study of the theory and practice of this course, and can utilize biomedical optics methods to solve practical problems in the clinical medical engineering practice. From the dimension of teaching contents, based on the characteristics of biomedical engineering in medical colleges, the organic integration of engineering aspects, medical optical instruments, and biomedical aspects dispersed in human anatomy, human physiology, clinical medicine fundamental related to the biomedical optics is build. Noninvasive measurement of the human body composition and noninvasive optical imaging of the human body were taken as actual problems in biomedical optics fields. Typical medical applications such as eye optics and laser medicine were also integrated into the theory and practice teaching. From the dimension of teaching methods, referencing to organ-system based medical teaching mode, optical principle and instrument principle were taught by teachers from school of medical instruments, and the histological characteristics and clinical actual need in areas such as digestive diseases and urinary surgery were taught by teachers from school of basic medicine or clinical medicine of medical colleges. Furthermore, clinical application guidance would be provided by physician and surgeons in hospitals.

  14. Multiscale integration of -omic, imaging, and clinical data in biomedical informatics.

    Science.gov (United States)

    Phan, John H; Quo, Chang F; Cheng, Chihwen; Wang, May Dongmei

    2012-01-01

    This paper reviews challenges and opportunities in multiscale data integration for biomedical informatics. Biomedical data can come from different biological origins, data acquisition technologies, and clinical applications. Integrating such data across multiple scales (e.g., molecular, cellular/tissue, and patient) can lead to more informed decisions for personalized, predictive, and preventive medicine. However, data heterogeneity, community standards in data acquisition, and computational complexity are big challenges for such decision making. This review describes genomic and proteomic (i.e., molecular), histopathological imaging (i.e., cellular/tissue), and clinical (i.e., patient) data; it includes case studies for single-scale (e.g., combining genomic or histopathological image data), multiscale (e.g., combining histopathological image and clinical data), and multiscale and multiplatform (e.g., the Human Protein Atlas and The Cancer Genome Atlas) data integration. Numerous opportunities exist in biomedical informatics research focusing on integration of multiscale and multiplatform data.

  15. New software developments for quality mesh generation and optimization from biomedical imaging data.

    Science.gov (United States)

    Yu, Zeyun; Wang, Jun; Gao, Zhanheng; Xu, Ming; Hoshijima, Masahiko

    2014-01-01

    In this paper we present a new software toolkit for generating and optimizing surface and volumetric meshes from three-dimensional (3D) biomedical imaging data, targeted at image-based finite element analysis of some biomedical activities in a single material domain. Our toolkit includes a series of geometric processing algorithms including surface re-meshing and quality-guaranteed tetrahedral mesh generation and optimization. All methods described have been encapsulated into a user-friendly graphical interface for easy manipulation and informative visualization of biomedical images and mesh models. Numerous examples are presented to demonstrate the effectiveness and efficiency of the described methods and toolkit. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  16. In-line phase contrast micro-CT reconstruction for biomedical specimens.

    Science.gov (United States)

    Fu, Jian; Tan, Renbo

    2014-01-01

    X-ray phase contrast micro computed tomography (micro-CT) can non-destructively provide the internal structure information of soft tissues and low atomic number materials. It has become an invaluable analysis tool for biomedical specimens. Here an in-line phase contrast micro-CT reconstruction technique is reported, which consists of a projection extraction method and the conventional filter back-projection (FBP) reconstruction algorithm. The projection extraction is implemented by applying the Fourier transform to the forward projections of in-line phase contrast micro-CT. This work comprises a numerical study of the method and its experimental verification using a biomedical specimen dataset measured at an X-ray tube source micro-CT setup. The numerical and experimental results demonstrate that the presented technique can improve the imaging contrast of biomedical specimens. It will be of interest for a wide range of in-line phase contrast micro-CT applications in medicine and biology.

  17. Advancing community stakeholder engagement in biomedical HIV prevention trials: principles, practices and evidence.

    Science.gov (United States)

    Newman, Peter A; Rubincam, Clara

    2014-12-01

    Community stakeholder engagement is foundational to fair and ethically conducted biomedical HIV prevention trials. Concerns regarding the ethical engagement of community stakeholders in HIV vaccine trials and early terminations of several international pre-exposure prophylaxis trials have fueled the development of international guidelines, such as UNAIDS' good participatory practice (GPP). GPP aims to ensure that stakeholders are effectively involved in all phases of biomedical HIV prevention trials. We provide an overview of the six guiding principles in the GPP and critically examine them in relation to existing social and behavioral science research. In particular, we highlight the challenges involved in operationalizing these principles on the ground in various global contexts, with a focus on low-income country settings. Increasing integration of social science in biomedical HIV prevention trials will provide evidence to advance a science of community stakeholder engagement to support ethical and effective practices informed by local realities and sociocultural differences.

  18. Biomedical Information Extraction: Mining Disease Associated Genes from Literature

    Science.gov (United States)

    Huang, Zhong

    2014-01-01

    Disease associated gene discovery is a critical step to realize the future of personalized medicine. However empirical and clinical validation of disease associated genes are time consuming and expensive. In silico discovery of disease associated genes from literature is therefore becoming the first essential step for biomarker discovery to…

  19. User needs analysis and usability assessment of DataMed - a biomedical data discovery index.

    Science.gov (United States)

    Dixit, Ram; Rogith, Deevakar; Narayana, Vidya; Salimi, Mandana; Gururaj, Anupama; Ohno-Machado, Lucila; Xu, Hua; Johnson, Todd R

    2017-11-30

    To present user needs and usability evaluations of DataMed, a Data Discovery Index (DDI) that allows searching for biomedical data from multiple sources. We conducted 2 phases of user studies. Phase 1 was a user needs analysis conducted before the development of DataMed, consisting of interviews with researchers. Phase 2 involved iterative usability evaluations of DataMed prototypes. We analyzed data qualitatively to document researchers' information and user interface needs. Biomedical researchers' information needs in data discovery are complex, multidimensional, and shaped by their context, domain knowledge, and technical experience. User needs analyses validate the need for a DDI, while usability evaluations of DataMed show that even though aggregating metadata into a common search engine and applying traditional information retrieval tools are promising first steps, there remain challenges for DataMed due to incomplete metadata and the complexity of data discovery. Biomedical data poses distinct problems for search when compared to websites or publications. Making data available is not enough to facilitate biomedical data discovery: new retrieval techniques and user interfaces are necessary for dataset exploration. Consistent, complete, and high-quality metadata are vital to enable this process. While available data and researchers' information needs are complex and heterogeneous, a successful DDI must meet those needs and fit into the processes of biomedical researchers. Research directions include formalizing researchers' information needs, standardizing overviews of data to facilitate relevance judgments, implementing user interfaces for concept-based searching, and developing evaluation methods for open-ended discovery systems such as DDIs. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  20. Advances in biomedical signal and image processing – A systematic review

    Directory of Open Access Journals (Sweden)

    J. Rajeswari

    Full Text Available Biomedical signal and image processing establish a dynamic area of specialization in both academic as well as research aspects of biomedical engineering. The concepts of signal and image processing have been widely used for extracting the physiological information in implementing many clinical procedures for sophisticated medical practices and applications. In this paper, the relationship between electrophysiological signals, i.e., electrocardiogram (ECG, electromyogram (EMG, electroencephalogram (EEG and functional image processing and their derived interactions have been discussed. Examples have been investigated in various case studies such as neurosciences, functional imaging, and cardiovascular system, by using different algorithms and methods. The interaction between the extracted information obtained from multiple signals and modalities seems to be very promising. The advanced algorithms and methods in the area of information retrieval based on time-frequency representation have been investigated. Finally, some examples of algorithms have been discussed in which the electrophysiological signals and functional images have been properly extracted and have a significant impact on various biomedical applications. Keywords: Biomedical signals and images, Processing, Analysis

  1. COEUS: "semantic web in a box" for biomedical applications.

    Science.gov (United States)

    Lopes, Pedro; Oliveira, José Luís

    2012-12-17

    As the "omics" revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter's complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a "semantic web in a box" approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.

  2. Publications in biomedical and environmental sciences programs, 1981

    Energy Technology Data Exchange (ETDEWEB)

    Moody, J.B. (comp.)

    1982-07-01

    This bibliography contains 698 references to articles in journals, books, and reports published in the subject area of biomedical and environmental sciences during 1981. There are 520 references to articles published in journals and books and 178 references to reports. Staff members in the Biomedical and Environmental Sciences divisions have other publications not included in this bibliography; for example, theses, book reviews, abstracts published in journals or symposia proceedings, pending journal publications and reports such as monthly, bimonthly, and quarterly progress reports, contractor reports, and reports for internal distribution. This document is sorted by the division, and then alphabetically by author. The sorting by divisions separates the references by subject area in a simple way. The divisions represented in the order that they appear in the bibliography are Analytical Chemistry, Biology, Chemical Technology, Information R and D, Health and Safety Research, Instrumentation and Controls, Computer Sciences, Energy, Engineering Technology, Solid State, Central Management, Operations, and Environmental Sciences. Indexes are provided by author, title, and journal reference.

  3. The relevance of Heidegger's philosophy of technology for biomedical ethics.

    Science.gov (United States)

    Svenaeus, Fredrik

    2013-02-01

    Heidegger's thoughts on modern technology have received much attention in many disciplines and fields, but, with a few exceptions, the influence has been sparse in biomedical ethics. The reason for this might be that Heidegger's position has been misinterpreted as being generally hostile towards modern science and technology, and the fact that Heidegger himself never subjected medical technologies to scrutiny but was concerned rather with industrial technology and information technology. In this paper, Heidegger's philosophy of modern technology is introduced and then brought to bear on medical technology. Its main relevance for biomedical ethics is found to be that the field needs to focus upon epistemological and ontological questions in the philosophy of medicine related to the structure and goal of medical practice. Heidegger's philosophy can help us to see how the scientific attitude in medicine must always be balanced by and integrated into a phenomenological way of understanding the life-world concerns of patients. The difference between the scientific and the phenomenological method in medicine is articulated by Heidegger as two different ways of studying the human body: as biological organism and as lived body. Medicine needs to acknowledge the priority of the lived body in addressing health as a way of being-in-the-world and not as the absence of disease only. A critical development of Heidegger's position can provide us with a criterion for distinguishing the uses of medical technologies that are compatible with such an endeavor from the technological projects that are not.

  4. Cross Layer Interference Management in Wireless Biomedical Networks

    Directory of Open Access Journals (Sweden)

    Emmanouil G. Spanakis

    2014-04-01

    Full Text Available Interference, in wireless networks, is a central phenomenon when multiple uncoordinated links share a common communication medium. The study of the interference channel was initiated by Shannon in 1961 and since then this problem has been thoroughly elaborated at the Information theoretic level but its characterization still remains an open issue. When multiple uncoordinated links share a common medium the effect of interference is a crucial limiting factor for network performance. In this work, using cross layer cooperative communication techniques, we study how to compensate interference in the context of wireless biomedical networks, where many links transferring biomedical or other health related data may be formed and suffer from all other interfering transmissions, to allow successful receptions and improve the overall network performance. We define the interference limited communication range to be the critical communication region around a receiver, with a number of surrounding interfering nodes, within which a successful communication link can be formed. Our results indicate that we can achieve more successful transmissions by adapting the transmission rate and power, to the path loss exponent, and the selected mode of the underline communication technique allowing interference mitigation and when possible lower power consumption and increase achievable transmission rates.

  5. Publications in biomedical and environmental sciences programs, 1981

    International Nuclear Information System (INIS)

    Moody, J.B.

    1982-07-01

    This bibliography contains 698 references to articles in journals, books, and reports published in the subject area of biomedical and environmental sciences during 1981. There are 520 references to articles published in journals and books and 178 references to reports. Staff members in the Biomedical and Environmental Sciences divisions have other publications not included in this bibliography; for example, theses, book reviews, abstracts published in journals or symposia proceedings, pending journal publications and reports such as monthly, bimonthly, and quarterly progress reports, contractor reports, and reports for internal distribution. This document is sorted by the division, and then alphabetically by author. The sorting by divisions separates the references by subject area in a simple way. The divisions represented in the order that they appear in the bibliography are Analytical Chemistry, Biology, Chemical Technology, Information R and D, Health and Safety Research, Instrumentation and Controls, Computer Sciences, Energy, Engineering Technology, Solid State, Central Management, Operations, and Environmental Sciences. Indexes are provided by author, title, and journal reference

  6. [Self-archiving of biomedical papers in open access repositories].

    Science.gov (United States)

    Abad-García, M Francisca; Melero, Remedios; Abadal, Ernest; González-Teruel, Aurora

    2010-04-01

    Open-access literature is digital, online, free of charge, and free of most copyright and licensing restrictions. Self-archiving or deposit of scholarly outputs in institutional repositories (open-access green route) is increasingly present in the activities of the scientific community. Besides the benefits of open access for visibility and dissemination of science, it is increasingly more often required by funding agencies to deposit papers and any other type of documents in repositories. In the biomedical environment this is even more relevant by the impact scientific literature can have on public health. However, to make self-archiving feasible, authors should be aware of its meaning and the terms in which they are allowed to archive their works. In that sense, there are some tools like Sherpa/RoMEO or DULCINEA (both directories of copyright licences of scientific journals at different levels) to find out what rights are retained by authors when they publish a paper and if they allow to implement self-archiving. PubMed Central and its British and Canadian counterparts are the main thematic repositories for biomedical fields. In our country there is none of similar nature, but most of the universities and CSIC, have already created their own institutional repositories. The increase in visibility of research results and their impact on a greater and earlier citation is one of the most frequently advance of open access, but removal of economic barriers to access to information is also a benefit to break borders between groups.

  7. Resolving complex research data management issues in biomedical laboratories: Qualitative study of an industry-academia collaboration.

    Science.gov (United States)

    Myneni, Sahiti; Patel, Vimla L; Bova, G Steven; Wang, Jian; Ackerman, Christopher F; Berlinicke, Cynthia A; Chen, Steve H; Lindvall, Mikael; Zack, Donald J

    2016-04-01

    This paper describes a distributed collaborative effort between industry and academia to systematize data management in an academic biomedical laboratory. Heterogeneous and voluminous nature of research data created in biomedical laboratories make information management difficult and research unproductive. One such collaborative effort was evaluated over a period of four years using data collection methods including ethnographic observations, semi-structured interviews, web-based surveys, progress reports, conference call summaries, and face-to-face group discussions. Data were analyzed using qualitative methods of data analysis to (1) characterize specific problems faced by biomedical researchers with traditional information management practices, (2) identify intervention areas to introduce a new research information management system called Labmatrix, and finally to (3) evaluate and delineate important general collaboration (intervention) characteristics that can optimize outcomes of an implementation process in biomedical laboratories. Results emphasize the importance of end user perseverance, human-centric interoperability evaluation, and demonstration of return on investment of effort and time of laboratory members and industry personnel for success of implementation process. In addition, there is an intrinsic learning component associated with the implementation process of an information management system. Technology transfer experience in a complex environment such as the biomedical laboratory can be eased with use of information systems that support human and cognitive interoperability. Such informatics features can also contribute to successful collaboration and hopefully to scientific productivity. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  8. Optimizing biomedical science learning in a veterinary curriculum: a review.

    Science.gov (United States)

    Warren, Amy L; Donnon, Tyrone

    2013-01-01

    As veterinary medical curricula evolve, the time dedicated to biomedical science teaching, as well as the role of biomedical science knowledge in veterinary education, has been scrutinized. Aside from being mandated by accrediting bodies, biomedical science knowledge plays an important role in developing clinical, diagnostic, and therapeutic reasoning skills in the application of clinical skills, in supporting evidence-based veterinary practice and life-long learning, and in advancing biomedical knowledge and comparative medicine. With an increasing volume and fast pace of change in biomedical knowledge, as well as increased demands on curricular time, there has been pressure to make biomedical science education efficient and relevant for veterinary medicine. This has lead to a shift in biomedical education from fact-based, teacher-centered and discipline-based teaching to applicable, student-centered, integrated teaching. This movement is supported by adult learning theories and is thought to enhance students' transference of biomedical science into their clinical practice. The importance of biomedical science in veterinary education and the theories of biomedical science learning will be discussed in this article. In addition, we will explore current advances in biomedical teaching methodologies that are aimed to maximize knowledge retention and application for clinical veterinary training and practice.

  9. Legal capacity and biomedicine: Biomedical discrimination

    Directory of Open Access Journals (Sweden)

    Cvetić Radenka

    2011-01-01

    Full Text Available The article begins with the overview of the legal capacity as a general legal qualification recognized by the legal order guaranteeing the right to be a holder of rights and obligations. The article is then focused on the scope of the absolute Constitutional guarantee of the right to legal personality as well as on the Constitutional prohibition of discrimination which gives rise to the general equality before the Constitution and the law. The focus of this article is the moment when the legal capacity, or legal personality, is considered to be acquired. It then moves to the issue whether limiting the access to techniques of assisted reproduction (biomedical conception is contrary to the general rules on legal capacity, and whether this is a genuine form of biomedical discrimination.

  10. Diamond-based materials for biomedical applications

    CERN Document Server

    Narayan, Roger

    2013-01-01

    Carbon is light-weight, strong, conductive and able to mimic natural materials within the body, making it ideal for many uses within biomedicine. Consequently a great deal of research and funding is being put into this interesting material with a view to increasing the variety of medical applications for which it is suitable. Diamond-based materials for biomedical applications presents readers with the fundamental principles and novel applications of this versatile material. Part one provides a clear introduction to diamond based materials for medical applications. Functionalization of diamond particles and surfaces is discussed, followed by biotribology and biological behaviour of nanocrystalline diamond coatings, and blood compatibility of diamond-like carbon coatings. Part two then goes on to review biomedical applications of diamond based materials, beginning with nanostructured diamond coatings for orthopaedic applications. Topics explored include ultrananocrystalline diamond for neural and ophthalmologi...

  11. Leveraging the national cyberinfrastructure for biomedical research.

    Science.gov (United States)

    LeDuc, Richard; Vaughn, Matthew; Fonner, John M; Sullivan, Michael; Williams, James G; Blood, Philip D; Taylor, James; Barnett, William

    2014-01-01

    In the USA, the national cyberinfrastructure refers to a system of research supercomputer and other IT facilities and the high speed networks that connect them. These resources have been heavily leveraged by scientists in disciplines such as high energy physics, astronomy, and climatology, but until recently they have been little used by biomedical researchers. We suggest that many of the 'Big Data' challenges facing the medical informatics community can be efficiently handled using national-scale cyberinfrastructure. Resources such as the Extreme Science and Discovery Environment, the Open Science Grid, and Internet2 provide economical and proven infrastructures for Big Data challenges, but these resources can be difficult to approach. Specialized web portals, support centers, and virtual organizations can be constructed on these resources to meet defined computational challenges, specifically for genomics. We provide examples of how this has been done in basic biology as an illustration for the biomedical informatics community.

  12. Low-level radioactive biomedical wastes

    International Nuclear Information System (INIS)

    Casarett, G.W.

    A summary of the management and hazards of low-level radioactive biomedical wastes is presented. The volume, disposal methods, current problems, regulatory agencies, and possible solutions to disposal problems are discussed. The benefits derived from using radioactivity in medicine are briefly described. Potential health risks are discussed. The radioactivity in most of the radioactive biomedical waste is a small fraction of that contained naturally in the human body or in the natural environment. Benefit-risk-cost considerations are presented. The cost of managing these wastes is getting so high that a new perspective for comparison of radioactivity (facts, risks, costs, benefits and trade-offs) and alternate approaches to minimize the risk and cost and maximize the benefits is suggested

  13. Combinatorial nanodiamond in pharmaceutical and biomedical applications.

    Science.gov (United States)

    Lim, Dae Gon; Prim, Racelly Ena; Kim, Ki Hyun; Kang, Eunah; Park, Kinam; Jeong, Seong Hoon

    2016-11-30

    One of the newly emerging carbon materials, nanodiamond (ND), has been exploited for use in traditional electric materials and this has extended into biomedical and pharmaceutical applications. Recently, NDs have attained significant interests as a multifunctional and combinational drug delivery system. ND studies have provided insights into granting new potentials with their wide ranging surface chemistry, complex formation with biopolymers, and combination with biomolecules. The studies that have proved ND inertness, biocompatibility, and low toxicity have made NDs much more feasible for use in real in vivo applications. This review gives an understanding of NDs in biomedical engineering and pharmaceuticals, focusing on the classified introduction of ND/drug complexes. In addition, the diverse potential applications that can be obtained with chemical modification are presented. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Biomedical Applications of Nanodiamonds: An Overview.

    Science.gov (United States)

    Passeri, D; Rinaldi, F; Ingallina, C; Carafa, M; Rossi, M; Terranova, M L; Marianecci, C

    2015-02-01

    Nanodiamonds are a novel class of nanomaterials which have raised much attention for application in biomedical field, as they combine the possibility of being produced on large scale using relatively inexpensive synthetic processes, of being fluorescent as a consequence of the presence of nitrogen vacancies, of having their surfaces functionalized, and of having good biocompatibility. Among other applications, we mainly focus on drug delivery, including cell interaction, targeting, cancer therapy, gene and protein delivery. In addition, nanodiamonds for bone and dental implants and for antibacterial use is discussed. Techniques for detection and imaging of nanodiamonds in biological tissues are also reviewed, including electron microscopy, fluorescence microscopy, Raman mapping, atomic force microscopy, thermal imaging, magnetic resonance imaging, and positron emission tomography, either in vitro, in vivo, or ex vivo. Toxicological aspects related to the use of nanodiamonds are also discussed. Finally, patents, preclinical and clinical trials based on the use of nanodiamonds for biomedical applications are reviewed.

  15. Design and analysis of biomedical studies

    DEFF Research Database (Denmark)

    Hansen, Merete Kjær

    been allocated this field. It is utterly important to utilize these ressources responsibly and efficiently by constantly striving to ensure high-quality biomedical studies. This involves the use of a sound statistical methodology regarding both the design and analysis of biomedical studies. The focus...... have conducted a literature study strongly indicating that this structure commonly is neglected in the statistical analysis. Based on this closed-form expressions for the approximate type I error rate are formulated. The type I error rates are assessed for a number of factor combinations as they appear...... in practice and in all cases the type I error rates are demonstrated to be severely inflated. Prior to conducting a study it is important to perform power and sample size determinations to ensure that reliable conclusions can be drawn from the statistical analysis. We have formulated closed-form expressions...

  16. Emerging applications of nanoparticles: Biomedical and environmental

    Science.gov (United States)

    Gulati, Shivani; Sachdeva, M.; Bhasin, K. K.

    2018-05-01

    Nanotechnology finds a wide range of applications from energy production to industrial fabrication processes to biomedical applications. Nanoparticles (NPs) can be engineered to possess unique compositions and functionalities to empower novel tools and techniques that have not existed previously in biomedical research. The unique size and shape dependent physicochemical properties along with their unique spectral and optical properties have prompted the development of a wide variety of potential applications in the field of diagnostics and medicines. In the plethora of scientific and technological fields, environmental safety is also a big concern. For this purpose, nanomaterials have been functionalized to cope up the existing pollution, improving manufacturing methods to reduce the generation of new pollution, and making alternative and more cost effective energy sources.

  17. Potential of Starch Nanocomposites for Biomedical Applications

    Science.gov (United States)

    Zakaria, N. H.; Muhammad, N.; Abdullah, M. M. A. B.

    2017-06-01

    In recent years, the development of biodegradable materials from renewable sources based on polymeric biomaterials have grown rapidly due to increase environmental concerns and the shortage of petroleum sources. In this regard, naturally renewable polymers such as starch has shown great potential as environmental friendly materials. Besides, the unique properties of starch such as biodegradable and non-toxic, biocompatible and solubility make them useful for a various biomedical applications. Regardless of their unique properties, starch materials are known to have limitations in term of poor processability, low mechanical properties, poor long term stability and high water sensitivity. In order to overcome these limitations, the incorporation of nano size fillers into starch materials (nanocomposites) has been introduced. This review aims to give an overview about structure and characteristics of starch, modification of starch by nanocomposites and their potential for biomedical applications.

  18. Harnessing supramolecular peptide nanotechnology in biomedical applications.

    Science.gov (United States)

    Chan, Kiat Hwa; Lee, Wei Hao; Zhuo, Shuangmu; Ni, Ming

    2017-01-01

    The harnessing of peptides in biomedical applications is a recent hot topic. This arises mainly from the general biocompatibility of peptides, as well as from the ease of tunability of peptide structure to engineer desired properties. The ease of progression from laboratory testing to clinical trials is evident from the plethora of examples available. In this review, we compare and contrast how three distinct self-assembled peptide nanostructures possess different functions. We have 1) nanofibrils in biomaterials that can interact with cells, 2) nanoparticles that can traverse the bloodstream to deliver its payload and also be bioimaged, and 3) nanotubes that can serve as cross-membrane conduits and as a template for nanowire formation. Through this review, we aim to illustrate how various peptides, in their various self-assembled nanostructures, possess great promise in a wide range of biomedical applications and what more can be expected.

  19. Biomedical hydrogels biochemistry, manufacture and medical applications

    CERN Document Server

    Rimmer, Steve

    2011-01-01

    Hydrogels are very important for biomedical applications because they can be chemically manipulated to alter and control the hydrogel's interaction with cells and tissues. Their flexibility and high water content is similar to that of natural tissue, making them extremely suitable for biomaterials applications. Biomedical hydrogels explores the diverse range and use of hydrogels, focusing on processing methods and novel applications in the field of implants and prostheses. Part one of this book concentrates on the processing of hydrogels, covering hydrogel swelling behaviour, superabsorbent cellulose-based hydrogels and regulation of novel hydrogel products, as well as chapters focusing on the structure and properties of hydrogels and different fabrication technologies. Part two covers existing and novel applications of hydrogels, including chapters on spinal disc and cartilage replacement implants, hydrogels for ophthalmic prostheses and hydrogels for wound healing applications. The role of hydrogels in imag...

  20. Application of infrared to biomedical sciences

    CERN Document Server

    Etehadtavakol, Mahnaz

    2017-01-01

    The book covers the latest updates in the application of infrared to biomedical sciences, a non-invasive, contactless, safe and easy approach imaging of skin and tissue temperatures. Its diagnostic procedure allows practitioners to identify the locations of abnormal chemical and blood vessel activity such as angiogenesis in body tissue. Its non-invasive approach works by applying the technology of the infrared camera and state-of-the-art software, where high-resolution digital infrared imaging technology benefits highly from enhanced image production, standardized image interpretation protocols, computerized comparison and storage, and sophisticated image enhancement and analysis. The book contains contributions from global prominent scientists in the area of infrared applications in biomedical studies. The target audience includes academics, practitioners, clinicians and students working in the area of infrared imaging in biomedicine.

  1. Medical and biomedical applications of shock waves

    CERN Document Server

    Loske, Achim M

    2017-01-01

    This book provides current, comprehensive, and clear explanations of the physics behind medical and biomedical applications of shock waves. Extracorporeal shock wave lithotripsy is one of the greatest medical advances of our time, and its techniques and clinical devices are continuously evolving. Further research continues to improve the understanding of calculi fragmentation and tissue-damaging mechanisms. Shock waves are also used in orthopedics and traumatology. Possible applications in oncology, cardiology, dentistry, gene therapy, cell transfection, transformation of fungi and bacteria, as well as the inactivation of microorganisms are promising approaches for clinical treatment, industrial applications and research. Medical and Biomedical Applications of Shock Waves is useful as a guide for students, technicians and researchers working in universities and laboratories. Chemists, biologists, physicians and veterinarians, involved in research or clinical practice will find useful advice, but also engineer...

  2. Bibliography of astatine chemistry and biomedical applications

    International Nuclear Information System (INIS)

    Berei, K.; Vasaros, L.

    1992-02-01

    An overall bibliography is presented on astatine chemistry and on the biomedical applications of its 211 At isotope. The references were grouped in the following chapters: General reviews; Discovery, Natural Occurence; Nuclear Data; Preparation, Handling, Radiation Risk; Physico-chemical Properties; Astatine Compounds and Chemical Reactions; Biological Effects and Applications. Entries are sorted alphabetically by authors name in each chapter, and cross-references to other chapters are provided if appropriate. (R.P.)

  3. Production and Biomedical Applications of Probiotic Biosurfactants.

    Science.gov (United States)

    Fariq, Anila; Saeed, Ayesha

    2016-04-01

    Biosurfactants have been widely used for environmental and industrial applications. However, their use in medical field is still limited. Probiotic biosurfactants possess an immense antimicrobial, anti-adhesive, antitumor, and antibiofilm potential. Moreover, they have an additional advantage over conventional microbial surfactants because probiotics are an integral part of normal human microflora and their biosurfactants are innocuous to human. So, they can be effectively exploited for medicinal use. Present review is aimed to discourse the production and biomedical applications of probiotic biosurfactants.

  4. Biomedical application of the nuclear microprobe

    International Nuclear Information System (INIS)

    Lindh, U.

    1987-01-01

    The Studsvik Nuclear Microprobe (SMP) has mainly been devoted to applications in the biomedical field. Its ultimate resolution is reached at 2.9x2.9 μm 2 with a proton current of 100 pA. With this performance the SMP has been used in a wide range of disciplines covering environmental hygiene, toxicology, various aspects of internal medicine and trace element physiology. Examples of recent applications in these fields are described. (orig.)

  5. Implantable biomedical microsystems design principles and applications

    CERN Document Server

    Bhunia, Swarup; Sawan, Mohamad

    2015-01-01

    Research and innovation in areas such as circuits, microsystems, packaging, biocompatibility, miniaturization, power supplies, remote control, reliability, and lifespan are leading to a rapid increase in the range of devices and corresponding applications in the field of wearable and implantable biomedical microsystems, which are used for monitoring, diagnosing, and controlling the health conditions of the human body. This book provides comprehensive coverage of the fundamental design principles and validation for implantable microsystems, as well as several major application areas. Each co

  6. Nanodiamonds of Laser Synthesis for Biomedical Applications.

    Science.gov (United States)

    Perevedentseva, E; Peer, D; Uvarov, V; Zousman, B; Levinson, O

    2015-02-01

    In recent decade detonation nanodiamonds (DND), discovered 50 years ago and used in diverse technological processes, have been actively applied in biomedical research as a drug and gene delivery carrier, a contrast agent for bio-imaging and diagnostics and an adsorbent for protein separation and purification. In this work we report about nanodiamonds of high purity produced by laser assisted technique, compare them with DND and consider the prospect and advantages of their use in the said applications.

  7. Opal web services for biomedical applications.

    Science.gov (United States)

    Ren, Jingyuan; Williams, Nadya; Clementi, Luca; Krishnan, Sriram; Li, Wilfred W

    2010-07-01

    Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal's programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239,814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

  8. Immune-deficient animals in biomedical research

    International Nuclear Information System (INIS)

    Rygaard, J.; Brunner, N.; Groem, N.; Spang-Thomsen, M.

    1987-01-01

    This book presents paper given at a workshop on immune-dificient animals in biomedical research. Topics presented included the following: differential recovery of antibody production potential after sublethal whole-body irradiation of mice; increased levels of plasma DNA in nude mice transplanted with human tumors; and transplantation of exocrine pancreatic carcinomas to nude mice: A model to investigate immunoscintigraphy, radioimmunotherapy and drug sensitivity

  9. Determination of death: Metaphysical and biomedical discourse

    Directory of Open Access Journals (Sweden)

    Irayda Jakušovaitė

    2016-01-01

    Full Text Available The prominence of biomedical criteria relying on brain death reduces the impact of metaphysical, anthropological, psychosocial, cultural, religious, and legal aspects disclosing the real value and essence of human life. The aim of this literature review is to discuss metaphysical and biomedical approaches toward death and their complimentary relationship in the determination of death. A critical appraisal of theoretical and scientific evidence and legal documents supported analytical discourse. In the metaphysical discourse of death, two main questions about what human death is and how to determine the fact of death clearly separate the ontological and epistemological aspects of death. During the 20th century, various understandings of human death distinguished two different approaches toward the human: the human is a subject of activities or a subject of the human being. Extinction of the difference between the entities and the being, emphasized as rational–logical instrumentation, is not sufficient to understand death thoroughly. Biological criteria of death are associated with biological features and irreversible loss of certain cognitive capabilities. Debating on the question “Does a brain death mean death of a human being?” two approaches are considering: the body-centrist and the mind-centrist. By bridging those two alternatives human death appears not only as biomedical, but also as metaphysical phenomenon. It was summarized that a predominance of clinical criteria for determination of death in practice leads to medicalization of death and limits the holistic perspective toward individual's death. Therefore, the balance of metaphysical and biomedical approaches toward death and its determination would decrease the medicalization of the concept of death.

  10. Electrosprayed calcium phosphate coatings for biomedical purposes.

    OpenAIRE

    Leeuwenburgh, S.C.G.

    2006-01-01

    In this thesis, the suitability of the Electrostatic Spray Deposition (ESD) technique was studied for biomedical purposes, i.e., deposition of calcium phosphate (CaP) coatings onto titanium substrates. Using ESD, which is a simple and cheap deposition method for inorganic and organic coatings, it was possible to obtain thin CaP layers with an extremely wide range of chemical and morphological characteristics. Various CaP phases and phase mixtures were deposited and a broad diversity of coatin...

  11. Determination of death: Metaphysical and biomedical discourse.

    Science.gov (United States)

    Jakušovaitė, Irayda; Luneckaitė, Žydrunė; Peičius, Eimantas; Bagdonaitė, Živilė; Riklikienė, Olga; Stankevičius, Edgaras

    2016-01-01

    The prominence of biomedical criteria relying on brain death reduces the impact of metaphysical, anthropological, psychosocial, cultural, religious, and legal aspects disclosing the real value and essence of human life. The aim of this literature review is to discuss metaphysical and biomedical approaches toward death and their complimentary relationship in the determination of death. A critical appraisal of theoretical and scientific evidence and legal documents supported analytical discourse. In the metaphysical discourse of death, two main questions about what human death is and how to determine the fact of death clearly separate the ontological and epistemological aspects of death. During the 20th century, various understandings of human death distinguished two different approaches toward the human: the human is a subject of activities or a subject of the human being. Extinction of the difference between the entities and the being, emphasized as rational-logical instrumentation, is not sufficient to understand death thoroughly. Biological criteria of death are associated with biological features and irreversible loss of certain cognitive capabilities. Debating on the question "Does a brain death mean death of a human being?" two approaches are considering: the body-centrist and the mind-centrist. By bridging those two alternatives human death appears not only as biomedical, but also as metaphysical phenomenon. It was summarized that a predominance of clinical criteria for determination of death in practice leads to medicalization of death and limits the holistic perspective toward individual's death. Therefore, the balance of metaphysical and biomedical approaches toward death and its determination would decrease the medicalization of the concept of death. Copyright © 2016 The Lithuanian University of Health Sciences. Production and hosting by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

  12. Ethical Issues of Artificial Biomedical Applications

    OpenAIRE

    Alexiou , Athanasios; Psixa , Maria; Vlamos , Panagiotis

    2011-01-01

    Part 12: Medical Applications of ANN and Ethics of AI; International audience; While the plethora of artificial biomedical applications is enriched and combined with the possibilities of artificial intelligence, bioinformatics and nanotechnology, the variability in the ideological use of such concepts is associated with bioethical issues and several legal aspects. The convergence of bioethics and computer ethics, attempts to illustrate and approach problems, occurring by the fusion of human a...

  13. Design of biomedical devices and systems

    CERN Document Server

    King, Paul H

    2008-01-01

    Introduction to Biomedical Engineering Design. Fundamental Design Tools. Design Team Management, Reporting, and Documentation. Product Definition. Product Documentation. Product Development. Hardware Development Methods and Tools. Software Development Methods and Tools. Human Factors. Industrial Design. Biomaterials and Material Testing. Safety Engineering: Devices and Processes. Testing. Analysis of Test Data. Reliability and Liability. Food and Drug Administration. Regulations and Standards. Licensing, Patents, Copyrights, and Trade Secrets. Manufacturing and Quality Control. Miscellaneous Issues. Product Issues. Professional Issues. Design Case Studies. Future Design Issues.

  14. Harnessing supramolecular peptide nanotechnology in biomedical applications

    OpenAIRE

    Chan, Kiat Hwa; Lee, Wei Hao; Zhuo, Shuangmu; Ni, Ming

    2017-01-01

    Kiat Hwa Chan,1 Wei Hao Lee,2 Shuangmu Zhuo,3 Ming Ni3 1Division of Science, Yale-NUS College, Singapore; 2Department of Chemistry, Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, MD, USA; 3Fujian Provincial Key Laboratory for Photonics Technology, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, People’s Republic of China Abstract: The harnessing of peptides in biomedic...

  15. University of Vermont Center for Biomedical Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Bernstein, Dr. Ira [University of Vermont and State Agricultural College

    2013-08-02

    This grant was awarded in support of Phase 2 of the University of Vermont Center for Biomedical Imaging. Phase 2 outlined several specific aims including: The development of expertise in MRI and fMRI imaging and their applications The acquisition of peer reviewed extramural funding in support of the Center The development of a Core Imaging Advisory Board, fee structure and protocol review and approval process.

  16. Functional supramolecular polymers for biomedical applications.

    Science.gov (United States)

    Dong, Ruijiao; Zhou, Yongfeng; Huang, Xiaohua; Zhu, Xinyuan; Lu, Yunfeng; Shen, Jian

    2015-01-21

    As a novel class of dynamic and non-covalent polymers, supramolecular polymers not only display specific structural and physicochemical properties, but also have the ability to undergo reversible changes of structure, shape, and function in response to diverse external stimuli, making them promising candidates for widespread applications ranging from academic research to industrial fields. By an elegant combination of dynamic/reversible structures with exceptional functions, functional supramolecular polymers are attracting increasing attention in various fields. In particular, functional supramolecular polymers offer several unique advantages, including inherent degradable polymer backbones, smart responsiveness to various biological stimuli, and the ease for the incorporation of multiple biofunctionalities (e.g., targeting and bioactivity), thereby showing great potential for a wide range of applications in the biomedical field. In this Review, the trends and representative achievements in the design and synthesis of supramolecular polymers with specific functions are summarized, as well as their wide-ranging biomedical applications such as drug delivery, gene transfection, protein delivery, bio-imaging and diagnosis, tissue engineering, and biomimetic chemistry. These achievements further inspire persistent efforts in an emerging interdisciplin-ary research area of supramolecular chemistry, polymer science, material science, biomedical engineering, and nanotechnology. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Building the biomedical data science workforce.

    Directory of Open Access Journals (Sweden)

    Michelle C Dunn

    2017-07-01

    Full Text Available This article describes efforts at the National Institutes of Health (NIH from 2013 to 2016 to train a national workforce in biomedical data science. We provide an analysis of the Big Data to Knowledge (BD2K training program strengths and weaknesses with an eye toward future directions aimed at any funder and potential funding recipient worldwide. The focus is on extramurally funded programs that have a national or international impact rather than the training of NIH staff, which was addressed by the NIH's internal Data Science Workforce Development Center. From its inception, the major goal of BD2K was to narrow the gap between needed and existing biomedical data science skills. As biomedical research increasingly relies on computational, mathematical, and statistical thinking, supporting the training and education of the workforce of tomorrow requires new emphases on analytical skills. From 2013 to 2016, BD2K jump-started training in this area for all levels, from graduate students to senior researchers.

  18. IEEE International Symposium on Biomedical Imaging.

    Science.gov (United States)

    2017-01-01

    The IEEE International Symposium on Biomedical Imaging (ISBI) is a scientific conference dedicated to mathematical, algorithmic, and computational aspects of biological and biomedical imaging, across all scales of observation. It fosters knowledge transfer among different imaging communities and contributes to an integrative approach to biomedical imaging. ISBI is a joint initiative from the IEEE Signal Processing Society (SPS) and the IEEE Engineering in Medicine and Biology Society (EMBS). The 2018 meeting will include tutorials, and a scientific program composed of plenary talks, invited special sessions, challenges, as well as oral and poster presentations of peer-reviewed papers. High-quality papers are requested containing original contributions to the topics of interest including image formation and reconstruction, computational and statistical image processing and analysis, dynamic imaging, visualization, image quality assessment, and physical, biological, and statistical modeling. Accepted 4-page regular papers will be published in the symposium proceedings published by IEEE and included in IEEE Xplore. To encourage attendance by a broader audience of imaging scientists and offer additional presentation opportunities, ISBI 2018 will continue to have a second track featuring posters selected from 1-page abstract submissions without subsequent archival publication.

  19. Electroactive polymers for healthcare and biomedical applications

    Science.gov (United States)

    Bauer, Siegfried

    2017-04-01

    Electroactivity was noticed early in biological substances, including proteins, polynucleotides and enzymes, even piezoand pyroelectricity were found in wool, hair, wood, bone and tendon. Recently, ferroelectricity has been identified in a surprisingly large number of biologically relevant materials, including hydroxyapatite, aortic walls and elastin. Inspired by the variety of natural electroactive materials, a wealth of new elastomers and polymers were designed recently, including an all organic elastomer electret and self-healing dielectric elastomers. Let's further draw inspiration from nature and widen the utilization of electroactive polymers towards (mobile) healthcare and biomedical applications. Ferroelectrets, internally charged polymer foams with a strong piezoelectric thickness coefficient are employed in biomedical sensing, for example as blood pressure and pulse sensor, as vital signs monitor or for the detection of tonicclonic seizures. Piezo- and pyroelectric polymers are booming in printed electronics research. They provide electronic skin the ability to "feel" pressure and temperature changes, or to generate electrical energy from vibrations and motions, even from contractile and relaxation motions of the heart and lung. Dielectric elastomers are pioneered by StretchSense as wearable motion capture sensors, monitoring pressure, stretch, bend and shear, quantifying comfort in sports and healthcare. On the cellular level, electroactive polymer arrays are used to study mechanotransduction of individual cells. Ionic electroactive polymers show potential to be used in implantable electroactive biomedical devices. Already with the currently available science and technology, we are at the verge of witnessing the demonstration of truly complex bionic systems.

  20. Innovations in biomedical nanoengineering: nanowell array biosensor

    Science.gov (United States)

    Seo, YoungTae; Jeong, Sunil; Lee, JuKyung; Choi, Hak Soo; Kim, Jonghan; Lee, HeaYeon

    2018-04-01

    Nanostructured biosensors have pioneered biomedical engineering by providing highly sensitive analyses of biomolecules. The nanowell array (NWA)-based biosensing platform is particularly innovative, where the small size of NWs within the array permits extremely profound sensing of a small quantity of biomolecules. Undoubtedly, the NWA geometry of a gently-sloped vertical wall is critical for selective docking of specific proteins without capillary resistances, and nanoprocessing has contributed to the fabrication of NWA electrodes on gold substrate such as molding process, e-beam lithography, and krypton-fluoride (KrF) stepper semiconductor method. The Lee group at the Mara Nanotech has established this NW-based biosensing technology during the past two decades by engineering highly sensitive electrochemical sensors and providing a broad range of detection methods from large molecules (e.g., cells or proteins) to small molecules (e.g., DNA and RNA). Nanosized gold dots in the NWA enhance the detection of electrochemical biosensing to the range of zeptomoles in precision against the complementary target DNA molecules. In this review, we discuss recent innovations in biomedical nanoengineering with a specific focus on novel NWA-based biosensors. We also describe our continuous efforts in achieving a label-free detection without non-specific binding while maintaining the activity and stability of immobilized biomolecules. This research can lay the foundation of a new platform for biomedical nanoengineering systems.

  1. Successful aging: considering non-biomedical constructs

    Directory of Open Access Journals (Sweden)

    Carver LF

    2016-11-01

    Full Text Available Lisa F Carver,1 Diane Buchanan2 1Department of Sociology, Queen’s University Kingston, ON, Canada; 2School of Nursing, Queen’s University Kingston, ON, Canada Objectives: Successful aging continues to be applied in a variety of contexts and is defined using a number of different constructs. Although previous reviews highlight the multidimensionality of successful aging, a few have focused exclusively on non-biomedical factors, as was done here. Methods: This scoping review searched Ovid Medline database for peer-reviewed English-language articles published between 2006 and 2015, offering a model of successful aging and involving research with older adults. Results: Seventy-two articles were reviewed. Thirty-five articles met the inclusion criteria. Common non-biomedical constructs associated with successful aging included engagement, optimism and/or positive attitude, resilience, spirituality and/or religiosity, self-efficacy and/or self-esteem, and gerotranscendence. Discussion: Successful aging is a complex process best described using a multidimensional model. Given that the majority of elders will experience illness and/or disease during the life course, public health initiatives that promote successful aging need to employ non-biomedical constructs, facilitating the inclusion of elders living with disease and/or disability. Keywords: successful aging, resilience, gerotranscendence, engagement, optimism

  2. Inorganic nanolayers: structure, preparation, and biomedical applications.

    Science.gov (United States)

    Saifullah, Bullo; Hussein, Mohd Zobir B

    2015-01-01

    Hydrotalcite-like compounds are two-dimensional inorganic nanolayers also known as clay minerals or anionic clays or layered double hydroxides/layered hydroxy salts, and have emerged as a single type of material with numerous biomedical applications, such as drug delivery, gene delivery, cosmetics, and biosensing. Inorganic nanolayers are promising materials due to their fascinating properties, such as ease of preparation, ability to intercalate different type of anions (inorganic, organic, biomolecules, and even genes), high thermal stability, delivery of intercalated anions in a sustained manner, high biocompatibility, and easy biodegradation. Inorganic nanolayers have been the focus for researchers over the last decade, resulting in widening application horizons, especially in the field of biomedical science. These nanolayers have been widely applied in drug and gene delivery. They have also been applied in biosensing technology, and most recently in bioimaging science. The suitability of inorganic nanolayers for application in drug delivery, gene delivery, biosensing technology, and bioimaging science makes them ideal materials to be applied for theranostic purposes. In this paper, we review the structure, methods of preparation, and latest advances made by inorganic nanolayers in such biomedical applications as drug delivery, gene delivery, biosensing, and bioimaging.

  3. Biomedical Applications of Zinc Oxide Nanomaterials

    Science.gov (United States)

    Zhang, Yin; Nayak, Tapas R.; Hong, Hao; Cai, Weibo

    2013-01-01

    Nanotechnology has witnessed tremendous advancement over the last several decades. Zinc oxide (ZnO), which can exhibit a wide variety of nanostructures, possesses unique semiconducting, optical, and piezoelectric properties hence has been investigated for a wide variety of applications. One of the most important features of ZnO nanomaterials is low toxicity and biodegradability. Zn2+ is an indispensable trace element for adults (~10 mg of Zn2+ per day is recommended) and it is involved in various aspects of metabolism. Chemically, the surface of ZnO is rich in -OH groups, which can be readily functionalized by various surface decorating molecules. In this review article, we summarized the current status of the use of ZnO nanomaterials for biomedical applications, such as biomedical imaging (which includes fluorescence, magnetic resonance, positron emission tomography, as well as dual-modality imaging), drug delivery, gene delivery, and biosensing of a wide array of molecules of interest. Research in biomedical applications of ZnO nanomaterials will continue to flourish over the next decade, and much research effort will be needed to develop biocompatible/biodegradable ZnO nanoplatforms for potential clinical translation. PMID:24206130

  4. NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

    Science.gov (United States)

    Martínez-Romero, Marcos; Jonquet, Clement; O'Connor, Martin J; Graybeal, John; Pazos, Alejandro; Musen, Mark A

    2017-06-07

    Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios. Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability

  5. The Importance of Proper Citation of References in Biomedical Articles

    Science.gov (United States)

    Masic, Izet

    2013-01-01

    In scientific circles, the reference is the information that is necessary to the reader in identifying and finding used sources. The basic rule when listing the sources used is that references must be accurate, complete and should be consistently applied. On the other hand, quoting implies verbatim written or verbal repetition of parts of the text or words written by others that can be checked in original. Authors of every new scientific article need to explain how their study or research fits with previous one in the same or similar fields. A typical article in the health sciences refers to approximately 20-30 other articles published in peer reviewed journals, cite once or hundreds times. Citations typically appear in two formats: a) as in-text citations where the sources of information are briefly identified in the text; or b) in the reference list at the end of the publication (book chapter, manuscript, article, etc.) that provides full bibliographic information for each source. Group of publishers met in Vancouver in 1978 and decided to prescribe uniform technical propositions for publication. Adopted in the 1979 by the National Library of Medicine in Bethesda, then the International Committee of Medical Journals Editors (ICMJE), whose review in 1982 entered the official application by 300 international biomedical journals. Authors writing articles for publication in biomedical publications used predominantly citation styles: Vancouver style, Harward style, PubMed style, ICMJE, APA, etc. The paper gives examples of all of these styles of citation to the authors in order to facilitate their applications. Also in this paper is given the review about the problem of plagiarism which becomes more common in the writing of scientific and technical articles in biomedicine. PMID:24167381

  6. The importance of proper citation of references in biomedical articles.

    Science.gov (United States)

    Masic, Izet

    2013-01-01

    In scientific circles, the reference is the information that is necessary to the reader in identifying and finding used sources. The basic rule when listing the sources used is that references must be accurate, complete and should be consistently applied. On the other hand, quoting implies verbatim written or verbal repetition of parts of the text or words written by others that can be checked in original. Authors of every new scientific article need to explain how their study or research fits with previous one in the same or similar fields. A typical article in the health sciences refers to approximately 20-30 other articles published in peer reviewed journals, cite once or hundreds times. Citations typically appear in two formats: a) as in-text citations where the sources of information are briefly identified in the text; or b) in the reference list at the end of the publication (book chapter, manuscript, article, etc.) that provides full bibliographic information for each source. Group of publishers met in Vancouver in 1978 and decided to prescribe uniform technical propositions for publication. Adopted in the 1979 by the National Library of Medicine in Bethesda, then the International Committee of Medical Journals Editors (ICMJE), whose review in 1982 entered the official application by 300 international biomedical journals. Authors writing articles for publication in biomedical publications used predominantly citation styles: Vancouver style, Harward style, PubMed style, ICMJE, APA, etc. The paper gives examples of all of these styles of citation to the authors in order to facilitate their applications. Also in this paper is given the review about the problem of plagiarism which becomes more common in the writing of scientific and technical articles in biomedicine.

  7. The biomedical disciplines and the structure of biomedical and clinical knowledge.

    Science.gov (United States)

    Nederbragt, H

    2000-11-01

    The relation between biomedical knowledge and clinical knowledge is discussed by comparing their respective structures. The knowledge of a disease as a biological phenomenon is constructed by the interaction of facts and theories from the main biomedical disciplines: epidemiology, diagnostics, clinical trial, therapy development and pathogenesis. Although these facts and theories are based on probabilities and extrapolations, the interaction provides a reliable and coherent structure, comparable to a Kuhnian paradigma. In the structure of clinical knowledge, i.e. knowledge of the patient with the disease, not only biomedical knowledge contributes to the structure but also economic and social relations, ethics and personal experience. However, the interaction between each of the participating "knowledges" in clinical knowledge is not based on mutual dependency and accumulation of different arguments from each, as in biomedical knowledge, but on competition and partial exclusion. Therefore, the structure of biomedical knowledge is different from that of clinical knowledge. This difference is used as the basis for a discussion in which the place of technology, evidence-based medicine and the gap between scientific and clinical knowledge are evaluated.

  8. The BioLexicon: a large-scale terminological resource for biomedical text mining

    Directory of Open Access Journals (Sweden)

    Thompson Paul

    2011-10-01

    Full Text Available Abstract Background Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events. Results This article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is

  9. The BioLexicon: a large-scale terminological resource for biomedical text mining

    Science.gov (United States)

    2011-01-01

    Background Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events) involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events. Results This article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized) together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is modelled using the Lexical

  10. CALL FOR PAPERS: Special cluster in Biomedical Optics: honouring Professor Valery Tuchin, Saratov University

    Science.gov (United States)

    Wang, Ruikang K.; Priezzhev, Alexander; Fantini, Sergio

    2004-07-01

    To honour Professor Valery Tuchin, one of the pioneers in biomedical optics, Journal of Physics D: Applied Physics invites manuscript submissions on topics in biomedical optics, for publication in a Special section in May 2005. Papers may cover a variety of topics related to photon propagation in turbid media, spectroscopy and imaging. This Special cluster will reflect the diversity, breadth and impact of Professor Tuchin's contributions to the field of biomedical optics over the course of his distinguished career. Biomedical optics is a recently emerged discipline providing a broad variety of optical techniques and instruments for diagnostic, therapeutic and basic science applications. Together with contributions from other pioneers in the field, Professor Tuchin's work on fundamental and experimental aspects in tissue optics contributed enormously to the formation of this exciting field. Although general submissions in biomedical optics are invited, the Special cluster Editors especially encourage submissions in areas that are explicitly or implicitly influenced by Professor Tuchin's contributions to the field of biomedical optics. Manuscripts submitted to this Special cluster of Journal of Physics D: Applied Physics will be refereed according to the normal criteria and procedures of the journal, in accordance with the following schedule: Deadline for receipt of contributed papers: 31 November 2004 Deadline for acceptance and completion of refereeing process: 28 February 2005 Publication of special issue: May 2005 Please submit your manuscript electronically to jphysd@iop.org or via the Web site at www.iop.org/Journals. Otherwise, please send a copy of your typescript, a set of original figures and a cover letter to: The Publishing Administrator, Journal of Physics D: Applied Physics, Institute of Physics Publishing, Dirac House, Temple Back, Bristol BS1 6BE, United Kingdom. Further information on how to submit may be obtained upon request by e-mailing the

  11. Biomedical text mining for research rigor and integrity: tasks, challenges, directions.

    Science.gov (United States)

    Kilicoglu, Halil

    2017-06-13

    An estimated quarter of a trillion US dollars is invested in the biomedical research enterprise annually. There is growing alarm that a significant portion of this investment is wasted because of problems in reproducibility of research findings and in the rigor and integrity of research conduct and reporting. Recent years have seen a flurry of activities focusing on standardization and guideline development to enhance the reproducibility and rigor of biomedical research. Research activity is primarily communicated via textual artifacts, ranging from grant applications to journal publications. These artifacts can be both the source and the manifestation of practices leading to research waste. For example, an article may describe a poorly designed experiment, or the authors may reach conclusions not supported by the evidence presented. In this article, we pose the question of whether biomedical text mining techniques can assist the stakeholders in the biomedical research enterprise in doing their part toward enhancing research integrity and rigor. In particular, we identify four key areas in which text mining techniques can make a significant contribution: plagiarism/fraud detection, ensuring adherence to reporting guidelines, managing information overload and accurate citation/enhanced bibliometrics. We review the existing methods and tools for specific tasks, if they exist, or discuss relevant research that can provide guidance for future work. With the exponential increase in biomedical research output and the ability of text mining approaches to perform automatic tasks at large scale, we propose that such approaches can support tools that promote responsible research practices, providing significant benefits for the biomedical research enterprise. Published by Oxford University Press 2017. This work is written by a US Government employee and is in the public domain in the US.

  12. The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.

    Science.gov (United States)

    Malone, James; Brown, Andy; Lister, Allyson L; Ison, Jon; Hull, Duncan; Parkinson, Helen; Stevens, Robert

    2014-01-01

    Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility. The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications. The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user's needs. The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com.

  13. [The long pilgrimage of Spanish biomedical journals toward excellence. Who helps? Quality, impact and research merit].

    Science.gov (United States)

    Alfonso, Fernando

    2010-03-01

    Biomedical journals must adhere to strict standards of editorial quality. In a globalized academic scenario, biomedical journals must compete firstly to publish the most relevant original research and secondly to obtain the broadest possible visibility and the widest dissemination of their scientific contents. The cornerstone of the scientific process is still the peer-review system but additional quality criteria should be met. Recently access to medical information has been revolutionized by electronic editions. Bibliometric databases such as MEDLINE, the ISI Web of Science and Scopus offer comprehensive online information on medical literature. Classically, the prestige of biomedical journals has been measured by their impact factor but, recently, other indicators such as SCImago SJR or the Eigenfactor are emerging as alternative indices of a journal's quality. Assessing the scholarly impact of research and the merits of individual scientists remains a major challenge. Allocation of authorship credit also remains controversial. Furthermore, in our Kafkaesque world, we prefer to count rather than read the articles we judge. Quantitative publication metrics (research output) and citations analyses (scientific influence) are key determinants of the scientific success of individual investigators. However, academia is embracing new objective indicators (such as the "h" index) to evaluate scholarly merit. The present review discusses some editorial issues affecting biomedical journals, currently available bibliometric databases, bibliometric indices of journal quality and, finally, indicators of research performance and scientific success. Copyright 2010 SEEN. Published by Elsevier Espana. All rights reserved.

  14. [International regulation of ethics committees on biomedical research as protection mechanisms for people: analysis of the Additional Protocol to the Convention on Human Rights and Biomedicine, concerning Biomedical Research of the Council of Europe].

    Science.gov (United States)

    de Lecuona, Itziar

    2013-01-01

    The article explores and analyses the content of the Council of Europe's Additional Protocol to the Convention on Human Rights and Biomedicine concerning Biomedical Research regarding the standard legal instrument in biomedical research, issued by an international organization with leadership in bioethics. This implies ethics committees are mechanisms of protection of humans in biomedical research and not mere bureaucratic agencies and that a sound inescapable international regulatory framework exists for States to regulate biomedical research. The methodology used focuses on the analysis of the background, the context in which it is made and the nature and scope of the Protocol. It also identifies and analyses the characteristics and functions of ethics committees in biomedical research and, in particular, the information that should be provided to this bodies to develop their functions previously, during and at the end of research projects. This analysis will provide guidelines, suggestions and conclusions for the awareness and training of members of these committees in order to influence the daily practice. This paper may also be of interest to legal practitioners who work in different areas of biomedical research. From this practical perspective, the article examines the legal treatment of the Protocol to meet new challenges and classic issues in research: the treatment of human biological samples, the use of placebos, avoiding double standards, human vulnerability, undue influence and conflicts of interest, among others. Also, from a critical view, this work links the legal responses to develop work procedures that are required for an effective performance of the functions assigned of ethics committees in biomedical research. An existing international legal response that lacks doctrinal standards and provides little support should, however, serve as a guide and standard to develop actions that allow ethics committees -as key bodies for States- to advance in

  15. Computational Biomechanics Theoretical Background and BiologicalBiomedical Problems

    CERN Document Server

    Tanaka, Masao; Nakamura, Masanori

    2012-01-01

    Rapid developments have taken place in biological/biomedical measurement and imaging technologies as well as in computer analysis and information technologies. The increase in data obtained with such technologies invites the reader into a virtual world that represents realistic biological tissue or organ structures in digital form and allows for simulation and what is called “in silico medicine.” This volume is the third in a textbook series and covers both the basics of continuum mechanics of biosolids and biofluids and the theoretical core of computational methods for continuum mechanics analyses. Several biomechanics problems are provided for better understanding of computational modeling and analysis. Topics include the mechanics of solid and fluid bodies, fundamental characteristics of biosolids and biofluids, computational methods in biomechanics analysis/simulation, practical problems in orthopedic biomechanics, dental biomechanics, ophthalmic biomechanics, cardiovascular biomechanics, hemodynamics...

  16. Raman Plus X: Biomedical Applications of Multimodal Raman Spectroscopy.

    Science.gov (United States)

    Das, Nandan K; Dai, Yichuan; Liu, Peng; Hu, Chuanzhen; Tong, Lieshu; Chen, Xiaoya; Smith, Zachary J

    2017-07-07

    Raman spectroscopy is a label-free method of obtaining detailed chemical information about samples. Its compatibility with living tissue makes it an attractive choice for biomedical analysis, yet its translation from a research tool to a clinical tool has been slow, hampered by fundamental Raman scattering issues such as long integration times and limited penetration depth. In this review we detail the how combining Raman spectroscopy with other techniques yields multimodal instruments that can help to surmount the translational barriers faced by Raman alone. We review Raman combined with several optical and non-optical methods, including fluorescence, elastic scattering, OCT, phase imaging, and mass spectrometry. In each section we highlight the power of each combination along with a brief history and presentation of representative results. Finally, we conclude with a perspective detailing both benefits and challenges for multimodal Raman measurements, and give thoughts on future directions in the field.

  17. Biomedical hypothesis generation by text mining and gene prioritization.

    Science.gov (United States)

    Petric, Ingrid; Ligeti, Balazs; Gyorffy, Balazs; Pongor, Sandor

    2014-01-01

    Text mining methods can facilitate the generation of biomedical hypotheses by suggesting novel associations between diseases and genes. Previously, we developed a rare-term model called RaJoLink (Petric et al, J. Biomed. Inform. 42(2): 219-227, 2009) in which hypotheses are formulated on the basis of terms rarely associated with a target domain. Since many current medical hypotheses are formulated in terms of molecular entities and molecular mechanisms, here we extend the methodology to proteins and genes, using a standardized vocabulary as well as a gene/protein network model. The proposed enhanced RaJoLink rare-term model combines text mining and gene prioritization approaches. Its utility is illustrated by finding known as well as potential gene-disease associations in ovarian cancer using MEDLINE abstracts and the STRING database.

  18. Biomedical Research Institute, Biomedical Research Foundation of Northwest Louisiana, Shreveport, Louisiana

    International Nuclear Information System (INIS)

    1992-01-01

    Department of Energy (DOE) has prepared an Environmental Assessment (EA), DOE/EA-0789, evaluating the environmental impacts of construction and operation of a Biomedical Research Institute (BRI) at the Louisiana State University (LSU) Medical Center, Shreveport, Louisiana. The purpose of the BRI is to accelerate the development of biomedical research in cardiovascular disease, molecular biology, and neurobiology. Based on the analyses in the EA, DOE has determined that the proposed action does not constitute a major Federal action significantly affecting the quality of the human environment within the meaning of the National Environmental Policy Act of 1969 (NEPA). Therefore, the preparation of an Environmental Impact Statement is not required

  19. The development of biomedical engineering as experienced by one biomedical engineer.

    Science.gov (United States)

    Newell, Jonathan C

    2012-12-12

    This personal essay described the development of the field of Biomedical Engineering from its early days, from the perspective of one who lived through that development. It describes the making of a major invention using data that had been rejected by other scientists, the re-discovery of an obscure fact of physiology and its use in developing a major medical instrument, the development of a new medical imaging modality, and the near-death rescue of a research project. The essay concludes with comments about the development and present status of impedance imaging, and recent changes in the evolution of biomedical engineering as a field.

  20. Synergies and Distinctions between Computational Disciplines in Biomedical Research: Perspective from the Clinical and Translational Science Award Programs

    Science.gov (United States)

    Bernstam, Elmer V.; Hersh, William R.; Johnson, Stephen B.; Chute, Christopher G.; Nguyen, Hien; Sim, Ida; Nahm, Meredith; Weiner, Mark; Miller, Perry; DiLaura, Robert P.; Overcash, Marc; Lehmann, Harold P.; Eichmann, David; Athey, Brian D.; Scheuermann, Richard H.; Anderson, Nick; Starren, Justin B.; Harris, Paul A.; Smith, Jack W.; Barbour, Ed; Silverstein, Jonathan C.; Krusch, David A.; Nagarajan, Rakesh; Becich, Michael J.

    2010-01-01

    Clinical and translational research increasingly requires computation. Projects may involve multiple computationally-oriented groups including information technology (IT) professionals, computer scientists and biomedical informaticians. However, many biomedical researchers are not aware of the distinctions among these complementary groups, leading to confusion, delays and sub-optimal results. Although written from the perspective of clinical and translational science award (CTSA) programs within academic medical centers, the paper addresses issues that extend beyond clinical and translational research. The authors describe the complementary but distinct roles of operational IT, research IT, computer science and biomedical informatics using a clinical data warehouse as a running example. In general, IT professionals focus on technology. The authors distinguish between two types of IT groups within academic medical centers: central or administrative IT (supporting the administrative computing needs of large organizations) and research IT (supporting the computing needs of researchers). Computer scientists focus on general issues of computation such as designing faster computers or more efficient algorithms, rather than specific applications. In contrast, informaticians are concerned with data, information and knowledge. Biomedical informaticians draw on a variety of tools, including but not limited to computers, to solve information problems in health care and biomedicine. The paper concludes with recommendations regarding administrative structures that can help to maximize the benefit of computation to biomedical research within academic health centers. PMID:19550198

  1. Blockchain distributed ledger technologies for biomedical and health care applications.

    Science.gov (United States)

    Kuo, Tsung-Ting; Kim, Hyeon-Eui; Ohno-Machado, Lucila

    2017-11-01

    To introduce blockchain technologies, including their benefits, pitfalls, and the latest applications, to the biomedical and health care domains. Biomedical and health care informatics researchers who would like to learn about blockchain technologies and their applications in the biomedical/health care domains. The covered topics include: (1) introduction to the famous Bitcoin crypto-currency and the underlying blockchain technology; (2) features of blockchain; (3) review of alternative blockchain technologies; (4) emerging nonfinancial distributed ledger technologies and applications; (5) benefits of blockchain for biomedical/health care applications when compared to traditional distributed databases; (6) overview of the latest biomedical/health care applications of blockchain technologies; and (7) discussion of the potential challenges and proposed solutions of adopting blockchain technologies in biomedical/health care domains. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.

  2. 3rd International Conference on Nanotechnologies and Biomedical Engineering

    CERN Document Server

    Tiginyanu, Ion

    2016-01-01

    This volume presents the proceedings of the 3rd International Conference on Nanotechnologies and Biomedical Engineering which was held on September 23-26, 2015 in Chisinau, Republic of Moldova. ICNBME-2015 continues the series of International Conferences in the field of nanotechnologies and biomedical engineering. It aims at bringing together scientists and engineers dealing with fundamental and applied research for reporting on the latest theoretical developments and applications involved in the fields. Topics include Nanotechnologies and nanomaterials Plasmonics and metamaterials Bio-micro/nano technologies Biomaterials Biosensors and sensors systems Biomedical instrumentation Biomedical signal processing Biomedical imaging and image processing Molecular, cellular and tissue engineering Clinical engineering, health technology management and assessment; Health informatics, e-health and telemedicine Biomedical engineering education Nuclear and radiation safety and security Innovations and technology transfer...

  3. Building a biomedical cyberinfrastructure for collaborative research.

    Science.gov (United States)

    Schad, Peter A; Mobley, Lee Rivers; Hamilton, Carol M

    2011-05-01

    For the potential power of genome-wide association studies (GWAS) and translational medicine to be realized, the biomedical research community must adopt standard measures, vocabularies, and systems to establish an extensible biomedical cyberinfrastructure. Incorporating standard measures will greatly facilitate combining and comparing studies via meta-analysis. Incorporating consensus-based and well-established measures into various studies should reduce the variability across studies due to attributes of measurement, making findings across studies more comparable. This article describes two well-established consensus-based approaches to identifying standard measures and systems: PhenX (consensus measures for phenotypes and eXposures), and the Open Geospatial Consortium (OGC). NIH support for these efforts has produced the PhenX Toolkit, an assembled catalog of standard measures for use in GWAS and other large-scale genomic research efforts, and the RTI Spatial Impact Factor Database (SIFD), a comprehensive repository of geo-referenced variables and extensive meta-data that conforms to OGC standards. The need for coordinated development of cyberinfrastructure to support measures and systems that enhance collaboration and data interoperability is clear; this paper includes a discussion of standard protocols for ensuring data compatibility and interoperability. Adopting a cyberinfrastructure that includes standard measures and vocabularies, and open-source systems architecture, such as the two well-established systems discussed here, will enhance the potential of future biomedical and translational research. Establishing and maintaining the cyberinfrastructure will require a fundamental change in the way researchers think about study design, collaboration, and data storage and analysis. Copyright © 2011 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  4. 5th International Conference on Biomedical Engineering in Vietnam

    CERN Document Server

    Phuong, Tran

    2015-01-01

    This volume presents the proceedings of the Fifth International Conference on the Development of Biomedical Engineering in Vietnam which was held from June 16-18, 2014 in Ho Chi Minh City. The volume reflects the progress of Biomedical Engineering and discusses problems and solutions. I aims identifying new challenges, and shaping future directions for research in biomedical engineering fields including medical instrumentation, bioinformatics, biomechanics, medical imaging, drug delivery therapy, regenerative medicine and entrepreneurship in medical devices.

  5. Quality assurance in biomedical neutron activation analysis

    International Nuclear Information System (INIS)

    1984-01-01

    The summary report represents an attempt to identify some of the possible sources of error in in vitro neutron activation analysis of trace elements applied to specimens of biomedical origin and to advise on practical means to avoid them. The report is intended as guidance for all involved in analysis, including sample collection and preparation for analysis. All these recommendations constitute part of quality assurance which is here taken to encompass the two concepts - quality control and quality assessment. Quality control is the mechanism established to control errors, while quality assessment is the mechanism used to verify that the analytical procedure is operating within acceptable limits

  6. CMT for biomedical and other applications

    Energy Technology Data Exchange (ETDEWEB)

    Spanne, P. [ESRF, Grenoble (France)

    1997-02-01

    This session includes two presentations describing applications for x-ray tomography using synchrotron radiation for biomedical uses and fluid flow modeling, and outlines advantages for using monoenergetic x-rays. Contrast mechanisms are briefly described and several graphs of absorbed doses and scattering of x-rays are included. Also presented are schematic diagrams of computerized tomographic instrumentation with camera head. A brief description of goals for a real time tomographic system and expected improvements to the system are described. Color photomicrographs of the Berea Sandstone and human bone are provided, as well as a 3-D microtomographic reconstruction of a human vertebra sample.

  7. Research on pressure sensors for biomedical instruments

    Science.gov (United States)

    Angell, J. B.

    1975-01-01

    The development of a piezo-resistive pressure transducer is discussed suitable for recording pressures typically encountered in biomedical applications. The pressure transducer consists of a thin silicon diaphragm containing four strain-sensitive resistors, and is fabricated using silicon monolithic integrated-circuit technology. The pressure transducers can be as small as 0.7 mm outer diameter, and are, as a result, suitable for mounting at the tip of a catheter. Pressure-induced stress in the diaphragm is sensed by the resistors, which are interconnected to form a Wheatstone bridge.

  8. Engineered magnetic nanoparticles for biomedical applications.

    Science.gov (United States)

    Canfarotta, Francesco; Piletsky, Sergey A

    2014-02-01

    In the past decades, magnetic nanoparticles (MNPs) have been used in wide range of diverse applications, ranging from separation to sensing. Here, synthesis and applications of functionalized MNPs in the biomedical field are discussed, in particular in drug delivery, imaging, and cancer therapy, highlighting also recent progresses in the development of multifunctional and stimuli-responsive MNPs. The role of their size, composition, and surface functionalization is analyzed, together with their biocompatibility issues. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Qality assurance program for biomedical radiography

    International Nuclear Information System (INIS)

    Korolyuk, I.P.; Gurvich, A.M.

    1986-01-01

    Essence and purposes of quality assurance program (QAP) in biomedical radiography of population are considered. This program can be determined as organizational and executive activity of radiological service personnel providing the necessary for diagnosis quality of investigation at minimum radiation loads to patients and personnel and the lowest cost of the investigation. QAP includes quality control of technical means and of investigation implementation. Attention is paid to means and methods of quality control. QAP organizational problems are discussed. Necessity of further investigations and technical developments in this direction is noted

  10. High performance flexible electronics for biomedical devices.

    Science.gov (United States)

    Salvatore, Giovanni A; Munzenrieder, Niko; Zysset, Christoph; Kinkeldei, Thomas; Petti, Luisa; Troster, Gerhard

    2014-01-01

    Plastic electronics is soft, deformable and lightweight and it is suitable for the realization of devices which can form an intimate interface with the body, be implanted or integrated into textile for wearable and biomedical applications. Here, we present flexible electronics based on amorphous oxide semiconductors (a-IGZO) whose performance can achieve MHz frequency even when bent around hair. We developed an assembly technique to integrate complex electronic functionalities into textile while preserving the softness of the garment. All this and further developments can open up new opportunities in health monitoring, biotechnology and telemedicine.

  11. Selective laser sintering in biomedical engineering.

    Science.gov (United States)

    Mazzoli, Alida

    2013-03-01

    Selective laser sintering (SLS) is a solid freeform fabrication technique, developed by Carl Deckard for his master's thesis at the University of Texas, patented in 1989. SLS manufacturing is a technique that produces physical models through a selective solidification of a variety of fine powders. SLS technology is getting a great amount of attention in the clinical field. In this paper the characteristics features of SLS and the materials that have been developed for are reviewed together with a discussion on the principles of the above-mentioned manufacturing technique. The applications of SLS in tissue engineering, and at-large in the biomedical field, are reviewed and discussed.

  12. Data Analysis in Experimental Biomedical Research

    DEFF Research Database (Denmark)

    Markovich, Dmitriy

    This thesis covers two non-related topics in experimental biomedical research: data analysis in thrombin generation experiments (collaboration with Novo Nordisk A/S), and analysis of images and physiological signals in the context of neurovascular signalling and blood flow regulation in the brain...... to critically assess and compare obtained results. We reverse engineered the data analysis performed by CAT, a de facto standard assay in the field. This revealed a number of possibilities to improve its methods of data analysis. We found that experimental calibration data is described well with textbook...

  13. Functionalized conjugated polyelectrolytes design and biomedical applications

    CERN Document Server

    Wang, Shu

    2014-01-01

    Functionalized Conjugated Polyelectrolytes presents a comprehensive review of these polyelectrolytes and their biomedical applications. Basic aspects like molecular design and optoelectronic properties are covered in the first chapter. Emphasis is placed on the various applications including sensing (chemical and biological), disease diagnosis, cell imaging, drug/gene delivery and disease treatment. This book explores a multi-disciplinary topic of interest to researchers working in the fields of chemistry, materials, biology and medicine. It also offers an integrated perspective on both basic research and application issues. Functionalized conjugated polyelectrolyte materials, which have already drawn considerable interest, will become a major new direction for biomedicine development.

  14. [Dendrimers in biomedical sciences and nanotechnology].

    Science.gov (United States)

    Sekowski, Szymon; Miłowska, Katarzyna; Gabryelak, Teresa

    2008-12-30

    Dendrimers are relatively new, hyper-branched polymers that have many interesting abilities. Dendrimers could be used, for example, as drug or gene carriers, contrast agents, sensors for different metal ions, and in developing innovation technology. These spherical polymers are also characterized by pharmacological activity against different bacterial and viral diseases. Dendrimers are currently being intensively investigated as anti-prion and anti-amyloid fibril agents. They can be used to build specific dendrimer films to be applied in modern technology. This review describes different uses of dendrimer particles in biomedical sciences and nanotechnology and shows advantages of their application.

  15. Research groups in biomedical sciences. Some recommendations

    Directory of Open Access Journals (Sweden)

    Ricardo Cardona

    2015-07-01

    Full Text Available Despite the growing number of scientific publications reflecting a greater number of people interested in the biomedical sciences, many research groups disappear secondary to poor internal organization. From the review of the available literature, we generate a series of recommendations that may be useful for the creation of a research group or to improve the productivity of an existing group. Fluid communication between its members with a common overall policy framework allows the creation of a good foundation that will lead to the consolidation of the group.

  16. Introduction to Statistics for Biomedical Engineers

    CERN Document Server

    Ropella, Kristina

    2007-01-01

    There are many books written about statistics, some brief, some detailed, some humorous, some colorful, and some quite dry. Each of these texts is designed for a specific audience. Too often, texts about statistics have been rather theoretical and intimidating for those not practicing statistical analysis on a routine basis. Thus, many engineers and scientists, who need to use statistics much more frequently than calculus or differential equations, lack sufficient knowledge of the use of statistics. The audience that is addressed in this text is the university-level biomedical engineering stud

  17. EVALUATION OF BIOMEDICAL WASTE MANAGEMENT PRACTICES IN MULTI-SPECIALITY TERTIARY HOSPITAL

    Directory of Open Access Journals (Sweden)

    Shalini Srivastav

    2010-06-01

    Full Text Available Background: Biomedical Waste (BMW, collection and proper disposal has become a significant concern for both the medical and the general community The scientific “Hospital waste Management “is of vital importance as its improper management poses risks to the health care workers ,waste handlers patients, community in general and largely the environment. Objectives: (i To assess current practices of Bio-medical Waste management including generation, collection, transportation storage, treatment and disposal technologies in tertiary health care center. (ii To assess health andsafetypracticesfor the health care personnel involved in Bio-Medical waste Management. Materials and Methods: Waste management practices in tertiary care-centre was studied during May 2010 June 2010. The information/data regarding Bio-Medical Waste Management practices and safety was collected by way of semi structured interview, proforma being the one used for WASTE AUDITING QUESTIONNAIRE. The information collected was verified by personal observations of waste management practices in each ward of hospital. Results : SRMS-IMS generates 1. 25Kgs waste per bed per day and maximum waste is generated in wards. The institute has got separate color coded bins in each ward for collection of waste but segregation practices needs to be more refined. The safety measures taken by health care workers was not satisfactory it was not due to unavailability of Personal protective measures but because of un-awareness of health hazards which may occur due to improper waste management practices. Thus it is concluded that there should be strict implementation of a waste management policy set up in the institute, training and motivation must be given paramount importance to meet the current needs and standard of bio-medical waste management.

  18. Biomedical imaging graduate curricula and courses: report from the 2005 Whitaker Biomedical Engineering Educational Summit.

    Science.gov (United States)

    Louie, Angelique; Izatt, Joseph; Ferrara, Katherine

    2006-02-01

    We present an overview of graduate programs in biomedical imaging that are currently available in the US. Special attention is given to the emerging technologies of molecular imaging and biophotonics. Discussions from the workshop on Graduate Imaging at the 2005 Whitaker Educational Summit meeting are summarized.

  19. Signal and image analysis for biomedical and life sciences

    CERN Document Server

    Sun, Changming; Pham, Tuan D; Vallotton, Pascal; Wang, Dadong

    2014-01-01

    With an emphasis on applications of computational models for solving modern challenging problems in biomedical and life sciences, this book aims to bring collections of articles from biologists, medical/biomedical and health science researchers together with computational scientists to focus on problems at the frontier of biomedical and life sciences. The goals of this book are to build interactions of scientists across several disciplines and to help industrial users apply advanced computational techniques for solving practical biomedical and life science problems. This book is for users in t

  20. Accreditation of Biomedical Engineering Programs in Europe - Challenge and Opportunity

    National Research Council Canada - National Science Library

    Nagel, Joachim

    2001-01-01

    Today, more than 100 universities and polytechnic schools in Europe offer educational programs in Biomedical Engineering at all academic levels, but without any international coordination of contents...