Diet and psychological health.

PubMed

Miller, M

1996-09-01

This article reviews research that suggests a relationship between diet and psychological symptoms. Mind-body dualism (as it relates to clinical practice) and the limited role of nutrition in mainstream biomedical training and treatment are discussed as background issues. Two areas of inquiry that have generated relevant research findings in this area are reviewed: (1) orthomolecular theory and vitamin deficiencies, and (2) clinical ecology/environmental medicine theory and the impact of "food allergies." Although clinical case reports and promising research findings have been reported, the impact of diet on psychological health is neither widely accepted nor integrated into mental health treatment methods. Ongoing research findings in brain biochemistry and psychoneuroimmunology point to communication pathways that can provide a clearer understanding of the links between nutritional intake, central nervous system and immune function, and psychological health status. These findings may lead to greater acceptance of dietary treatment approaches among health practitioners addressing psychological disorders.

Incorporating collaboratory concepts into informatics in support of translational interdisciplinary biomedical research

PubMed Central

Lee, E. Sally; McDonald, David W.; Anderson, Nicholas; Tarczy-Hornoch, Peter

2008-01-01

Due to its complex nature, modern biomedical research has become increasingly interdisciplinary and collaborative in nature. Although a necessity, interdisciplinary biomedical collaboration is difficult. There is, however, a growing body of literature on the study and fostering of collaboration in fields such as computer supported cooperative work (CSCW) and information science (IS). These studies of collaboration provide insight into how to potentially alleviate the difficulties of interdisciplinary collaborative research. We, therefore, undertook a cross cutting study of science and engineering collaboratories to identify emergent themes. We review many relevant collaboratory concepts: (a) general collaboratory concepts across many domains: communication, common workspace and coordination, and data sharing and management, (b) specific collaboratory concepts of particular biomedical relevance: data integration and analysis, security structure, metadata and data provenance, and interoperability and data standards, (c) environmental factors that support collaboratories: administrative and management structure, technical support, and available funding as critical environmental factors, and (d) future considerations for biomedical collaboration: appropriate training and long-term planning. In our opinion, the collaboratory concepts we discuss can guide planning and design of future collaborative infrastructure by biomedical informatics researchers to alleviate some of the difficulties of interdisciplinary biomedical collaboration. PMID:18706852

Applicability Analysis of Validation Evidence for Biomedical Computational Models

DOE PAGES

Pathmanathan, Pras; Gray, Richard A.; Romero, Vicente J.; ...

2017-09-07

Computational modeling has the potential to revolutionize medicine the way it transformed engineering. However, despite decades of work, there has only been limited progress to successfully translate modeling research to patient care. One major difficulty which often occurs with biomedical computational models is an inability to perform validation in a setting that closely resembles how the model will be used. For example, for a biomedical model that makes in vivo clinically relevant predictions, direct validation of predictions may be impossible for ethical, technological, or financial reasons. Unavoidable limitations inherent to the validation process lead to challenges in evaluating the credibilitymore » of biomedical model predictions. Therefore, when evaluating biomedical models, it is critical to rigorously assess applicability, that is, the relevance of the computational model, and its validation evidence to the proposed context of use (COU). However, there are no well-established methods for assessing applicability. In this paper, we present a novel framework for performing applicability analysis and demonstrate its use with a medical device computational model. The framework provides a systematic, step-by-step method for breaking down the broad question of applicability into a series of focused questions, which may be addressed using supporting evidence and subject matter expertise. The framework can be used for model justification, model assessment, and validation planning. While motivated by biomedical models, it is relevant to a broad range of disciplines and underlying physics. Finally, the proposed applicability framework could help overcome some of the barriers inherent to validation of, and aid clinical implementation of, biomedical models.« less

Applicability Analysis of Validation Evidence for Biomedical Computational Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pathmanathan, Pras; Gray, Richard A.; Romero, Vicente J.

Computational modeling has the potential to revolutionize medicine the way it transformed engineering. However, despite decades of work, there has only been limited progress to successfully translate modeling research to patient care. One major difficulty which often occurs with biomedical computational models is an inability to perform validation in a setting that closely resembles how the model will be used. For example, for a biomedical model that makes in vivo clinically relevant predictions, direct validation of predictions may be impossible for ethical, technological, or financial reasons. Unavoidable limitations inherent to the validation process lead to challenges in evaluating the credibilitymore » of biomedical model predictions. Therefore, when evaluating biomedical models, it is critical to rigorously assess applicability, that is, the relevance of the computational model, and its validation evidence to the proposed context of use (COU). However, there are no well-established methods for assessing applicability. In this paper, we present a novel framework for performing applicability analysis and demonstrate its use with a medical device computational model. The framework provides a systematic, step-by-step method for breaking down the broad question of applicability into a series of focused questions, which may be addressed using supporting evidence and subject matter expertise. The framework can be used for model justification, model assessment, and validation planning. While motivated by biomedical models, it is relevant to a broad range of disciplines and underlying physics. Finally, the proposed applicability framework could help overcome some of the barriers inherent to validation of, and aid clinical implementation of, biomedical models.« less

Development and Evaluation of Thesauri-Based Bibliographic Biomedical Search Engine

ERIC Educational Resources Information Center

Alghoson, Abdullah

2017-01-01

Due to the large volume and exponential growth of biomedical documents (e.g., books, journal articles), it has become increasingly challenging for biomedical search engines to retrieve relevant documents based on users' search queries. Part of the challenge is the matching mechanism of free-text indexing that performs matching based on…

Bioethical conflicts between Muslim patients and German physicians and the principles of biomedical ethics.

PubMed

Ilkilic, Ilhan

2002-01-01

In the age of globalisation, more and more people who are members of different religions and cultures live in the same society. This situation tends to create many conflicts in different areas of life and not least in the health care system, a fact which raises a number of bioethical issues. The cultural and religious differences between patient and physician can be a cause of bioethical conflicts and therefore represent a challenge for biomedical ethics. The confrontation between Turkish Muslin patients and the German health care system is a convenient example of this situation. The Muslim Turks came to Germany 40 years ago as industrial workers. Their value system had been shaped by traditional and Islamic parameters in Turkey. With this value system, they now found themselves in the German modern health care system. In many fields of modern medicine there are areas of potential conflict of values, where a Muslin patient will argue differently from a secular or Christian person. In an ethical conflict between two individuals who are members of different cultures, it is necessary to make sure that the ethical concept which is to be used for resolving the problem is relevant. In this particular case, both the Islamic legal responses (fatwa) and the classical theories of biomedical ethics are often insufficient. This paper tries to give a brief outline of these bioethical conflicts and discuss these conflicts with regard to the principle of respect for autonomy in the concept of "principilism," as introduced by T.L. Beauchamp and J.F. Childress. The central question is whether this bioethical concept is able to analyse and to help solve the kinds of ethical conflicts which involve transcultural dimensions. This question is discussed with some consideration of the ongoing debate about universalism versus relativism in biomedical ethics.

View from... Photonics Meets Biology Summer School: The bio-mission of diode lasers

NASA Astrophysics Data System (ADS)

Won, Rachel

2015-12-01

Diode lasers represent a viable alternative to light sources used in many biomedical applications. Their ongoing development will further increase their importance, offering not only multiple wavelength ranges, but also higher power levels.

Biomedical databases: protecting privacy and promoting research.

PubMed

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.

Space Product Development (SPD)

NASA Image and Video Library

2003-01-12

Experiments to seek solutions for a range of biomedical issues are at the heart of several investigations that will be hosted by the Commercial Instrumentation Technology Associates (ITA), Inc. Biomedical Experiments (CIBX-2) payload. CIBX-2 is unique, encompassing more than 20 separate experiments including cancer research, commercial experiments, and student hands-on experiments from 10 schools as part of ITA's ongoing University Among the Stars program. Valerie Cassanto of ITA checks the Canadian Protein Crystallization Experiment (CAPE) carried by STS-86 to Mir in 1997. The experiments are sponsored by NASA's Space Product Development Program (SPD).

Biomedical research and aerospace technology applications

NASA Technical Reports Server (NTRS)

1971-01-01

The accomplishments and activities of an Applications Team for biomedical subjects are presented. The team attempts to couple the technological problems and requirements in medicine with the relevant aerospace technology and, in particular, NASA-generated technology. The team actively engages in identifying these problems through direct contact with medical staffs or problem originators. The identification and specification of medical problems is followed by a search for technology which may be relevant to solutions to these problems.

Using Biomedically Relevant Multimedia Content in an Introductory Physics Course for Life Science and Pre-Health Students

ERIC Educational Resources Information Center

Mylott, Elliot; Kutschera, Ellynne; Dunlap, Justin C.; Christensen, Warren; Widenhorn, Ralf

2016-01-01

We will describe a one-quarter pilot algebra-based introductory physics course for pre-health and life science majors. The course features videos with biomedical experts and cogent biomedically inspired physics content. The materials were used in a flipped classroom as well as an all-online environment where students interacted with multimedia…

Behavioral Health and Performance at NASA JSC: Recent Successes and Future Plan for BHP Research and Operations

NASA Technical Reports Server (NTRS)

Leveton, L. B.; VanderArk, S. T.

2014-01-01

The Behavioral Health and Performance discipline at NASA Johnson Space Center is organized into two distinct Divisions (Biomedical Research and Environmental Science Division and Space and Clinical Operations Division) but is integrated and interrelated in its day-to-day work. Ongoing operations supporting NASA's spaceflight goals benefit from the research portfolios that address risks to mission success. Similarly, these research portfolios are informed by operations to ensure investigations stay relevant given the dynamic environment of spaceflight. There are many success stories that can be presented where initial work begun as a BHP Research project, and funded through the Human Research Program, was fully implemented in operations or addressed an operational need. Examples include improving effectiveness of the debriefings used within Mission Control by the Mission Operations Directorate and countermeasures for fatigue management. There is also ongoing collaboration with research and operations for developing selection methods for future generation astronauts, and to enhance and inform the current family support function. The objective of this panel is to provide examples of recent success stories, describe areas where close collaboration is benefitting ongoing research and operations, and summarize how this will come together as NASA plans for the one year ISS mission - a unique opportunity for both BHP operations and research to learn more about preparing and supporting crewmembers for extended missions in space. The proposed panel will be comprised of six presentations, each describing a unique aspect of research or operations and the benefits to current and future spaceflight.

Environmental/Biomedical Terminology Index

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 groupedmore » 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).« less

The SWAN biomedical discourse ontology.

PubMed

Ciccarese, Paolo; Wu, Elizabeth; Wong, Gwen; Ocana, Marco; Kinoshita, June; Ruttenberg, Alan; Clark, Tim

2008-10-01

Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. SWAN (Semantic Web Applications in Neuromedicine) is an interdisciplinary project to develop a practical, common, semantically structured, framework for biomedical discourse initially applied, but not limited, to significant problems in Alzheimer Disease (AD) research. The SWAN ontology has been developed in the context of building a series of applications for biomedical researchers, as well as in extensive discussions and collaborations with the larger bio-ontologies community. In this paper, we present and discuss the SWAN ontology of biomedical discourse. We ground its development theoretically, present its design approach, explain its main classes and their application, and show its relationship to other ongoing activities in biomedicine and bio-ontologies.

Enhancing biomedical text summarization using semantic relation extraction.

PubMed

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.

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).

PubMed

Jiang, Xiangying; Ringwald, Martin; Blake, Judith; Shatkay, Hagit

2017-01-01

The Gene Expression Database (GXD) is a comprehensive online database within the Mouse Genome Informatics resource, aiming to provide available information about endogenous gene expression during mouse development. The information stems primarily from many thousands of biomedical publications that database curators must go through and read. Given the very large number of biomedical papers published each year, automatic document classification plays an important role in biomedical research. Specifically, an effective and efficient document classifier is needed for supporting the GXD annotation workflow. We present here an effective yet relatively simple classification scheme, which uses readily available tools while employing feature selection, aiming to assist curators in identifying publications relevant to GXD. We examine the performance of our method over a large manually curated dataset, consisting of more than 25 000 PubMed abstracts, of which about half are curated as relevant to GXD while the other half as irrelevant to GXD. In addition to text from title-and-abstract, we also consider image captions, an important information source that we integrate into our method. We apply a captions-based classifier to a subset of about 3300 documents, for which the full text of the curated articles is available. The results demonstrate that our proposed approach is robust and effectively addresses the GXD document classification. Moreover, using information obtained from image captions clearly improves performance, compared to title and abstract alone, affirming the utility of image captions as a substantial evidence source for automatically determining the relevance of biomedical publications to a specific subject area. www.informatics.jax.org. © The Author(s) 2017. Published by Oxford University Press.

Biomedical Biopolymers, their Origin and Evolution in Biomedical Sciences: A Systematic Review

PubMed Central

Yadav, Harsh; Shah, Veena Gowri; Shah, Gaurav; Dhaka, Gaurav

2015-01-01

Biopolymers provide a plethora of applications in the pharmaceutical and medical applications. A material that can be used for biomedical applications like wound healing, drug delivery and tissue engineering should possess certain properties like biocompatibility, biodegradation to non-toxic products, low antigenicity, high bio-activity, processability to complicated shapes with appropriate porosity, ability to support cell growth and proliferation and appropriate mechanical properties, as well as maintaining mechanical strength. This paper reviews biodegradable biopolymers focusing on their potential in biomedical applications. Biopolymers most commonly used and most abundantly available have been described with focus on the properties relevant to biomedical importance. PMID:26501034

Astronaut William Gregory activates Liquids Mixing Apparatus

NASA Technical Reports Server (NTRS)

2003-01-01

Experiments to seek solutions for a range of biomedical issues are at the heart of several investigations that will be hosted by the Commercial Instrumentation Technology Associates (ITA), Inc. Biomedical Experiments (CIBX-2) payload. CIBX-2 is unique, encompassing more than 20 separate experiments including cancer research, commercial experiments, and student hands-on experiments from 10 schools as part of ITA's ongoing University Among the Stars program. Astronaut William G. Gregory activates Liquids Mixing Apparatus (LMA) vials during STS-67. Other LMAs hang at top on the face of the middeck locker array. The experiments are sponsored under NASA's Space Product Development Program (SPD).

Space Product Development (SPD)

NASA Image and Video Library

2003-01-12

Experiments to seek solutions for a range of biomedical issues are at the heart of several investigations that will be hosted by the Commercial Instrumentation Technology Associates (ITA), Inc. Biomedical Experiments (CIBX-2) payload. CIBX-2 is unique, encompassing more than 20 separate experiments including cancer research, commercial experiments, and student hands-on experiments from 10 schools as part of ITA's ongoing University Among the Stars program. Astronaut William G. Gregory activates Liquids Mixing Apparatus (LMA) vials during STS-67. Other LMAs hang at top on the face of the middeck locker array. The experiments are sponsored under NASA's Space Product Development Program (SPD).

Lignin biopolymer based triboelectric nanogenerators

NASA Astrophysics Data System (ADS)

Bao, Yukai; Wang, Ruoxing; Lu, Yunmei; Wu, Wenzhuo

2017-07-01

Ongoing research in triboelectric nanogenerators (TENGs) focuses on increasing power generation, but obstacles concerning economical and eco-friendly utilization of TENGs continue to prevail. Being the second most abundant biopolymer on earth, lignin offers a valuable opportunity for low-cost TENG applications in biomedical devices, benefitting from its biodegradability and biocompatibility. Here, we develop for the first time a lignin biopolymer based TENGs for harvesting mechanical energy in the environment, which shows great potential for self-powered biomedical devices among other applications and opens doors to new technologies that utilize otherwise wasted materials for economically feasible and ecologically friendly production of energy devices.

Single cell biology beyond the era of antibodies: relevance, challenges, and promises in biomedical research.

PubMed

Abraham, Parvin; Maliekal, Tessy Thomas

2017-04-01

Research of the past two decades has proved the relevance of single cell biology in basic research and translational medicine. Successful detection and isolation of specific subsets is the key to understand their functional heterogeneity. Antibodies are conventionally used for this purpose, but their relevance in certain contexts is limited. In this review, we discuss some of these contexts, posing bottle neck for different fields of biology including biomedical research. With the advancement of chemistry, several methods have been introduced to overcome these problems. Even though microfluidics and microraft array are newer techniques exploited for single cell biology, fluorescence-activated cell sorting (FACS) remains the gold standard technique for isolation of cells for many biomedical applications, like stem cell therapy. Here, we present a comprehensive and comparative account of some of the probes that are useful in FACS. Further, we illustrate how these techniques could be applied in biomedical research. It is postulated that intracellular molecular markers like nucleostemin (GNL3), alkaline phosphatase (ALPL) and HIRA can be used for improving the outcome of cardiac as well as bone regeneration. Another field that could utilize intracellular markers is diagnostics, and we propose the use of specific peptide nucleic acid probes (PNPs) against certain miRNAs for cancer surgical margin prediction. The newer techniques for single cell biology, based on intracellular molecules, will immensely enhance the repertoire of possible markers for the isolation of cell types useful in biomedical research.

Toward human organ printing: Charleston Bioprinting Symposium.

PubMed

Mironov, Vladimir

2006-01-01

The First Annual Charleston Bioprinting Symposium was organized by the Bioprinting Research Center of the Medical University of South Carolina (MUSC) and convened July 21, 2006, in Charleston, South Carolina. In broad terms, bioprinting is the application of rapid prototyping technology to the biomedical field. More specifically, it is defined as the layer by layer deposition of biologically relevant material. The 2006 Symposium included four sessions: Computer-aided design and Bioprinting, Bioprinting Technologies; Hydrogel for Bioprinting and, finally, a special session devoted to ongoing research projects at the MUSC Bioprinting Research Center. The Symposium highlight was the presentation of the multidisciplinary Charleston Bioengineered Kidney Project. This symposium demonstrated that bioprinting or robotic biofabrication is one of the most exciting and fast-emerging branches in the tissue engineering field. Robotic biofabrication will eventually lead to industrial production of living human organs suitable for clinical transplantation. The symposium demonstrated that although there are still many technological challenges, organ printing is a rapidly evolving feasible technology.

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

PubMed

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.

Magnetic microbubble: A biomedical platform co-constructed from magnetics and acoustics

NASA Astrophysics Data System (ADS)

Yang, Fang; Gu, Zhu-Xiao; Jin, Xin; Wang, Hao-Yao; Gu, Ning

2013-10-01

Generation of magnetic micrbubbles and their basic magnetic and acoustic mechanism are reviewed. The ultrasound (US) and magnetic resonance (MR) dual imaging, the controlled therapeutic delivery, as well as theranostic multifunctions are all introduced based on recent research results. Some on-going research is also discussed.

Enhancing Biomedical Text Summarization Using Semantic Relation Extraction

PubMed Central

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. PMID:21887336

Advances in nano-scaled biosensors for biomedical applications.

PubMed

Wang, Jianling; Chen, Guihua; Jiang, Hui; Li, Zhiyong; Wang, Xuemei

2013-08-21

Recently, a growing amount of attention has been focused on the utility of biosensors for biomedical applications. Combined with nanomaterials and nanostructures, nano-scaled biosensors are installed for biomedical applications, such as pathogenic bacteria monitoring, virus recognition, disease biomarker detection, among others. These nano-biosensors offer a number of advantages and in many respects are ideally suited to biomedical applications, which could be made as extremely flexible devices, allowing biomedical analysis with speediness, excellent selectivity and high sensitivity. This minireview discusses the literature published in the latest years on the advances in biomedical applications of nano-scaled biosensors for disease bio-marking and detection, especially in bio-imaging and the diagnosis of pathological cells and viruses, monitoring pathogenic bacteria, thus providing insight into the future prospects of biosensors in relevant clinical applications.

A Roadmap for caGrid, an Enterprise Grid Architecture for Biomedical Research

PubMed Central

Saltz, Joel; Hastings, Shannon; Langella, Stephen; Oster, Scott; Kurc, Tahsin; Payne, Philip; Ferreira, Renato; Plale, Beth; Goble, Carole; Ervin, David; Sharma, Ashish; Pan, Tony; Permar, Justin; Brezany, Peter; Siebenlist, Frank; Madduri, Ravi; Foster, Ian; Shanbhag, Krishnakant; Mead, Charlie; Hong, Neil Chue

2012-01-01

caGrid is a middleware system which combines the Grid computing, the service oriented architecture, and the model driven architecture paradigms to support development of interoperable data and analytical resources and federation of such resources in a Grid environment. The functionality provided by caGrid is an essential and integral component of the cancer Biomedical Informatics Grid (caBIG™) program. This program is established by the National Cancer Institute as a nationwide effort to develop enabling informatics technologies for collaborative, multi-institutional biomedical research with the overarching goal of accelerating translational cancer research. Although the main application domain for caGrid is cancer research, the infrastructure provides a generic framework that can be employed in other biomedical research and healthcare domains. The development of caGrid is an ongoing effort, adding new functionality and improvements based on feedback and use cases from the community. This paper provides an overview of potential future architecture and tooling directions and areas of improvement for caGrid and caGrid-like systems. This summary is based on discussions at a roadmap workshop held in February with participants from biomedical research, Grid computing, and high performance computing communities. PMID:18560123

A roadmap for caGrid, an enterprise Grid architecture for biomedical research.

PubMed

Saltz, Joel; Hastings, Shannon; Langella, Stephen; Oster, Scott; Kurc, Tahsin; Payne, Philip; Ferreira, Renato; Plale, Beth; Goble, Carole; Ervin, David; Sharma, Ashish; Pan, Tony; Permar, Justin; Brezany, Peter; Siebenlist, Frank; Madduri, Ravi; Foster, Ian; Shanbhag, Krishnakant; Mead, Charlie; Chue Hong, Neil

2008-01-01

caGrid is a middleware system which combines the Grid computing, the service oriented architecture, and the model driven architecture paradigms to support development of interoperable data and analytical resources and federation of such resources in a Grid environment. The functionality provided by caGrid is an essential and integral component of the cancer Biomedical Informatics Grid (caBIG) program. This program is established by the National Cancer Institute as a nationwide effort to develop enabling informatics technologies for collaborative, multi-institutional biomedical research with the overarching goal of accelerating translational cancer research. Although the main application domain for caGrid is cancer research, the infrastructure provides a generic framework that can be employed in other biomedical research and healthcare domains. The development of caGrid is an ongoing effort, adding new functionality and improvements based on feedback and use cases from the community. This paper provides an overview of potential future architecture and tooling directions and areas of improvement for caGrid and caGrid-like systems. This summary is based on discussions at a roadmap workshop held in February with participants from biomedical research, Grid computing, and high performance computing communities.

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

PubMed

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.

The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine.

PubMed

Hesselager, Marianne O; Codrea, Marius C; Sun, Zhi; Deutsch, Eric W; Bennike, Tue B; Stensballe, Allan; Bundgaard, Louise; Moritz, Robert L; Bendixen, Emøke

2016-02-01

Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this article demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Pig PeptideAtlas: a resource for systems biology in animal production and biomedicine

PubMed Central

Hesselager, Marianne O.; Codrea, Marius C.; Sun, Zhi; Deutsch, Eric W.; Bennike, Tue B.; Stensballe, Allan; Bundgaard, Louise; Moritz, Robert L.; Bendixen, Emøke

2016-01-01

Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system wide observations, and cross species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this manuscript demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research. PMID:26699206

Space Product Development (SPD)

NASA Image and Video Library

2003-01-12

Experiments to seek solutions for a range of biomedical issues are at the heart of several investigations that will be hosted by the Commercial Instrumentation Technology Associates (ITA), Inc. Biomedical Experiments (CIBX-2) payload. CIBX-2 is unique, encompassing more than 20 separate experiments including cancer research, commercial experiments, and student hands-on experiments from 10 schools as part of ITA's ongoing University Among the Stars program. Student Marnix Aklian and ITA's Mark Bem prepare biological samples for flight as part of ITA's hands-on student outreach program on STS-95. Similar activities are a part of the CIBX-2 payload. The experiments are sponsored by NASA's Space Product Development Program (SPD).

Space Product Development (SPD)

NASA Image and Video Library

2003-01-12

Experiments to seek solutions for a range of biomedical issues are at the heart of several investigations that will be hosted by the Commercial Instrumentation Technology Associates (ITA), Inc. The biomedical experiments CIBX-2 payload is unique, encompassing more than 20 separate experiments including cancer research, commercial experiments, and student hands-on experiments from 10 schools as part of ITA's ongoing University Among the stars program. Here, Astronaut Story Musgrave activates the CMIX-5 (Commercial MDA ITA experiment) payload in the Space Shuttle mid deck during the STS-80 mission in 1996 which is similar to CIBX-2. The experiments are sponsored by NASA's Space Product Development Program (SPD).

Biomedical informatics and translational medicine.

PubMed

Sarkar, Indra Neil

2010-02-26

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.

Women in biomedical engineering and health informatics.

PubMed

McGregor, Carolyn; Frize, Monique

2008-01-01

A valuable session for anyone whether student or not, interested in learning more about Biomedical Engineering and Health Informatics as a career choice for women. Prominent women within the domains Biomedical Engineering and Health Informatics will present their research and their humanitarian interests that motivate them. Utilise the fantastic networking opportunity that will conclude this session to build and establish new professional networks with other women interested in your fields of expertise. Bring your contact details and be ready to make new contacts that are relevant for you.

Translation of biomedical prevention strategies for HIV: Prospects and pitfalls

PubMed Central

Vermund, Sten H.; Tique, José A.; Cassell, Holly M.; Johnson, Megan E.; Ciampa, Philip J.; Audet, Carolyn M.

2013-01-01

Early achievements in biomedical approaches for HIV prevention included physical barriers (condoms), clean injection equipment (both for medical use and for injection drug users), blood and blood product safety, and prevention of mother to child transmission. In recent years, antiretroviral drugs to reduce risk of transmission (when the infected person takes the medicines; treatment as prevention or TasP) or reduce risk of acquisition (when the seronegative person takes them; pre-exposure prophylaxis or PrEP) have proven efficacious. Circumcision of men has also been a major tool relevant for higher prevalence regions such as sub-Saharan Africa. Well-established prevention strategies in the control of sexually transmitted diseases and tuberculosis are highly relevant for HIV (i.e., screening, linkage to care, early treatment, and contact tracing). Unfortunately, only slow progress is being made in some available HIV prevention strategies such as family planning for HIV-infected women who do not want more children and prevention mother-to-child HIV transmission. Current studies seek to integrate strategies into approaches that combine biomedical, behavioral, and structural methods to achieve prevention synergies. This review identifies the major biomedical approaches demonstrated to be efficacious that are now available. We also highlight the need for behavioral risk reduction and adherence as essential components of any biomedical approach. PMID:23673881

Renovating Alzheimer's: "Constructive" Reflections on the New Clinical and Research Diagnostic Guidelines

ERIC Educational Resources Information Center

George, Daniel R.; Qualls, Sara H.; Camp, Cameron J.; Whitehouse, Peter J.

2013-01-01

The development of disease concepts for conditions such as Alzheimer's disease (AD) is an ongoing social process that evolves over time. The biomedical paradigm about AD that has informed our culture's understanding of brain aging for the past several decades is currently undergoing a major and timely renovation in the early 21st century. This…

Race and Genetics: Controversies in Biomedical, Behavioral, and Forensic Sciences

ERIC Educational Resources Information Center

Ossorio, Pilar; Duster, Troy

2005-01-01

Among biomedical scientists, there is a great deal of controversy over the nature of race, the relevance of racial categories for research, and the proper methods of using racial variables. This article argues that researchers and scholars should avoid a binary-type argument, in which the question is whether to use race always or never.…

British Journal of Biomedical Science in 2015: what have we learned?

PubMed

Blann, Andrew; Nation, Brian

2016-01-01

In 2015, the British Journal of Biomedical Science published 47 reports on topics relating to the various disciplines within biomedical science. Of these, the majority were in infection science (15 in microbiology and two in virology) and blood science (seven in biochemistry, four in haematology, three in immunology and one in transplantation), with a smaller number in cellular sciences (four reports) and with one review across disciplines. The present report will summarise key aspects of these publications that are of greatest relevance to laboratory scientists.

Virtual firm as a role-playing tool for biomedical education.

PubMed

Blagosklonov, Oleg; Soto-Romero, Georges; Guyon, Florent; Courjal, Nadège; Euphrasie, Sebatien; Yahiaoui, Reda; Butterlin, Nadia

2006-01-01

The paper describes design of a role-playing tool based on the experience of the practice firm which allows participants to obtain relevant and practical on-the-job experience. The students played the roles of the employees and the applicants for vacant positions at the virtual firm - a small business specialized in biomedical sector - founded to design the demonstration vehicle for a biomedical device. We found that this innovative concept may be used to improve the young engineers performance and to facilitate their post-graduate integration.

Developing a comprehensive system for content-based retrieval of image and text data from a national survey

NASA Astrophysics Data System (ADS)

Antani, Sameer K.; Natarajan, Mukil; Long, Jonathan L.; Long, L. Rodney; Thoma, George R.

2005-04-01

The article describes the status of our ongoing R&D at the U.S. National Library of Medicine (NLM) towards the development of an advanced multimedia database biomedical information system that supports content-based image retrieval (CBIR). NLM maintains a collection of 17,000 digitized spinal X-rays along with text survey data from the Second National Health and Nutritional Examination Survey (NHANES II). These data serve as a rich data source for epidemiologists and researchers of osteoarthritis and musculoskeletal diseases. It is currently possible to access these through text keyword queries using our Web-based Medical Information Retrieval System (WebMIRS). CBIR methods developed specifically for biomedical images could offer direct visual searching of these images by means of example image or user sketch. We are building a system which supports hybrid queries that have text and image-content components. R&D goals include developing algorithms for robust image segmentation for localizing and identifying relevant anatomy, labeling the segmented anatomy based on its pathology, developing suitable indexing and similarity matching methods for images and image features, and associating the survey text information for query and retrieval along with the image data. Some highlights of the system developed in MATLAB and Java are: use of a networked or local centralized database for text and image data; flexibility to incorporate new research work; provides a means to control access to system components under development; and use of XML for structured reporting. The article details the design, features, and algorithms in this third revision of this prototype system, CBIR3.

A Road Less Traveled By: Exploring a Decade of Ellman Chemistry

PubMed Central

Shelat, Anang A.; Guy, R. Kiplin

2009-01-01

The Ellman group has been one of the most influential in the development and widespread adoption of combinatorial chemistry techniques for biomedical research. Their work has included substantial methodological development for library synthesis with a particular focus on new scaffolds rationally targeted to biomolecules of interest and biologically relevant natural products. Herein we analyze a representative set of libraries from this group with respect to their biological and biomedical relevance in comparison to existing drugs and probe compounds. This analysis reveals that the Ellman group has not only provided new methodologies to the community but also provided libraries with unique potential for further biological study. PMID:18343129

Recommending images of user interests from the biomedical literature

NASA Astrophysics Data System (ADS)

Clukey, Steven; Xu, Songhua

2013-03-01

Every year hundreds of thousands of biomedical images are published in journals and conferences. Consequently, finding images relevant to one's interests becomes an ever daunting task. This vast amount of literature creates a need for intelligent and easy-to-use tools that can help researchers effectively navigate through the content corpus and conveniently locate materials of their interests. Traditionally, literature search tools allow users to query content using topic keywords. However, manual query composition is often time and energy consuming. A better system would be one that can automatically deliver relevant content to a researcher without having the end user manually manifest one's search intent and interests via search queries. Such a computer-aided assistance for information access can be provided by a system that first determines a researcher's interests automatically and then recommends images relevant to the person's interests accordingly. The technology can greatly improve a researcher's ability to stay up to date in their fields of study by allowing them to efficiently browse images and documents matching their needs and interests among the vast amount of the biomedical literature. A prototype system implementation of the technology can be accessed via http://www.smartdataware.com.

[Social constructionism in primary health care: an integrative review].

PubMed

Cadoná, Eliane; Scarparo, Helena

2015-09-01

This study sets out to analyze scientific articles in order to investigate how researchers in the area of Social Constructionism define "health" in Primary Health Care. An integrative review of the literature was conducted along with a decision to concentrate on those works with narrative experiences and research studies. The database researched was the Brazilian Virtual Health Library, with experiences in the scope of Primary Health Care. The effectiveness of this step resulted in 12 articles. Data were analyzed and discussed based on the perspectives of social constructionism, which generated two central themes. They were: citizenship exercises - promoting health in collective spaces; health practices - overcoming the dichotomies and absolute truths. This study revealed the relevance of the notion of shared responsibility on meanings of health contained in the texts analyzed. The researchers claim that it is possible to expand health practices into collective action to facilitate ongoing dialogue between health users and workers. However, the dominance of biomedical discourse is criticized by the researchers, because that paradigm still promotes practices of care focused on illness.

Cancer Control Research among Cambodian Americans in Washington

PubMed Central

Taylor, Victoria M.; Jackson, J. Carey; Tu, Shin-Ping

2006-01-01

Purpose We summarized previous and ongoing cancer control research among Cambodian immigrants in Washington. Methods A literature review of articles and published abstracts was conducted. Findings Cambodian Americans have a limited understanding of Western biomedical concepts, and low levels of cancer screening participation. Conclusions Culturally appropriate cancer control interventions for Cambodian Americans should be developed, implemented, and evaluated. PMID:11567509

Challenging Medical Students with an Interim Assessment: A Positive Effect on Formal Examination Score in a Randomized Controlled Study

ERIC Educational Resources Information Center

Bekkink, Marleen Olde; Donders, Rogier; van Muijen, Goos N. P.; Ruiter, Dirk J.

2012-01-01

Until now, positive effects of assessment at a medical curriculum level have not been demonstrated. This study was performed to determine whether an interim assessment, taken during a small group work session of an ongoing biomedical course, results in students' increased performance at the formal course examination. A randomized controlled trial…

Biomedical research leaders: report on needs, opportunities, difficulties, education and training, and evaluation.

PubMed Central

Wilson, S H; Merkle, S; Brown, D; Moskowitz, J; Hurley, D; Brown, D; Bailey, B J; McClain, M; Misenhimer, M; Buckalew, J; Burks, T

2000-01-01

The National Association of Physicians for the Environment (NAPE) has assumed a leadership role in protecting environmental health in recent years. The Committee of Biomedical Research Leaders was convened at the recent NAPE Leadership Conference: Biomedical Research and the Environment held on 1--2 November 1999, at the National Institutes of Health, Bethesda, Maryland. This report summarizes the discussion of the committee and its recommendations. The charge to the committee was to raise and address issues that will promote and sustain environmental health, safety, and energy efficiency within the biomedical community. Leaders from every important research sector (industry laboratories, academic health centers and institutes, hospitals and care facilities, Federal laboratories, and community-based research facilities) were gathered in this committee to discuss issues relevant to promoting environmental health. The conference and this report focus on the themes of environmental stewardship, sustainable development and "best greening practices." Environmental stewardship, an emerging theme within and outside the biomedical community, symbolizes the effort to provide an integrated, synthesized, and concerted effort to protect the health of the environment in both the present and the future. The primary goal established by the committee is to promote environmentally responsible leadership in the biomedical research community. Key outcomes of the committee's discussion and deliberation were a) the need for a central organization to evaluate, promote, and oversee efforts in environmental stewardship; and b) immediate need to facilitate efficient information transfer relevant to protecting the global environment through a database/clearinghouse. Means to fulfill these needs are discussed in this report. PMID:11121363

Biomedical research leaders: report on needs, opportunities, difficulties, education and training, and evaluation.

PubMed

Wilson, S H; Merkle, S; Brown, D; Moskowitz, J; Hurley, D; Brown, D; Bailey, B J; McClain, M; Misenhimer, M; Buckalew, J; Burks, T

2000-12-01

The National Association of Physicians for the Environment (NAPE) has assumed a leadership role in protecting environmental health in recent years. The Committee of Biomedical Research Leaders was convened at the recent NAPE Leadership Conference: Biomedical Research and the Environment held on 1--2 November 1999, at the National Institutes of Health, Bethesda, Maryland. This report summarizes the discussion of the committee and its recommendations. The charge to the committee was to raise and address issues that will promote and sustain environmental health, safety, and energy efficiency within the biomedical community. Leaders from every important research sector (industry laboratories, academic health centers and institutes, hospitals and care facilities, Federal laboratories, and community-based research facilities) were gathered in this committee to discuss issues relevant to promoting environmental health. The conference and this report focus on the themes of environmental stewardship, sustainable development and "best greening practices." Environmental stewardship, an emerging theme within and outside the biomedical community, symbolizes the effort to provide an integrated, synthesized, and concerted effort to protect the health of the environment in both the present and the future. The primary goal established by the committee is to promote environmentally responsible leadership in the biomedical research community. Key outcomes of the committee's discussion and deliberation were a) the need for a central organization to evaluate, promote, and oversee efforts in environmental stewardship; and b) immediate need to facilitate efficient information transfer relevant to protecting the global environment through a database/clearinghouse. Means to fulfill these needs are discussed in this report.

A LDA-based approach to promoting ranking diversity for genomics information retrieval.

PubMed

Chen, Yan; Yin, Xiaoshi; Li, Zhoujun; Hu, Xiaohua; Huang, Jimmy Xiangji

2012-06-11

In the biomedical domain, there are immense data and tremendous increase of genomics and biomedical relevant publications. The wealth of information has led to an increasing amount of interest in and need for applying information retrieval techniques to access the scientific literature in genomics and related biomedical disciplines. In many cases, the desired information of a query asked by biologists is a list of a certain type of entities covering different aspects that are related to the question, such as cells, genes, diseases, proteins, mutations, etc. Hence, it is important of a biomedical IR system to be able to provide relevant and diverse answers to fulfill biologists' information needs. However traditional IR model only concerns with the relevance between retrieved documents and user query, but does not take redundancy between retrieved documents into account. This will lead to high redundancy and low diversity in the retrieval ranked lists. In this paper, we propose an approach which employs a topic generative model called Latent Dirichlet Allocation (LDA) to promoting ranking diversity for biomedical information retrieval. Different from other approaches or models which consider aspects on word level, our approach assumes that aspects should be identified by the topics of retrieved documents. We present LDA model to discover topic distribution of retrieval passages and word distribution of each topic dimension, and then re-rank retrieval results with topic distribution similarity between passages based on N-size slide window. We perform our approach on TREC 2007 Genomics collection and two distinctive IR baseline runs, which can achieve 8% improvement over the highest Aspect MAP reported in TREC 2007 Genomics track. The proposed method is the first study of adopting topic model to genomics information retrieval, and demonstrates its effectiveness in promoting ranking diversity as well as in improving relevance of ranked lists of genomics search. Moreover, we proposes a distance measure to quantify how much a passage can increase topical diversity by considering both topical importance and topical coefficient by LDA, and the distance measure is a modified Euclidean distance.

Commercial Instrumentation Technology Associates Inc. Biomedical Experiments Payload (CIBX-2)

NASA Technical Reports Server (NTRS)

Morrison, Dennis; Edmundson, Allen; Robinson, Keith (Technical Monitor)

2002-01-01

Experiments to find solutions for a range of biomedical issues are being hosted by the Commercial Instrumentation Technology Associates Inc. (ITA) Biomedical Experiments (CIBX-2) payload. This research encompasses more than 20 separate experiments including cancer research, commercial experiments and hands-on student experiments from 10 schools as part of ITA's ongoing University Among the Stars program. Protein crystal growth experiments will address the structure of urokinase - a protein that has been identified as a key enzyme in the spread of brain, lung, colon, prostate and breast cancers. Crystals of Bence Jones, a protein associated with bone cancer, will also be grown. Understanding their structures may help scientists develop treatments. In a related area, the Microencapsulation of Drugs (MEPS) is an anti-cancer drug delivery system, based on a 10-year partnership with NASA's Johnson Space Center. On this mission, the co-encapsulation of antibodies and immune stimulants will be made in submicron microcapsules to target pulmonary and bacterial infections.

Novartis School Lab: bringing young people closer to the world of research and discovering the excitement of science.

PubMed

Michel, Christiane Röckl; Standke, Gesche; Naef, Reto

2012-01-01

The Novartis School Lab (http://www.novartis.ch/schullabor) is an institution with an old tradition. The School Lab reaches about 5000 students through internal courses and an additional 5000 children at public science events where they can enjoy hands-on science in disciplines of biomedical research. The subjects range from chemistry, physics, molecular biology and genetics to toxicology and medical topics. The Novartis School Lab offers a variety of activities for youngsters aged 10-20 ranging from lab courses for school classes, continuing education for teachers and development of teaching kits, support for individual research projects to outreach for public science events. Innovation and adaptation to changes of current needs are essential aspects for the Novartis School Lab. Ongoing activities to shape the Novartis Biomedical Learning Lab include design of new teaching experiments, exploration into additional disciplines of biomedical science and the creation of a fascinating School Lab of the future.

Stereotyping at the undergraduate level revealed during interprofessional learning between future doctors and biomedical scientists.

PubMed

Lewitt, Moira S; Ehrenborg, Ewa; Scheja, Max; Brauner, Annelie

2010-01-01

Interprofessional education (IPE) involving undergraduate health professionals is expected to promote collaboration in their later careers. The role of IPE between doctors and biomedical scientists has not been explored at the undergraduate level. Our aim was to introduce IPE sessions for medical and biomedical students in order to identify the benefits and barriers to these groups learning together. Medical and biomedical students together discussed laboratory results, relevant literature, and ideas for developing new diagnostic tools. The programme was evaluated with questionnaires and interviews. While there was general support for the idea of IPE, medical and biomedical students responded differently. Biomedical students were more critical, wanted more explicit learning objectives and felt that their professional role was often misunderstood. The medical students were more enthusiastic but regarded the way the biomedical students communicated concerns about their perceived role as a barrier to effective interprofessional learning. We conclude that stereotyping, which can impede effective collaborations between doctors and biomedical scientists, is already present at the undergraduate level and may be a barrier to IPE. Effective learning opportunities should be supported at the curriculum level and be designed to specifically enable a broad appreciation of each other's future professional roles.

Multi-field query expansion is effective for biomedical dataset retrieval.

PubMed

Bouadjenek, Mohamed Reda; Verspoor, Karin

2017-01-01

In the context of the bioCADDIE challenge addressing information retrieval of biomedical datasets, we propose a method for retrieval of biomedical data sets with heterogenous schemas through query reformulation. In particular, the method proposed transforms the initial query into a multi-field query that is then enriched with terms that are likely to occur in the relevant datasets. We compare and evaluate two query expansion strategies, one based on the Rocchio method and another based on a biomedical lexicon. We then perform a comprehensive comparative evaluation of our method on the bioCADDIE dataset collection for biomedical retrieval. We demonstrate the effectiveness of our multi-field query method compared to two baselines, with MAP improved from 0.2171 and 0.2669 to 0.2996. We also show the benefits of query expansion, where the Rocchio expanstion method improves the MAP for our two baselines from 0.2171 and 0.2669 to 0.335. We show that the Rocchio query expansion method slightly outperforms the one based on the biomedical lexicon as a source of terms, with an improvement of roughly 3% for MAP. However, the query expansion method based on the biomedical lexicon is much less resource intensive since it does not require computation of any relevance feedback set or any initial execution of the query. Hence, in term of trade-off between efficiency, execution time and retrieval accuracy, we argue that the query expansion method based on the biomedical lexicon offers the best performance for a prototype biomedical data search engine intended to be used at a large scale. In the official bioCADDIE challenge results, although our approach is ranked seventh in terms of the infNDCG evaluation metric, it ranks second in term of P@10 and NDCG. Hence, the method proposed here provides overall good retrieval performance in relation to the approaches of other competitors. Consequently, the observations made in this paper should benefit the development of a Data Discovery Index prototype or the improvement of the existing one. © The Author(s) 2017. Published by Oxford University Press.

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

PubMed

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 and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available (both via the user interface at http://bioportal.bioontology.org/recommender , and via a Web service API).

Multi-field query expansion is effective for biomedical dataset retrieval

PubMed Central

2017-01-01

Abstract In the context of the bioCADDIE challenge addressing information retrieval of biomedical datasets, we propose a method for retrieval of biomedical data sets with heterogenous schemas through query reformulation. In particular, the method proposed transforms the initial query into a multi-field query that is then enriched with terms that are likely to occur in the relevant datasets. We compare and evaluate two query expansion strategies, one based on the Rocchio method and another based on a biomedical lexicon. We then perform a comprehensive comparative evaluation of our method on the bioCADDIE dataset collection for biomedical retrieval. We demonstrate the effectiveness of our multi-field query method compared to two baselines, with MAP improved from 0.2171 and 0.2669 to 0.2996. We also show the benefits of query expansion, where the Rocchio expanstion method improves the MAP for our two baselines from 0.2171 and 0.2669 to 0.335. We show that the Rocchio query expansion method slightly outperforms the one based on the biomedical lexicon as a source of terms, with an improvement of roughly 3% for MAP. However, the query expansion method based on the biomedical lexicon is much less resource intensive since it does not require computation of any relevance feedback set or any initial execution of the query. Hence, in term of trade-off between efficiency, execution time and retrieval accuracy, we argue that the query expansion method based on the biomedical lexicon offers the best performance for a prototype biomedical data search engine intended to be used at a large scale. In the official bioCADDIE challenge results, although our approach is ranked seventh in terms of the infNDCG evaluation metric, it ranks second in term of P@10 and NDCG. Hence, the method proposed here provides overall good retrieval performance in relation to the approaches of other competitors. Consequently, the observations made in this paper should benefit the development of a Data Discovery Index prototype or the improvement of the existing one. PMID:29220457

G-Bean: an ontology-graph based web tool for biomedical literature retrieval

PubMed Central

2014-01-01

Background Currently, most people use NCBI's PubMed to search the MEDLINE database, an important bibliographical information source for life science and biomedical information. However, PubMed has some drawbacks that make it difficult to find relevant publications pertaining to users' individual intentions, especially for non-expert users. To ameliorate the disadvantages of PubMed, we developed G-Bean, a graph based biomedical search engine, to search biomedical articles in MEDLINE database more efficiently. Methods G-Bean addresses PubMed's limitations with three innovations: (1) Parallel document index creation: a multithreaded index creation strategy is employed to generate the document index for G-Bean in parallel; (2) Ontology-graph based query expansion: an ontology graph is constructed by merging four major UMLS (Version 2013AA) vocabularies, MeSH, SNOMEDCT, CSP and AOD, to cover all concepts in National Library of Medicine (NLM) database; a Personalized PageRank algorithm is used to compute concept relevance in this ontology graph and the Term Frequency - Inverse Document Frequency (TF-IDF) weighting scheme is used to re-rank the concepts. The top 500 ranked concepts are selected for expanding the initial query to retrieve more accurate and relevant information; (3) Retrieval and re-ranking of documents based on user's search intention: after the user selects any article from the existing search results, G-Bean analyzes user's selections to determine his/her true search intention and then uses more relevant and more specific terms to retrieve additional related articles. The new articles are presented to the user in the order of their relevance to the already selected articles. Results Performance evaluation with 106 OHSUMED benchmark queries shows that G-Bean returns more relevant results than PubMed does when using these queries to search the MEDLINE database. PubMed could not even return any search result for some OHSUMED queries because it failed to form the appropriate Boolean query statement automatically from the natural language query strings. G-Bean is available at http://bioinformatics.clemson.edu/G-Bean/index.php. Conclusions G-Bean addresses PubMed's limitations with ontology-graph based query expansion, automatic document indexing, and user search intention discovery. It shows significant advantages in finding relevant articles from the MEDLINE database to meet the information need of the user. PMID:25474588

G-Bean: an ontology-graph based web tool for biomedical literature retrieval.

PubMed

Wang, James Z; Zhang, Yuanyuan; Dong, Liang; Li, Lin; Srimani, Pradip K; Yu, Philip S

2014-01-01

Currently, most people use NCBI's PubMed to search the MEDLINE database, an important bibliographical information source for life science and biomedical information. However, PubMed has some drawbacks that make it difficult to find relevant publications pertaining to users' individual intentions, especially for non-expert users. To ameliorate the disadvantages of PubMed, we developed G-Bean, a graph based biomedical search engine, to search biomedical articles in MEDLINE database more efficiently. G-Bean addresses PubMed's limitations with three innovations: (1) Parallel document index creation: a multithreaded index creation strategy is employed to generate the document index for G-Bean in parallel; (2) Ontology-graph based query expansion: an ontology graph is constructed by merging four major UMLS (Version 2013AA) vocabularies, MeSH, SNOMEDCT, CSP and AOD, to cover all concepts in National Library of Medicine (NLM) database; a Personalized PageRank algorithm is used to compute concept relevance in this ontology graph and the Term Frequency - Inverse Document Frequency (TF-IDF) weighting scheme is used to re-rank the concepts. The top 500 ranked concepts are selected for expanding the initial query to retrieve more accurate and relevant information; (3) Retrieval and re-ranking of documents based on user's search intention: after the user selects any article from the existing search results, G-Bean analyzes user's selections to determine his/her true search intention and then uses more relevant and more specific terms to retrieve additional related articles. The new articles are presented to the user in the order of their relevance to the already selected articles. Performance evaluation with 106 OHSUMED benchmark queries shows that G-Bean returns more relevant results than PubMed does when using these queries to search the MEDLINE database. PubMed could not even return any search result for some OHSUMED queries because it failed to form the appropriate Boolean query statement automatically from the natural language query strings. G-Bean is available at http://bioinformatics.clemson.edu/G-Bean/index.php. G-Bean addresses PubMed's limitations with ontology-graph based query expansion, automatic document indexing, and user search intention discovery. It shows significant advantages in finding relevant articles from the MEDLINE database to meet the information need of the user.

Rules and management of biomedical waste at Vivekananda Polyclinic: a case study.

PubMed

Gupta, Saurabh; Boojh, Ram; Mishra, Ajai; Chandra, Hem

2009-02-01

Hospitals and other healthcare establishments have a "duty of care" for the environment and for public health, and have particular responsibilities in relation to the waste they produce (i.e., biomedical waste). Negligence, in terms of biomedical waste management, significantly contributes to polluting the environment, affects the health of human beings, and depletes natural and financial resources. In India, in view of the serious situation of biomedical waste management, the Ministry of Environment and Forests, within the Government of India, ratified the Biomedical Waste (Management and Handling) Rules, in July 1998. The present paper provides a brief description of the biomedical waste (Management and Handling) Rules 1998, and the current biomedical waste management practices in one of the premier healthcare establishments of Lucknow, the Vivekananda Polyclinic. The objective in undertaking this study was to analyse the biomedical waste management system, including policy, practice (i.e., storage, collection, transportation and disposal), and compliance with the standards prescribed under the regulatory framework. The analysis consisted of interviews with medical authorities, doctors, and paramedical staff involved in the management of the biomedical wastes in the Polyclinic. Other important stakeholders that were consulted and interviewed included environmental engineers (looking after the Biomedical Waste Cell) of the State Pollution Control Board, and randomly selected patients and visitors to the Polyclinic. A general survey of the facilities of the Polyclinic was undertaken to ascertain the efficacy of the implemented measures. The waste was quantified based on random samples collected from each ward. It was found that, although the Polyclinic in general abides by the prescribed regulations for the treatment and disposal of biomedical waste, there is a need to further build the capacity of the Polyclinic and its staff in terms of providing state-of-the-art facilities and on-going training in order to develop a model biomedical waste management system in the Polyclinic. There is also a need to create awareness among all other stakeholders about the importance of biomedical waste management and related regulations. Furthermore, healthcare waste management should go beyond data compilation, enforcement of regulations, and acquisition of better equipment. It should be supported through appropriate education, training, and the commitment of the healthcare staff and management and healthcare managers within an effective policy and legislative framework.

Trends in Biophysical Research and Their Implications for Medical Libraries

PubMed Central

Chen, Ching-chih

1973-01-01

This is a statistical survey of the trends in biophysical research as reflected by papers presented at four Biophysical Society (BPS) annual meetings between 1958 and 1972 and by the funding sources of the reported projects. The study reveals that biophysical research has grown quite substantially, particularly since 1968. Although biophysics is truly interdisciplinary, since 1968 there has been more pronounced emphasis on biomedically oriented problems and a tendency toward more specific and more highly specialized problems. Between 1958 and 1972, most biophysicists were academic researchers, 50% of whom were biomedical scientists. Over three quarters of the ongoing biophysical research projects during this period were supported by governmental agencies, and among them, the National Institutes of Health was the largest single funding source. PMID:4573970

Poland: biomedical ethics in a socialist state.

PubMed

Szawarski, Zbigniew

1987-06-01

In one of a Hastings Center Report series of four country reports, a professor of ethics discusses the Polish approach to ethical issues in health care. Szawarski begins by outlining five factors that influence the practice of medicine in Poland: a socialist form of government, the influence of the Roman Catholic Church, an ongoing economic crisis, the legacy of the Nazi death camps, and a lack of formal instruction in biomedical ethics. He then discusses three current ethical concerns of physicians, patients, and the public: regulation of physician conduct, abortion, and in vitro fertilization. There is little formal public debate of the issues, however, and physicians seem committed to upholding traditional medical codes of ethics without analyzing underlying moral principles and justifications.

A Suggested Model for Building Robust Biomedical Implants Registries.

PubMed

Aloufi, Bader; Alshagathrah, Fahad; Househ, Mowafa

2017-01-01

Registries are an essential source of information for clinical and non-clinical decision-makers; because they provide evidence for post-market clinical follow-up and early detection of safety signals for biomedical implants. Yet, many of todays biomedical implants registries are facing a variety of challenges relating to a poorly designed dataset, the reliability of inputted data and low clinician and patient participation. The purpose of this paper is to present a best practice model for the implementation and use of biomedical implants registries to monitor the safety and effectiveness of implantable medical devices. Based on a literature review and an analysis of multiple national relevant registries, we identified six factors that address contemporary challenges and are believed to be the keys for building a successful biomedical implants registry, which include: sustainable development, international comparability, data reliability, purposeful design, ease of patient participation, and collaborative development at the national level.

Ethical considerations in bipolar disorders.

PubMed

Richa, S; Chammay, R; Dargél, A; Henry, C; Masson, M

2018-06-01

The implications of biomedical ethics principles extend to both medical care and biomedical research. They are particularly relevant for psychiatry in which pathologies are often chronic and disabling. Bipolar disorders impact the ability to make judgements and to take decisions during mood episodes and remain a stigmatised condition. Early interventions, even those in the prodromal phase, pose ethical questions for both clinicians and researchers. The degree of patients' autonomy in their clinical care must also now be considered from a biomedical ethics perspective. Copyright © 2018 L'Encéphale, Paris. Published by Elsevier Masson SAS. All rights reserved.

CPTAC Accelerates Precision Proteomics Biomedical Research | Office of Cancer Clinical Proteomics Research

Cancer.gov

The accurate quantitation of proteins or peptides using Mass Spectrometry (MS) is gaining prominence in the biomedical research community as an alternative method for analyte measurement. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigators have been at the forefront in the promotion of reproducible MS techniques, through the development and application of standardized proteomic methods for protein quantitation on biologically relevant samples.

Quantum cascade lasers (QCLs) in biomedical spectroscopy.

PubMed

Schwaighofer, Andreas; Brandstetter, Markus; Lendl, Bernhard

2017-10-02

Quantum cascade lasers (QCL) are the first room temperature semiconductor laser source for the mid-IR spectral region, triggering substantial development for the advancement of mid-IR spectroscopy. Mid-IR spectroscopy in general provides rapid, label-free and objective analysis, particularly important in the field of biomedical analysis. Due to their unique properties, QCLs offer new possibilities for development of analytical methods to enable quantification of clinically relevant concentration levels and to support medical diagnostics. Compared to FTIR spectroscopy, novel and elaborated measurement techniques can be implemented that allow miniaturized and portable instrumentation. This review illustrates the characteristics of QCLs with a particular focus on their benefits for biomedical analysis. Recent applications of QCL-based spectroscopy for analysis of a variety of clinically relevant samples including breath, urine, blood, interstitial fluid, and biopsy samples are summarized. Further potential for technical advancements is discussed in combination with future prospects for employment of QCL-based devices in routine and point-of-care diagnostics.

BUILDing BLaST: promoting rural students' biomedical research careers using a culturally responsive, one health approach.

PubMed

Taylor, Barbara E; Reynolds, Arleigh J; Etz, Kathy E; MacCalla, Nicole M G; Cotter, Paul A; DeRuyter, Tiffany L; Hueffer, Karsten

2017-01-01

Most postsecondary institutions in the state of Alaska (USA) have a broad mission to serve diverse students, many of whom come from schools in rural villages that are accessible only by plane, boat, or snowmobile. The major research university, the University of Alaska in Fairbanks (UAF), serves a population whereby 40% are from groups recognized as underrepresented in the biomedical workforce. The purpose of this article is to describe the Building Infrastructure Leading to Diversity (BUILD)-supported program in the state of Alaska that seeks to engage students from rural areas with a culturally relevant approach that is centered on the One Health paradigm, integrating human, animal, and environmental health. The Biomedical Learning and Student Training (BLaST) program distinguished by broad themes that address recruitment, retention, and success of students in biomedical programs, especially for students from rural backgrounds. Targeted rural outreach emphasizes that biomedical research includes research on the integration of human, animal, and environmental health. This One Health perspective gives personal relevance and connection to biomedical research. This outreach is expected to benefit student recruitment, as well as foster family and community support for pursuit of college degrees. BLaST promotes integration of research into undergraduate curricula through curriculum development, and by creating a new class of instructors, laboratory research and teaching technicians, who provide research mentorship, course instruction, and comprehensive advising. Finally, BLaST facilitates early and sustained undergraduate research experiences in collaborations with graduate students and faculty. BLaST's approach is highly adapted to the Alaskan educational and physical environment, but components and concepts could be adapted to other rural areas as a means to engage students from rural backgrounds, who often have a closer relationship with the natural environment than urban students.

Rules and management of biomedical waste at Vivekananda Polyclinic: A case study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, Saurabh; Boojh, Ram; Mishra, Ajai

Hospitals and other healthcare establishments have a 'duty of care' for the environment and for public health, and have particular responsibilities in relation to the waste they produce (i.e., biomedical waste). Negligence, in terms of biomedical waste management, significantly contributes to polluting the environment, affects the health of human beings, and depletes natural and financial resources. In India, in view of the serious situation of biomedical waste management, the Ministry of Environment and Forests, within the Government of India, ratified the Biomedical Waste (Management and Handling) Rules, in July 1998. The present paper provides a brief description of the biomedicalmore » waste (Management and Handling) Rules 1998, and the current biomedical waste management practices in one of the premier healthcare establishments of Lucknow, the Vivekananda Polyclinic. The objective in undertaking this study was to analyse the biomedical waste management system, including policy, practice (i.e., storage, collection, transportation and disposal), and compliance with the standards prescribed under the regulatory framework. The analysis consisted of interviews with medical authorities, doctors, and paramedical staff involved in the management of the biomedical wastes in the Polyclinic. Other important stakeholders that were consulted and interviewed included environmental engineers (looking after the Biomedical Waste Cell) of the State Pollution Control Board, and randomly selected patients and visitors to the Polyclinic. A general survey of the facilities of the Polyclinic was undertaken to ascertain the efficacy of the implemented measures. The waste was quantified based on random samples collected from each ward. It was found that, although the Polyclinic in general abides by the prescribed regulations for the treatment and disposal of biomedical waste, there is a need to further build the capacity of the Polyclinic and its staff in terms of providing state-of-the-art facilities and on-going training in order to develop a model biomedical waste management system in the Polyclinic. There is also a need to create awareness among all other stakeholders about the importance of biomedical waste management and related regulations. Furthermore, healthcare waste management should go beyond data compilation, enforcement of regulations, and acquisition of better equipment. It should be supported through appropriate education, training, and the commitment of the healthcare staff and management and healthcare managers within an effective policy and legislative framework.« less

Relevance of bovine tuberculosis research to the understanding of human disease: Historical perspectives, approaches, and immunologic mechanisms

USDA-ARS?s Scientific Manuscript database

Pioneer studies on infectious disease and immunology by Jenner, Pasteur, Koch, Von Behring, Nocard, Roux, and Ehrlich forged a path for the dual-purpose with dual benefit approach, demonstrating a profound relevance of veterinary studies for biomedical applications. Tuberculosis (TB), primarily due ...

Magnetic Characterization of Iron Oxide Nanoparticles for Biomedical Applications.

PubMed

Maldonado-Camargo, Lorena; Unni, Mythreyi; Rinaldi, Carlos

2017-01-01

Iron oxide nanoparticles are of interest in a wide range of biomedical applications due to their response to applied magnetic fields and their unique magnetic properties. Magnetization measurements in constant and time-varying magnetic field are often carried out to quantify key properties of iron oxide nanoparticles. This chapter describes the importance of thorough magnetic characterization of iron oxide nanoparticles intended for use in biomedical applications. A basic introduction to relevant magnetic properties of iron oxide nanoparticles is given, followed by protocols and conditions used for measurement of magnetic properties, along with examples of data obtained from each measurement, and methods of data analysis.

Space Product Development (SPD)

NASA Image and Video Library

2003-01-12

Experiments to seek solutions for a range of biomedical issues are at the heart of several investigations that will be hosted by the Commercial Instrumentation Technology Associates (ITA), Inc. Biomedical Experiments (CIBX-2) payload. CIBX-2 is unique, encompassing more than 20 separate experiments including cancer research, commercial experiments, and student hands-on experiments from 10 schools as part of ITA's ongoing University Among the Stars program. This drawing depicts a cross-section of a set of Dual-Materials Dispersion Apparatus (DMDA) specimen wells, one of which can include a reverse osmosis membrane to dewater a protein solution and thus cause crystallization. Depending on individual needs, two or three wells may be used, the membrane may be absent, or other proprietary enhancements may be present. The experiments are sponsored by NASA's Space Product Development Program (SPD).

Dual-Materials Dispersion Apparatus

NASA Technical Reports Server (NTRS)

2003-01-01

Experiments to seek solutions for a range of biomedical issues are at the heart of several investigations that will be hosted by the Commercial Instrumentation Technology Associates (ITA), Inc. Biomedical Experiments (CIBX-2) payload. CIBX-2 is unique, encompassing more than 20 separate experiments including cancer research, commercial experiments, and student hands-on experiments from 10 schools as part of ITA's ongoing University Among the Stars program. This drawing depicts a cross-section of a set of Dual-Materials Dispersion Apparatus (DMDA) specimen wells, one of which can include a reverse osmosis membrane to dewater a protein solution and thus cause crystallization. Depending on individual needs, two or three wells may be used, the membrane may be absent, or other proprietary enhancements may be present. The experiments are sponsored by NASA's Space Product Development Program (SPD).

HIV Prevention Among Transgender Populations: Knowledge Gaps and Evidence for Action.

PubMed

Poteat, Tonia; Malik, Mannat; Scheim, Ayden; Elliott, Ayana

2017-08-01

The purpose of this review is to summarize the available evidence-based HIV prevention interventions tailored for transgender people. A limited number of evidence-based HIV prevention interventions have been tested with transgender populations. Most existing interventions target behavior change among transgender women, with only one HIV prevention program evaluated for transgender men. Studies addressing biomedical interventions for transgender women are ongoing. Few interventions address social and structural barriers to HIV prevention, such as stigma, discrimination, and poverty. Evidence-based multi-level interventions that address the structural, biomedical, and behavioral risks for HIV among transgender populations, including transgender men, are needed to address disparities in HIV prevalence. Future research should address not only pre-exposure prophylaxis uptake and condom use but also structural barriers that limit access to these prevention strategies.

Organizational principles of cloud storage to support collaborative biomedical research.

PubMed

Kanbar, Lara J; Shalish, Wissam; Robles-Rubio, Carlos A; Precup, Doina; Brown, Karen; Sant'Anna, Guilherme M; Kearney, Robert E

2015-08-01

This paper describes organizational guidelines and an anonymization protocol for the management of sensitive information in interdisciplinary, multi-institutional studies with multiple collaborators. This protocol is flexible, automated, and suitable for use in cloud-based projects as well as for publication of supplementary information in journal papers. A sample implementation of the anonymization protocol is illustrated for an ongoing study dealing with Automated Prediction of EXtubation readiness (APEX).

Responsive Biomaterials: Advances in Materials Based on Shape-Memory Polymers.

PubMed

Hardy, John G; Palma, Matteo; Wind, Shalom J; Biggs, Manus J

2016-07-01

Shape-memory polymers (SMPs) are morphologically responsive materials with potential for a variety of biomedical applications, particularly as devices for minimally invasive surgery and the delivery of therapeutics and cells for tissue engineering. A brief introduction to SMPs is followed by a discussion of the current progress toward the development of SMP-based biomaterials for clinically relevant biomedical applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature.

PubMed

Sutton, Victoria R; Hauser, Susan E

2005-01-01

MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information.

Using classification models for the generation of disease-specific medications from biomedical literature and clinical data repository.

PubMed

Wang, Liqin; Haug, Peter J; Del Fiol, Guilherme

2017-05-01

Mining disease-specific associations from existing knowledge resources can be useful for building disease-specific ontologies and supporting knowledge-based applications. Many association mining techniques have been exploited. However, the challenge remains when those extracted associations contained much noise. It is unreliable to determine the relevance of the association by simply setting up arbitrary cut-off points on multiple scores of relevance; and it would be expensive to ask human experts to manually review a large number of associations. We propose that machine-learning-based classification can be used to separate the signal from the noise, and to provide a feasible approach to create and maintain disease-specific vocabularies. We initially focused on disease-medication associations for the purpose of simplicity. For a disease of interest, we extracted potentially treatment-related drug concepts from biomedical literature citations and from a local clinical data repository. Each concept was associated with multiple measures of relevance (i.e., features) such as frequency of occurrence. For the machine purpose of learning, we formed nine datasets for three diseases with each disease having two single-source datasets and one from the combination of previous two datasets. All the datasets were labeled using existing reference standards. Thereafter, we conducted two experiments: (1) to test if adding features from the clinical data repository would improve the performance of classification achieved using features from the biomedical literature only, and (2) to determine if classifier(s) trained with known medication-disease data sets would be generalizable to new disease(s). Simple logistic regression and LogitBoost were two classifiers identified as the preferred models separately for the biomedical-literature datasets and combined datasets. The performance of the classification using combined features provided significant improvement beyond that using biomedical-literature features alone (p-value<0.001). The performance of the classifier built from known diseases to predict associated concepts for new diseases showed no significant difference from the performance of the classifier built and tested using the new disease's dataset. It is feasible to use classification approaches to automatically predict the relevance of a concept to a disease of interest. It is useful to combine features from disparate sources for the task of classification. Classifiers built from known diseases were generalizable to new diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge

PubMed Central

Wei, Wei; Ji, Zhanglong; He, Yupeng; Zhang, Kai; Ha, Yuanchi; Li, Qi; Ohno-Machado, Lucila

2018-01-01

Abstract The number and diversity of biomedical datasets grew rapidly in the last decade. A large number of datasets are stored in various repositories, with different formats. Existing dataset retrieval systems lack the capability of cross-repository search. As a result, users spend time searching datasets in known repositories, and they typically do not find new repositories. The biomedical and healthcare data discovery index ecosystem (bioCADDIE) team organized a challenge to solicit new indexing and searching strategies for retrieving biomedical datasets across repositories. We describe the work of one team that built a retrieval pipeline and examined its performance. The pipeline used online resources to supplement dataset metadata, automatically generated queries from users’ free-text questions, produced high-quality retrieval results and achieved the highest inferred Normalized Discounted Cumulative Gain among competitors. The results showed that it is a promising solution for cross-database, cross-domain and cross-repository biomedical dataset retrieval. Database URL: https://github.com/w2wei/dataset_retrieval_pipeline PMID:29688374

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

PubMed

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.

BioSig: The Free and Open Source Software Library for Biomedical Signal Processing

PubMed Central

Vidaurre, Carmen; Sander, Tilmann H.; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals. PMID:21437227

BioSig: the free and open source software library for biomedical signal processing.

PubMed

Vidaurre, Carmen; Sander, Tilmann H; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals.

Finding and accessing diagrams in biomedical publications.

PubMed

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.

[The relevance of qualitative techniques in biomedical research].

PubMed

de Camargo, Kenneth Rochel

2008-01-01

On observing how qualitative and quantitative studies are reported in the biomedical literature it becomes evident that, besides the virtual absence of the former, they are presented in different ways. Authors of qualitative studies seem to need almost invariably to explain why they choose a qualitative approach whereas that does not occur in quantitative studies. This paper takes Ludwik Fleck's comparative epistemology as a means of exploring those differences empirically, illustrating on the basis of two studies dealing with different aspects of biomedical practices how qualitative methods can elucidate a variety of questions pertaining to this field. The paper concludes presenting some structural characteristics of the biomedical field which on one hand, would not be explored properly without employing qualitative methods and, on the other hand, can help understanding the little value given to qualitative techniques in this area.

Integration of relational and textual biomedical sources. A pilot experiment using a semi-automated method for logical schema acquisition.

PubMed

García-Remesal, M; Maojo, V; Billhardt, H; Crespo, J

2010-01-01

Bringing together structured and text-based sources is an exciting challenge for biomedical informaticians, since most relevant biomedical sources belong to one of these categories. In this paper we evaluate the feasibility of integrating relational and text-based biomedical sources using: i) an original logical schema acquisition method for textual databases developed by the authors, and ii) OntoFusion, a system originally designed by the authors for the integration of relational sources. We conducted an integration experiment involving a test set of seven differently structured sources covering the domain of genetic diseases. We used our logical schema acquisition method to generate schemas for all textual sources. The sources were integrated using the methods and tools provided by OntoFusion. The integration was validated using a test set of 500 queries. A panel of experts answered a questionnaire to evaluate i) the quality of the extracted schemas, ii) the query processing performance of the integrated set of sources, and iii) the relevance of the retrieved results. The results of the survey show that our method extracts coherent and representative logical schemas. Experts' feedback on the performance of the integrated system and the relevance of the retrieved results was also positive. Regarding the validation of the integration, the system successfully provided correct results for all queries in the test set. The results of the experiment suggest that text-based sources including a logical schema can be regarded as equivalent to structured databases. Using our method, previous research and existing tools designed for the integration of structured databases can be reused - possibly subject to minor modifications - to integrate differently structured sources.

Literature-based discovery of diabetes- and ROS-related targets

PubMed Central

2010-01-01

Background Reactive oxygen species (ROS) are known mediators of cellular damage in multiple diseases including diabetic complications. Despite its importance, no comprehensive database is currently available for the genes associated with ROS. Methods We present ROS- and diabetes-related targets (genes/proteins) collected from the biomedical literature through a text mining technology. A web-based literature mining tool, SciMiner, was applied to 1,154 biomedical papers indexed with diabetes and ROS by PubMed to identify relevant targets. Over-represented targets in the ROS-diabetes literature were obtained through comparisons against randomly selected literature. The expression levels of nine genes, selected from the top ranked ROS-diabetes set, were measured in the dorsal root ganglia (DRG) of diabetic and non-diabetic DBA/2J mice in order to evaluate the biological relevance of literature-derived targets in the pathogenesis of diabetic neuropathy. Results SciMiner identified 1,026 ROS- and diabetes-related targets from the 1,154 biomedical papers (http://jdrf.neurology.med.umich.edu/ROSDiabetes/). Fifty-three targets were significantly over-represented in the ROS-diabetes literature compared to randomly selected literature. These over-represented targets included well-known members of the oxidative stress response including catalase, the NADPH oxidase family, and the superoxide dismutase family of proteins. Eight of the nine selected genes exhibited significant differential expression between diabetic and non-diabetic mice. For six genes, the direction of expression change in diabetes paralleled enhanced oxidative stress in the DRG. Conclusions Literature mining compiled ROS-diabetes related targets from the biomedical literature and led us to evaluate the biological relevance of selected targets in the pathogenesis of diabetic neuropathy. PMID:20979611

fastPACE Train-the-Trainer: A scalable new educational program to accelerate training in biomedical innovation, entrepreneurship, and commercialization.

PubMed

Servoss, Jonathan; Chang, Connie; Fay, Jonathan; Lota, Kanchan Sehgal; Mashour, George A; Ward, Kevin R

2017-10-01

The Institute of Medicine recommended the advance of innovation and entrepreneurship training programs within the Clinical & Translational Science Award (CTSA) program; however, there remains a gap in adoption by CTSA institutes. The University of Michigan's Michigan Institute for Clinical & Health Research and Fast Forward Medical Innovation (FFMI) partnered to develop a pilot program designed to teach CTSA hubs how to implement innovation and entrepreneurship programs at their home institutions. The program provided a 2-day onsite training experience combined with observation of an ongoing course focused on providing biomedical innovation, commercialization and entrepreneurial training to a medical academician audience (FFMI fast PACE). All 9 participating CTSA institutes reported a greater connection to biomedical research commercialization resources. Six launched their own version of the FFMI fast PACE course or modified existing programs. Two reported greater collaboration with their technology transfer offices. The FFMI fast PACE course and training program may be suitable for CTSA hubs looking to enhance innovation and entrepreneurship within their institutions and across their innovation ecosystems.

Minimization and management of wastes from biomedical research.

PubMed Central

Rau, E H; Alaimo, R J; Ashbrook, P C; Austin, S M; Borenstein, N; Evans, M R; French, H M; Gilpin, R W; Hughes, J; Hummel, S J; Jacobsohn, A P; Lee, C Y; Merkle, S; Radzinski, T; Sloane, R; Wagner, K D; Weaner, L E

2000-01-01

Several committees were established by the National Association of Physicians for the Environment to investigate and report on various topics at the National Leadership Conference on Biomedical Research and the Environment held at the 1--2 November 1999 at the National Institutes of Health in Bethesda, Maryland. This is the report of the Committee on Minimization and Management of Wastes from Biomedical Research. Biomedical research facilities contribute a small fraction of the total amount of wastes generated in the United States, and the rate of generation appears to be decreasing. Significant reductions in generation of hazardous, radioactive, and mixed wastes have recently been reported, even at facilities with rapidly expanding research programs. Changes in the focus of research, improvements in laboratory techniques, and greater emphasis on waste minimization (volume and toxicity reduction) explain the declining trend in generation. The potential for uncontrolled releases of wastes from biomedical research facilities and adverse impacts on the general environment from these wastes appears to be low. Wastes are subject to numerous regulatory requirements and are contained and managed in a manner protective of the environment. Most biohazardous agents, chemicals, and radionuclides that find significant use in research are not likely to be persistent, bioaccumulative, or toxic if they are released. Today, the primary motivations for the ongoing efforts by facilities to improve minimization and management of wastes are regulatory compliance and avoidance of the high disposal costs and liabilities associated with generation of regulated wastes. The committee concluded that there was no evidence suggesting that the anticipated increases in biomedical research will significantly increase generation of hazardous wastes or have adverse impacts on the general environment. This conclusion assumes the positive, countervailing trends of enhanced pollution prevention efforts by facilities and reductions in waste generation resulting from improvements in research methods will continue. PMID:11121362

The normative dimensions of extending the human lifespan by age-related biomedical innovations.

PubMed

Ehni, Hans-Joerg; Marckmann, Georg

2008-10-01

The current normative debate on age-related biomedical innovations and the extension of the human lifespan has important shortcomings. Mainly, the complexity of the different normative dimensions relevant for ethical and/or juridicial norms is not fully developed and the normative quality of teleological and deontological arguments is not properly distinguished. This article addresses some of these shortcomings and develops the outline of a more comprehensive normative framework covering all relevant dimensions. Such a frame necessarily has to include conceptions of a good life on the individual and societal levels. Furthermore, as a third dimension, a model for the access to and the just distribution of age-related biomedical innovations and technologies extending the human lifespan will be developed. It is argued that such a model has to include the different levels of the general philosophical theories of distributive justice, including social rights and theories of just health care. Furthermore, it has to show how these theories can be applied to the problem area of aging and extending the human lifespan.

Joint development of evidence-based medical record by doctors and patients through integrated Chinese and Western medicine on digestive system diseases.

PubMed

Li, Bo; Gao, Hong-yang; Gao, Rui; Zhao, Ying-pan; Li, Qing-na; Zhao, Yang; Tang, Xu-dong; Shang, Hong-cai

2016-02-01

Building the clinical therapeutic evaluation system by combing the evaluation given by doctors and patients can form a more comprehensive and objective evaluation system. A literature search on the practice of evidence-based evaluation was conducted in key biomedical databases, i.e. PubMed, Excerpt Medica Database, China Biology Medicine disc and China National Knowledge Infrastructure. However, no relevant study on the subjects of interest was identified. Therefore, drawing on the principles of narrative medicine and expert opinion from systems of Chinese medicine and Western medicine, we propose to develop and pilot-test a novel evidence-based medical record format that captures the perspectives of both patients and doctors in a clinical trial. Further, we seek to evaluate a strategic therapeutic approach that integrates the wisdom of Chinese medicine with the scientific basis of Western medicine in the treatment of digestive system disorders. Evaluation of therapeutic efficacy of remedies under the system of Chinese medicine is an imperative ongoing research. The present study intends to identify a novel approach to assess the synergistic benefits achievable from an integrated therapeutic approach combining Chinese and Western system of medicine to treat digestive system disorders.

Fault Tree Analysis: Investigation of Epidemic Hemorrhagic Fever Infection Acquired in Animal Laboratories in China.

PubMed

Liu, Xiao Yu; Xue, Kang Ning; Rong, Rong; Zhao, Chi Hong

2016-01-01

Epidemic hemorrhagic fever has been an ongoing threat to laboratory personnel involved in animal care and use. Laboratory transmissions and severe infections occurred over the past twenty years, even though the standards and regulations for laboratory biosafety have been issued, upgraded, and implemented in China. Therefore, there is an urgent need to identify risk factors and to seek effective preventive measures that can curb the incidences of epidemic hemorrhagic fever among laboratory personnel. In the present study, we reviewed literature that relevant to animals laboratory-acquired hemorrhagic fever infections reported from 1995 to 2015, and analyzed these incidences using fault tree analysis (FTA). The results of data analysis showed that purchasing of qualified animals and guarding against wild rats which could make sure the laboratory animals without hantaviruses, are the basic measures to prevent infections. During the process of daily management, the consciousness of personal protecting and the ability of personal protecting need to be further improved. Undoubtedly vaccination is the most direct and effective method, while it plays role after infection. So avoiding infections can't rely entirely on vaccination. Copyright © 2016 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

The nature of platinum in silicones for biomedical and healthcare use.

PubMed

Lambert, James M

2006-07-01

Silicone is an important biomaterial in many different biomedical and healthcare applications. Network formation in one type of silicone relies upon a chemical crosslinking reaction that typically employs a platinum catalyst. As a consequence, low concentrations of platinum may remain in certain medical devices designed for human use. The characteristics of platinum in silicone before, during, and after the crosslinking reaction have been well described in the literature. This review summarizes the relevant literature on the organometallic and analytical chemistry of platinum in silicone and thus provides a foundation for understanding the effects this platinum may have, if any, in the various biomedical and healthcare applications where it may be present.

Social Media and Mentoring in Biomedical Research Faculty Development.

PubMed

Teruya, Stacey Alan; Bazargan-Hejazi, Shahrzad

2014-09-01

To determine how effective and collegial mentoring in biomedical research faculty development may be implemented and facilitated through social media. The authors reviewed the literature for objectives, concerns, and limitations of career development for junior research faculty. They tabularized these as developmental goals, and aligned them with relevant social media strengths and capabilities facilitated through traditional and/or peer mentoring. The authors derived a model in which social media is leveraged to achieve developmental goals reflected in independent and shared projects, and in the creation and expansion of support and research networks. Social media may be successfully leveraged and applied in achieving developmental goals for biomedical research faculty, and potentially for those in other fields and disciplines.

Accessing Biomedical Literature in the Current Information Landscape

PubMed Central

Khare, Ritu; Leaman, Robert; Lu, Zhiyong

2015-01-01

i. Summary Biomedical and life sciences literature is unique because of its exponentially increasing volume and interdisciplinary nature. Biomedical literature access is essential for several types of users including biomedical researchers, clinicians, database curators, and bibliometricians. In the past few decades, several online search tools and literature archives, generic as well as biomedicine-specific, have been developed. We present this chapter in the light of three consecutive steps of literature access: searching for citations, retrieving full-text, and viewing the article. The first section presents the current state of practice of biomedical literature access, including an analysis of the search tools most frequently used by the users, including PubMed, Google Scholar, Web of Science, Scopus, and Embase, and a study on biomedical literature archives such as PubMed Central. The next section describes current research and the state-of-the-art systems motivated by the challenges a user faces during query formulation and interpretation of search results. The research solutions are classified into five key areas related to text and data mining, text similarity search, semantic search, query support, relevance ranking, and clustering results. Finally, the last section describes some predicted future trends for improving biomedical literature access, such as searching and reading articles on portable devices, and adoption of the open access policy. PMID:24788259

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

PubMed

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.

Emerging Ceramic-based Materials for Dentistry

PubMed Central

Denry, I.; Kelly, J.R.

2014-01-01

Our goal is to give an overview of a selection of emerging ceramics and issues for dental or biomedical applications, with emphasis on specific challenges associated with full-contour zirconia ceramics, and a brief synopsis on new machinable glass-ceramics and ceramic-based interpenetrating phase composites. Selected fabrication techniques relevant to dental or biomedical applications such as microwave sintering, spark plasma sintering, and additive manufacturing are also reviewed. Where appropriate, the authors have added their opinions and guidance. PMID:25274751

Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature

PubMed Central

Sutton, Victoria R.; Hauser, Susan E.

2005-01-01

MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information. PMID:16779415

Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval

PubMed Central

Karisani, Payam; Qin, Zhaohui S; Agichtein, Eugene

2018-01-01

Abstract The bioCADDIE dataset retrieval challenge brought together different approaches to retrieval of biomedical datasets relevant to a user’s query, expressed as a text description of a needed dataset. We describe experiments in applying a data-driven, machine learning-based approach to biomedical dataset retrieval as part of this challenge. We report on a series of experiments carried out to evaluate the performance of both probabilistic and machine learning-driven techniques from information retrieval, as applied to this challenge. Our experiments with probabilistic information retrieval methods, such as query term weight optimization, automatic query expansion and simulated user relevance feedback, demonstrate that automatically boosting the weights of important keywords in a verbose query is more effective than other methods. We also show that although there is a rich space of potential representations and features available in this domain, machine learning-based re-ranking models are not able to improve on probabilistic information retrieval techniques with the currently available training data. The models and algorithms presented in this paper can serve as a viable implementation of a search engine to provide access to biomedical datasets. The retrieval performance is expected to be further improved by using additional training data that is created by expert annotation, or gathered through usage logs, clicks and other processes during natural operation of the system. Database URL: https://github.com/emory-irlab/biocaddie PMID:29688379

The effects of utility evaluations, biomedical knowledge and modernization on intention to exclusively use biomedical health facilities among rural households in Mozambique.

PubMed

Mukolo, Abraham; Cooil, Bruce; Victor, Bart

2015-08-01

In resource-limited settings, the choice between utilizing biomedical health services and/or traditional healers is critical to the success of the public health mission. In the literature, this choice has been predicted to be influenced by three major factors: knowledge about biomedical etiologies; cultural modernization; and rational choice. The current study investigated all three of these predicted determinants, applying data from a general household survey conducted in 2010 in Zambézia Province of Mozambique involving 1045 randomly sampled rural households. Overall, more respondents (N = 802) intended to continue to supplement their biomedical healthcare with traditional healer services in comparison with those intending to utilize biomedical care exclusively (N = 243). The findings strongly supported the predicted association between rational utility (measured as satisfaction with the quality of service and results from past care) with the future intention to continue to supplement or utilize biomedical care exclusively. Odds of moving away from supplementation increase by a factor of 2.5 if the respondent reported seeing their condition improve under government/private biomedical care. Odds of staying with supplementation increase by a factor 3.1 if the respondent was satisfied with traditional care and a factor of 16 if the condition had improved under traditional care. Modernization variables (education, income, religion, and Portuguese language skills) were relevant and provided a significant component of the best scientific model. Amount of biomedical knowledge was not a significant predictor of choice. There was a small effect on choice from knowing the limitations of biomedical care. The findings have implications for public healthcare promotion activities in areas where biomedical care is introduced as an alternative to traditional healing. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuerteltaub, K. W.; Bench, G.; Buchholz, B. A.

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 integratedmore » 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 instruments.4.) Provide high throughput 14C BioAMS analysis for collaborative and service clients.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turteltaub, K. W.; Bench, G.; Buchholz, B. A.

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 integratedmore » 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 instruments.4.) Provide high throughput 14C BioAMS analysis for collaborative and service clients.« less

Towards a 21st century roadmap for biomedical research and ...

EPA Pesticide Factsheets

Decades of costly failures in translating drug candidates from preclinical disease models to human therapeutic use warrant reconsideration of the priority placed on animal models in biomedical research. Following an international workshop attended by experts from academia, government institutions, research funding bodies and the corporate and NGO sectors, this consensus report analyses, as case studies, five disease areas with major unmet needs for new treatments. In view of the scientifically driven transition towards a human pathways-based paradigm in toxicology, a similar paradigm shift appears to be justified in biomedical research. There is a pressing need for an approach that strategically implements advanced, human biology-based models and tools to understand disease pathways at multiple biological scales. We present recommendations to help achieve this. To discover and develop new therapies, we need 21-century roadmaps for biomedical research based on multiscale human disease pathways, and supported by policy and funding strategies that prioritise human relevance.

Animal Experiments in Biomedical Research: A Historical Perspective

PubMed Central

Franco, Nuno Henrique

2013-01-01

Simple Summary This article reviews the use of non-human animals in biomedical research from a historical viewpoint, providing an insight into the most relevant social and moral issues on this topic across time, as well as to how the current paradigm for ethically and publically acceptable use of animals in biomedicine has been achieved. Abstract The use of non-human animals in biomedical research has given important contributions to the medical progress achieved in our day, but it has also been a cause of heated public, scientific and philosophical discussion for hundreds of years. This review, with a mainly European outlook, addresses the history of animal use in biomedical research, some of its main protagonists and antagonists, and its effect on society from Antiquity to the present day, while providing a historical context with which to understand how we have arrived at the current paradigm regarding the ethical treatment of animals in research. PMID:26487317

Finding and Accessing Diagrams in Biomedical Publications

PubMed Central

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. PMID:23304318

[Biomedical research in Revista de Biologia Tropical].

PubMed

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.

An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition.

PubMed

Tsatsaronis, George; Balikas, Georgios; Malakasiotis, Prodromos; Partalas, Ioannis; Zschunke, Matthias; Alvers, Michael R; Weissenborn, Dirk; Krithara, Anastasia; Petridis, Sergios; Polychronopoulos, Dimitris; Almirantis, Yannis; Pavlopoulos, John; Baskiotis, Nicolas; Gallinari, Patrick; Artiéres, Thierry; Ngomo, Axel-Cyrille Ngonga; Heino, Norman; Gaussier, Eric; Barrio-Alvers, Liliana; Schroeder, Michael; Androutsopoulos, Ion; Paliouras, Georgios

2015-04-30

This article provides an overview of the first BIOASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BIOASQ assesses the ability of systems to semantically index very large numbers of biomedical scientific articles, and to return concise and user-understandable answers to given natural language questions by combining information from biomedical articles and ontologies. The 2013 BIOASQ competition comprised two tasks, Task 1a and Task 1b. In Task 1a participants were asked to automatically annotate new PUBMED documents with MESH headings. Twelve teams participated in Task 1a, with a total of 46 system runs submitted, and one of the teams performing consistently better than the MTI indexer used by NLM to suggest MESH headings to curators. Task 1b used benchmark datasets containing 29 development and 282 test English questions, along with gold standard (reference) answers, prepared by a team of biomedical experts from around Europe and participants had to automatically produce answers. Three teams participated in Task 1b, with 11 system runs. The BIOASQ infrastructure, including benchmark datasets, evaluation mechanisms, and the results of the participants and baseline methods, is publicly available. A publicly available evaluation infrastructure for biomedical semantic indexing and QA has been developed, which includes benchmark datasets, and can be used to evaluate systems that: assign MESH headings to published articles or to English questions; retrieve relevant RDF triples from ontologies, relevant articles and snippets from PUBMED Central; produce "exact" and paragraph-sized "ideal" answers (summaries). The results of the systems that participated in the 2013 BIOASQ competition are promising. In Task 1a one of the systems performed consistently better from the NLM's MTI indexer. In Task 1b the systems received high scores in the manual evaluation of the "ideal" answers; hence, they produced high quality summaries as answers. Overall, BIOASQ helped obtain a unified view of how techniques from text classification, semantic indexing, document and passage retrieval, question answering, and text summarization can be combined to allow biomedical experts to obtain concise, user-understandable answers to questions reflecting their real information needs.

FRATIS concept of operations : assessment of relevant prior and ongoing research and industry practices.

DOT National Transportation Integrated Search

2012-08-01

This report summarizes the state of the practice in freight-related advanced traveler information systems (ATIS) and assesses their relevance to the development of a Freight Advanced Traveler Information System (FRATIS). The report includes relevant ...

Measuring and understanding the attitudes of Australian gay and bisexual men towards biomedical HIV prevention using cross-sectional data and factor analyses.

PubMed

Wilkinson, Anna L; Draper, Bridget L; Pedrana, Alisa E; Asselin, Jason; Holt, Martin; Hellard, Margaret E; Stoové, Mark

2017-11-21

Contemporary responses to HIV embrace biomedical prevention, particularly treatment as prevention (TasP) and pre-exposure prophylaxis (PrEP). However, large-scale implementation of biomedical prevention should be ideally preceded by assessments of their community acceptability. We aimed to understand contemporary attitudes of gay and bisexual men (GBM) in Australia towards biomedical-based HIV prevention and propose a framework for their measurement and ongoing monitoring. A cross-sectional, online survey of GBM ≥18 years has been conducted annually in Victoria, Australia, since 2008. In 2016, 35 attitudinal items on biomedical HIV prevention were added. Items were scored on five-point Likert scales. We used principal factor analysis to identify key constructs related to GBM's attitudes to biomedical HIV prevention and use these to characterise levels of support for TasP and PrEP. A total of 462 HIV-negative or HIV-status-unknown men, not using PrEP, provided valid responses for all 35 attitudinal items. We extracted four distinct and interpretable factors we named: 'Confidence in PrEP', 'Judicious approach to PrEP', 'Treatment as prevention optimism' and 'Support for early treatment'. High levels of agreement were seen across PrEP-related items; 77.9% of men agreed that PrEP prevented HIV acquisition and 83.6% of men agreed that users were protecting themselves. However, the agreement levels for HIV TasP items were considerably lower, with <20% of men agreeing treatment (undetectable viral load) reduced HIV transmission risk. Better understanding of community attitudes is crucial for shaping policy and informing initiatives that aim to improve knowledge, acceptance and uptake of biomedical prevention. Our analyses suggest confidence in, acceptability of and community support for PrEP among GBM. However, strategies to address scepticism towards HIV treatment when used for prevention may be needed to optimise combination biomedical HIV prevention. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Medical Scenarios Relevant to Spaceflight

NASA Technical Reports Server (NTRS)

Bacal, Kira; Hurs, Victor; Doerr, Harold

2004-01-01

The Medical Operational Support Team (MOST) was tasked by the JSC Space Medicine and Life Sciences Directorate (SLSD) to incorporate medical simulation into 1) medical training for astronaut-crew medical officers (CMO) and medical flight control teams and 2) evaluations of procedures and resources required for medical care aboard the International Space Station (ISS). Development of evidence-based medical scenarios that mimic the physiology observed during spaceflight will be needed for the MOST to complete these two tasks. The MOST used a human patient simulator, the ISS-like resources in the Medical Simulation Laboratory (MSL), and evidence from space operations, military operations and medical literature to develop space relevant medical scenarios. These scenarios include conditions concerning airway management, Advanced Cardiac Life Support (ACLS) and mitigating anaphylactic symptoms. The MOST has used these space relevant medical scenarios to develop a preliminary space medical training regimen for NASA flight surgeons, Biomedical Flight Controllers (Biomedical Engineers; BME) and CMO-analogs. This regimen is conducted by the MOST in the MSL. The MOST has the capability to develop evidence-based space-relevant medical scenarios that can help SLSD I) demonstrate the proficiency of medical flight control teams to mitigate space-relevant medical events and 2) validate nextgeneration medical equipment and procedures for space medicine applications.

Compensatory neurofuzzy model for discrete data classification in biomedical

NASA Astrophysics Data System (ADS)

Ceylan, Rahime

2015-03-01

Biomedical data is separated to two main sections: signals and discrete data. So, studies in this area are about biomedical signal classification or biomedical discrete data classification. There are artificial intelligence models which are relevant to classification of ECG, EMG or EEG signals. In same way, in literature, many models exist for classification of discrete data taken as value of samples which can be results of blood analysis or biopsy in medical process. Each algorithm could not achieve high accuracy rate on classification of signal and discrete data. In this study, compensatory neurofuzzy network model is presented for classification of discrete data in biomedical pattern recognition area. The compensatory neurofuzzy network has a hybrid and binary classifier. In this system, the parameters of fuzzy systems are updated by backpropagation algorithm. The realized classifier model is conducted to two benchmark datasets (Wisconsin Breast Cancer dataset and Pima Indian Diabetes dataset). Experimental studies show that compensatory neurofuzzy network model achieved 96.11% accuracy rate in classification of breast cancer dataset and 69.08% accuracy rate was obtained in experiments made on diabetes dataset with only 10 iterations.

Using Biomedically Relevant Multimedia Content in an Introductory Physics Course for Life Science and Pre-health Students

NASA Astrophysics Data System (ADS)

Mylott, Elliot; Kutschera, Ellynne; Dunlap, Justin C.; Christensen, Warren; Widenhorn, Ralf

2016-04-01

We will describe a one-quarter pilot algebra-based introductory physics course for pre-health and life science majors. The course features videos with biomedical experts and cogent biomedically inspired physics content. The materials were used in a flipped classroom as well as an all-online environment where students interacted with multimedia materials online and prior to engaging in classroom activities. Pre-lecture questions on both the medical content covered in the video media and the physics concepts in the written material were designed to engage students and probe their understanding of physics. The course featured group discussion and peer-lead instruction. Following in-class instruction, students engaged with homework assignments which explore the connections of physics and the medical field in a quantitative manner. Course surveys showed a positive response by the vast majority of students. Students largely indicated that the course helped them to make a connection between physics and the biomedical field. The biomedical focus and different course format were seen as an improvement to previous traditional physics instruction.

Semantic Similarity in Biomedical Ontologies

PubMed Central

Pesquita, Catia; Faria, Daniel; Falcão, André O.; Lord, Phillip; Couto, Francisco M.

2009-01-01

In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization. We review semantic similarity measures applied to biomedical ontologies and propose their classification according to the strategies they employ: node-based versus edge-based and pairwise versus groupwise. We also present comparative assessment studies and discuss the implications of their results. We survey the existing implementations of semantic similarity measures, and we describe examples of applications to biomedical research. This will clarify how biomedical researchers can benefit from semantic similarity measures and help them choose the approach most suitable for their studies. Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application of automated annotation procedures to create corpora of higher quality and completeness than are currently available. Given that semantic similarity measures are directly dependent on these evolutions, we can expect to see them gaining more relevance and even becoming as essential as sequence similarity is today in biomedical research. PMID:19649320

Teleoperator/robot technology can help solve biomedical problems

NASA Technical Reports Server (NTRS)

Heer, E.; Bejczy, A. K.

1975-01-01

Teleoperator and robot technology appears to offer the possibility to apply these techniques to the benefit for the severely handicapped giving them greater self reliance and independence. Major problem areas in the development of prostheses and remotely controlled devices for the handicapped are briefly discussed, and the parallelism with problems in the development of teleoperator/robots identified. A brief description of specific ongoing and projected developments in the area of remotely controlled devices (wheelchairs and manipulators) is provided.

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

PubMed

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 increased to 86-97%; this indicates that researchers felt that only 3-14% of the necessary information for full figure comprehension was missing when full text was available to them. Clearly there is information in the abstract and in the full text that biomedical scientists deem important for understanding the figures that appear in full-text biomedical articles. We conclude that the texts that appear in full-text biomedical articles are useful for understanding the meaning of a figure, and an effective figure-mining system needs to unlock the information beyond figure legend. Our work provides important guidance to the figure mining systems that extract information only from figure and figure legend.

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

PubMed Central

2009-01-01

Background 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. Methods 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. Results 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 increased to 86–97%; this indicates that researchers felt that only 3–14% of the necessary information for full figure comprehension was missing when full text was available to them. Clearly there is information in the abstract and in the full text that biomedical scientists deem important for understanding the figures that appear in full-text biomedical articles. Conclusion We conclude that the texts that appear in full-text biomedical articles are useful for understanding the meaning of a figure, and an effective figure-mining system needs to unlock the information beyond figure legend. Our work provides important guidance to the figure mining systems that extract information only from figure and figure legend. PMID:19126221

Social Media and Mentoring in Biomedical Research Faculty Development

PubMed Central

Teruya, Stacey Alan; Bazargan-Hejazi, Shahrzad

2015-01-01

Purpose To determine how effective and collegial mentoring in biomedical research faculty development may be implemented and facilitated through social media. Method The authors reviewed the literature for objectives, concerns, and limitations of career development for junior research faculty. They tabularized these as developmental goals, and aligned them with relevant social media strengths and capabilities facilitated through traditional and/or peer mentoring. Results The authors derived a model in which social media is leveraged to achieve developmental goals reflected in independent and shared projects, and in the creation and expansion of support and research networks. Conclusions Social media may be successfully leveraged and applied in achieving developmental goals for biomedical research faculty, and potentially for those in other fields and disciplines. PMID:26120494

A Planetary Defense Gateway for Smart Discovery of relevant Information for Decision Support

NASA Technical Reports Server (NTRS)

Bambacus, Myra; Yang, Chaowei Phil; Leung, Ronald Y.; Barbee, Brent; Nuth, Joseph A.; Seery, Bernard; Jiang, Yongyao; Qin, Han; Li, Yun; Yu, Manzhu;

Semantic annotation in biomedicine: the current landscape.

PubMed

Jovanović, Jelena; Bagheri, Ebrahim

2017-09-22

The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing. This process is widely known as semantic annotation, and the tools that perform it are known as semantic annotators.Over the last dozen years, the biomedical research community has invested significant efforts in the development of biomedical semantic annotation technology. Aiming to establish grounds for further developments in this area, we review a selected set of state of the art biomedical semantic annotators, focusing particularly on general purpose annotators, that is, semantic annotation tools that can be customized to work with texts from any area of biomedicine. We also examine potential directions for further improvements of today's annotators which could make them even more capable of meeting the needs of real-world applications. To motivate and encourage further developments in this area, along the suggested and/or related directions, we review existing and potential practical applications and benefits of semantic annotators.

Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols.

PubMed

Campagne, Fabien

2008-02-29

The evaluation of information retrieval techniques has traditionally relied on human judges to determine which documents are relevant to a query and which are not. This protocol is used in the Text Retrieval Evaluation Conference (TREC), organized annually for the past 15 years, to support the unbiased evaluation of novel information retrieval approaches. The TREC Genomics Track has recently been introduced to measure the performance of information retrieval for biomedical applications. We describe two protocols for evaluating biomedical information retrieval techniques without human relevance judgments. We call these protocols No Title Evaluation (NT Evaluation). The first protocol measures performance for focused searches, where only one relevant document exists for each query. The second protocol measures performance for queries expected to have potentially many relevant documents per query (high-recall searches). Both protocols take advantage of the clear separation of titles and abstracts found in Medline. We compare the performance obtained with these evaluation protocols to results obtained by reusing the relevance judgments produced in the 2004 and 2005 TREC Genomics Track and observe significant correlations between performance rankings generated by our approach and TREC. Spearman's correlation coefficients in the range of 0.79-0.92 are observed comparing bpref measured with NT Evaluation or with TREC evaluations. For comparison, coefficients in the range 0.86-0.94 can be observed when evaluating the same set of methods with data from two independent TREC Genomics Track evaluations. We discuss the advantages of NT Evaluation over the TRels and the data fusion evaluation protocols introduced recently. Our results suggest that the NT Evaluation protocols described here could be used to optimize some search engine parameters before human evaluation. Further research is needed to determine if NT Evaluation or variants of these protocols can fully substitute for human evaluations.

Biomedical Approaches to HIV Prevention in Women.

PubMed

Heumann, Christine L

2018-04-17

Effective HIV prevention techniques for women are of critical importance, as nearly half of all HIV infections globally are in women. This article reviews the recent literature on biomedical approaches to HIV prevention in women. In trials in which women were adherent to oral pre-exposure prophylaxis (PrEP), PrEP was equally efficacious in men and women. However, in studies of oral PrEP exclusively in women, adherence was low, and it was not efficacious. In trials of topical PrEP, including vaginal tenofovir gel and the monthly dapivirine ring, efficacy was also dependent upon adherence. Treatment as prevention (TasP) is a very effective HIV prevention strategy, though limited in that it is not controlled by the HIV-uninfected partner. Adherence is an important factor in the efficacy of biomedical interventions for HIV prevention in women; continued research is needed to identify the most efficacious and acceptable agents for women. Oral PrEP is currently recommended for the following groups of HIV-negative women: heterosexual women in ongoing sexual relationships with a partner infected with or at substantial risk of HIV infection and women who inject drugs and share injection or drug preparation equipment.

Strom Thurmond Biomedical Research Center at the Medical Univesity for South Carolina Charleston, South Carolina

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1994-02-01

The Department of Energy (DOE) has prepared an Environmental Assessment (EA) evaluating the proposed construction and operation of the Strom Thurmond Biomedical Research Center (Center) at the Medical University of South Carolina (MUSC), Charleston, SC. The DOE is evaluating a grant proposal to authorize the MUSC to construct, equip and operate the lower two floors of the proposed nine-story Center as an expansion of on-going clinical research and out-patient diagnostic activities of the Cardiology Division of the existing Gazes Cardiac Research Institute. Based on the analysis in the EA, the DOE has determined that the proposed action does not constitutemore » a major federal action significantly affecting the quality of the human environment within the meaning of the NEPA. Therefore, the preparation of an Environmental Impact Statement is not required.« less

Explorative search of distributed bio-data to answer complex biomedical questions

PubMed Central

2014-01-01

Background The huge amount of biomedical-molecular data increasingly produced is providing scientists with potentially valuable information. Yet, such data quantity makes difficult to find and extract those data that are most reliable and most related to the biomedical questions to be answered, which are increasingly complex and often involve many different biomedical-molecular aspects. Such questions can be addressed only by comprehensively searching and exploring different types of data, which frequently are ordered and provided by different data sources. Search Computing has been proposed for the management and integration of ranked results from heterogeneous search services. Here, we present its novel application to the explorative search of distributed biomedical-molecular data and the integration of the search results to answer complex biomedical questions. Results A set of available bioinformatics search services has been modelled and registered in the Search Computing framework, and a Bioinformatics Search Computing application (Bio-SeCo) using such services has been created and made publicly available at http://www.bioinformatics.deib.polimi.it/bio-seco/seco/. It offers an integrated environment which eases search, exploration and ranking-aware combination of heterogeneous data provided by the available registered services, and supplies global results that can support answering complex multi-topic biomedical questions. Conclusions By using Bio-SeCo, scientists can explore the very large and very heterogeneous biomedical-molecular data available. They can easily make different explorative search attempts, inspect obtained results, select the most appropriate, expand or refine them and move forward and backward in the construction of a global complex biomedical query on multiple distributed sources that could eventually find the most relevant results. Thus, it provides an extremely useful automated support for exploratory integrated bio search, which is fundamental for Life Science data driven knowledge discovery. PMID:24564278

Rapid prototyping of multi-scale biomedical microdevices by combining additive manufacturing technologies.

PubMed

Hengsbach, Stefan; Lantada, Andrés Díaz

2014-08-01

The possibility of designing and manufacturing biomedical microdevices with multiple length-scale geometries can help to promote special interactions both with their environment and with surrounding biological systems. These interactions aim to enhance biocompatibility and overall performance by using biomimetic approaches. In this paper, we present a design and manufacturing procedure for obtaining multi-scale biomedical microsystems based on the combination of two additive manufacturing processes: a conventional laser writer to manufacture the overall device structure, and a direct-laser writer based on two-photon polymerization to yield finer details. The process excels for its versatility, accuracy and manufacturing speed and allows for the manufacture of microsystems and implants with overall sizes up to several millimeters and with details down to sub-micrometric structures. As an application example we have focused on manufacturing a biomedical microsystem to analyze the impact of microtextured surfaces on cell motility. This process yielded a relevant increase in precision and manufacturing speed when compared with more conventional rapid prototyping procedures.

A robust pointer segmentation in biomedical images toward building a visual ontology for biomedical article retrieval

NASA Astrophysics Data System (ADS)

You, Daekeun; Simpson, Matthew; Antani, Sameer; Demner-Fushman, Dina; Thoma, George R.

2013-01-01

Pointers (arrows and symbols) are frequently used in biomedical images to highlight specific image regions of interest (ROIs) that are mentioned in figure captions and/or text discussion. Detection of pointers is the first step toward extracting relevant visual features from ROIs and combining them with textual descriptions for a multimodal (text and image) biomedical article retrieval system. Recently we developed a pointer recognition algorithm based on an edge-based pointer segmentation method, and subsequently reported improvements made on our initial approach involving the use of Active Shape Models (ASM) for pointer recognition and region growing-based method for pointer segmentation. These methods contributed to improving the recall of pointer recognition but not much to the precision. The method discussed in this article is our recent effort to improve the precision rate. Evaluation performed on two datasets and compared with other pointer segmentation methods show significantly improved precision and the highest F1 score.

Characterizing semantic mappings adaptation via biomedical KOS evolution: a case study investigating SNOMED CT and ICD.

PubMed

Dos Reis, Julio Cesar; Pruski, Cédric; Da Silveira, Marcos; Reynaud-Delaître, Chantal

2013-01-01

Mappings established between Knowledge Organization Systems (KOS) increase semantic interoperability between biomedical information systems. However, biomedical knowledge is highly dynamic and changes affecting KOS entities can potentially invalidate part or the totality of existing mappings. Understanding how mappings evolve and what the impacts of KOS evolution on mappings are is therefore crucial for the definition of an automatic approach to maintain mappings valid and up-to-date over time. In this article, we study variations of a specific KOS complex change (split) for two biomedical KOS (SNOMED CT and ICD-9-CM) through a rigorous method of investigation for identifying and refining complex changes, and for selecting representative cases. We empirically analyze and explain their influence on the evolution of associated mappings. Results point out the importance of considering various dimensions of the information described in KOS, like the semantic structure of concepts, the set of relevant information used to define the mappings and the change operations interfering with this set of information.

Characterizing Semantic Mappings Adaptation via Biomedical KOS Evolution: A Case Study Investigating SNOMED CT and ICD

PubMed Central

Reis, Julio Cesar Dos; Pruski, Cédric; Da Silveira, Marcos; Reynaud-Delaître, Chantal

2013-01-01

Mappings established between Knowledge Organization Systems (KOS) increase semantic interoperability between biomedical information systems. However, biomedical knowledge is highly dynamic and changes affecting KOS entities can potentially invalidate part or the totality of existing mappings. Understanding how mappings evolve and what the impacts of KOS evolution on mappings are is therefore crucial for the definition of an automatic approach to maintain mappings valid and up-to-date over time. In this article, we study variations of a specific KOS complex change (split) for two biomedical KOS (SNOMED CT and ICD-9-CM) through a rigorous method of investigation for identifying and refining complex changes, and for selecting representative cases. We empirically analyze and explain their influence on the evolution of associated mappings. Results point out the importance of considering various dimensions of the information described in KOS, like the semantic structure of concepts, the set of relevant information used to define the mappings and the change operations interfering with this set of information. PMID:24551341

Unbridle biomedical research from the laboratory cage

PubMed Central

Lahvis, Garet P

2017-01-01

Many biomedical research studies use captive animals to model human health and disease. However, a surprising number of studies show that the biological systems of animals living in standard laboratory housing are abnormal. To make animal studies more relevant to human health, research animals should live in the wild or be able to roam free in captive environments that offer a natural range of both positive and negative experiences. Recent technological advances now allow us to study freely roaming animals and we should make use of them. PMID:28661398

Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature

PubMed Central

Chen, Guocai; Zhao, Jieyi; Cohen, Trevor; Tao, Cui; Sun, Jingchun; Xu, Hua; Bernstam, Elmer V.; Lawson, Andrew; Zeng, Jia; Johnson, Amber M.; Holla, Vijaykumar; Bailey, Ann M.; Lara-Guerra, Humberto; Litzenburger, Beate; Meric-Bernstam, Funda; Jim Zheng, W.

2015-01-01

Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene and article association. The core algorithm was implemented using a graphics processing unit-based MapReduce framework to handle big data and to improve performance. We conclude that Ontology Fingerprints can help disambiguate gene names mentioned in text and analyse the association between genes and articles. Database URL: http://www.ontologyfingerprint.org PMID:25858285

BIOSMILE web search: a web application for annotating biomedical entities and relations.

PubMed

Dai, Hong-Jie; Huang, Chi-Hsin; Lin, Ryan T K; Tsai, Richard Tzong-Han; Hsu, Wen-Lian

2008-07-01

BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along with snippets by order of relevancy to protein-protein interaction. Users can then select articles for further analysis, and BWS will find and mark up biomedical relations in the text. The analysis results can be viewed in the abstract text or in table form. To date, BWS has been field tested by over 30 biologists and questionnaires have shown that subjects are highly satisfied with its capabilities and usability. BWS is accessible free of charge at http://bioservices.cse.yzu.edu.tw/BWS.

Metal-containing and related polymers for biomedical applications.

PubMed

Yan, Yi; Zhang, Jiuyang; Ren, Lixia; Tang, Chuanbing

2016-10-07

A survey of the most recent progress in the biomedical applications of metal-containing polymers is given. Due to the unique optical, electrochemical, and magnetic properties, at least 30 different metal elements, most of them transition metals, are introduced into polymeric frameworks for interactions with biology-relevant substrates via various means. Inspired by the advance of metal-containing small molecular drugs and promoted by the great progress in polymer chemistry, metal-containing polymers have gained momentum during recent decades. According to their different applications, this review summarizes the following biomedical applications: (1) metal-containing polymers as drug delivery vehicles; (2) metal-containing polymeric drugs and biocides, including antimicrobial and antiviral agents, anticancer drugs, photodynamic therapy agents, radiotherapy agents and biocides; (3) metal-containing polymers as biosensors, and (4) metal-containing polymers in bioimaging.

20171015 - Generating Exposure-Relevant Measurement Data for Potential Use in Support of TSCA Requirements (ISES)

EPA Science Inventory

The EPA Office of Research and Development (ORD) has a number of ongoing projects which generate exposure measurements. These data may inform ongoing implementation of the amended Toxic Substances Control Act (TSCA). Exposure measurements include physical-chemical property inform...

Improve Biomedical Information Retrieval using Modified Learning to Rank Methods.

PubMed

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.

A combined pre-clinical meta-analysis and randomized confirmatory trial approach to improve data validity for therapeutic target validation.

PubMed

Kleikers, Pamela W M; Hooijmans, Carlijn; Göb, Eva; Langhauser, Friederike; Rewell, Sarah S J; Radermacher, Kim; Ritskes-Hoitinga, Merel; Howells, David W; Kleinschnitz, Christoph; Schmidt, Harald H H W

2015-08-27

Biomedical research suffers from a dramatically poor translational success. For example, in ischemic stroke, a condition with a high medical need, over a thousand experimental drug targets were unsuccessful. Here, we adopt methods from clinical research for a late-stage pre-clinical meta-analysis (MA) and randomized confirmatory trial (pRCT) approach. A profound body of literature suggests NOX2 to be a major therapeutic target in stroke. Systematic review and MA of all available NOX2(-/y) studies revealed a positive publication bias and lack of statistical power to detect a relevant reduction in infarct size. A fully powered multi-center pRCT rejects NOX2 as a target to improve neurofunctional outcomes or achieve a translationally relevant infarct size reduction. Thus stringent statistical thresholds, reporting negative data and a MA-pRCT approach can ensure biomedical data validity and overcome risks of bias.

Ethical issues in molecular medicine of relevance to surgeons

PubMed Central

Bernstein, Mark; Bampoe, Joseph; Daar, Abdallah S.

2004-01-01

The technology associated with the care of surgical patients and the level of sophistication of biomedical research accompanying it are evolving at a rapid pace. Both new and old bioethical issues are assuming increasing levels of prominence and importance, particularly in this age of molecular medicine. The authors explore bioethical issues pertinent and relevant to surgeons. Four specific areas that are exemplary by presenting both major scientific and ethical challenges are briefly addressed: privacy of information, stem cells, gene therapy, and conflict of interest in biomedical research. All of these can be generalized to all surgeons. As bioethical issues today play a greater role in surgical practice than they did even a decade ago, it is hoped that this brief review on ethical issues in molecular medicine will help stimulate present and future generations of surgeons in thinking about the ethical dimensions of their work. PMID:15646439

Customization of biomedical terminologies.

PubMed

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.

Document Exploration and Automatic Knowledge Extraction for Unstructured Biomedical Text

NASA Astrophysics Data System (ADS)

Chu, S.; Totaro, G.; Doshi, N.; Thapar, S.; Mattmann, C. A.; Ramirez, P.

2015-12-01

We describe our work on building a web-browser based document reader with built-in exploration tool and automatic concept extraction of medical entities for biomedical text. Vast amounts of biomedical information are offered in unstructured text form through scientific publications and R&D reports. Utilizing text mining can help us to mine information and extract relevant knowledge from a plethora of biomedical text. The ability to employ such technologies to aid researchers in coping with information overload is greatly desirable. In recent years, there has been an increased interest in automatic biomedical concept extraction [1, 2] and intelligent PDF reader tools with the ability to search on content and find related articles [3]. Such reader tools are typically desktop applications and are limited to specific platforms. Our goal is to provide researchers with a simple tool to aid them in finding, reading, and exploring documents. Thus, we propose a web-based document explorer, which we called Shangri-Docs, which combines a document reader with automatic concept extraction and highlighting of relevant terms. Shangri-Docsalso provides the ability to evaluate a wide variety of document formats (e.g. PDF, Words, PPT, text, etc.) and to exploit the linked nature of the Web and personal content by performing searches on content from public sites (e.g. Wikipedia, PubMed) and private cataloged databases simultaneously. Shangri-Docsutilizes Apache cTAKES (clinical Text Analysis and Knowledge Extraction System) [4] and Unified Medical Language System (UMLS) to automatically identify and highlight terms and concepts, such as specific symptoms, diseases, drugs, and anatomical sites, mentioned in the text. cTAKES was originally designed specially to extract information from clinical medical records. Our investigation leads us to extend the automatic knowledge extraction process of cTAKES for biomedical research domain by improving the ontology guided information extraction process. We will describe our experience and implementation of our system and share lessons learned from our development. We will also discuss ways in which this could be adapted to other science fields. [1] Funk et al., 2014. [2] Kang et al., 2014. [3] Utopia Documents, http://utopiadocs.com [4] Apache cTAKES, http://ctakes.apache.org

76 FR 49661 - Privacy Act; Implementation

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-11

...) because it is not always possible to detect the relevance or necessity of each piece of information in the... investigation of that individual is taking place, and the disclosure of which would weaken the on-going... individual relating to an on-going investigation. The conduct of a successful investigation leading to the...

Exposure Modeling Tools and Databases for Consideration for Relevance to the Amended TSCA (ISES)

EPA Science Inventory

The Agency’s Office of Research and Development (ORD) has a number of ongoing exposure modeling tools and databases. These efforts are anticipated to be useful in supporting ongoing implementation of the amended Toxic Substances Control Act (TSCA). Under ORD’s Chemic...

Self-assembly of inorganic nanoparticles: Ab ovo

NASA Astrophysics Data System (ADS)

Kotov, Nicholas A.

2017-09-01

There are numerous remarkable studies related to the self-organization of polymers, coordination compounds, microscale particles, biomolecules, macroscale particles, surfactants, and reactive molecules on surfaces. The focus of this paper is on the self-organization of nanoscale inorganic particles or simply nanoparticles (NPs). Although there are fascinating and profound discoveries made with other self-assembling structures, the ones involving NPs deserve particular attention because they (a) are omnipresent in Nature; (b) have relevance to numerous disciplines (physics, chemistry, biology, astronomy, Earth sciences, and others); (c) embrace most of the features, geometries, and intricacies observed for the self-organization of other chemical species; (d) offer new tools for studies of self-organization phenomena; and (e) have a large economic impact, extending from energy and construction industries, to optoelectronics, biomedical technologies, and food safety. Despite the overall success of the field it is necessary to step back from its multiple ongoing research venues and consider two questions: What is self-assembly of nanoparticles? and Why do we need to study it? The reason to bring them up is to achieve greater scientific depth in the understanding of these omnipresent phenomena and, perhaps, deepen their multifaceted impact. Contribution to the Focus Issue Self-assemblies of Inorganic and Organic Nanomaterials edited by Marie-Paule Pileni.

Lipopolysaccharide inhibits or accelerates biomedical titanium corrosion depending on environmental acidity

PubMed Central

Yu, Fei; Addison, Owen; Baker, Stephen J; Davenport, Alison J

2015-01-01

Titanium and its alloys are routinely used as biomedical implants and are usually considered to be corrosion resistant under physiological conditions. However, during inflammation, chemical modifications of the peri-implant environment including acidification occur. In addition certain biomolecules including lipopolysaccharide (LPS), a component of Gram-negative bacterial cell walls and driver of inflammation have been shown to interact strongly with Ti and modify its corrosion resistance. Gram-negative microbes are abundant in biofilms which form on dental implants. The objective was to investigate the influence of LPS on the corrosion properties of relevant biomedical Ti substrates as a function of environmental acidity. Inductively coupled plasma mass spectrometry was used to quantify Ti dissolution following immersion testing in physiological saline for three common biomedical grades of Ti (ASTM Grade 2, Grade 4 and Grade 5). Complementary electrochemical tests including anodic and cathodic polarisation experiments and potentiostatic measurements were also conducted. All three Ti alloys were observed to behave similarly and ion release was sensitive to pH of the immersion solution. However, LPS significantly inhibited Ti release under the most acidic conditions (pH 2), which may develop in localized corrosion sites, but promoted dissolution at pH 4–7, which would be more commonly encountered physiologically. The observed pattern of sensitivity to environmental acidity of the effect of LPS on Ti corrosion has not previously been reported. LPS is found extensively on the surfaces of skin and mucosal penetrating Ti implants and the findings are therefore relevant when considering the chemical stability of Ti implant surfaces in vivo. PMID:25634122

Building a more diverse biomedical engineering workforce: Biomedical engineering at the university of the district of Columbia, a historically black college & university.

PubMed

Thompson, Lara A; Adebayo, A Segun; Nian Zhang; Haghani, Sasan; Dowell, Kathleen; Shetty, Devdas

2016-08-01

Biomedical Engineering (BME) is a new, multidisciplinary, and rapidly growing field, however, the BME Workforce suffers from limited ethnic and gender diversity. Despite the demand and growth of this new field due to its public health importance, only 4 out of the 107 Historically Black Colleges and Universities (HBCUs) nationwide offers a Bachelor's of Science (B.S.) in Bio-Engineering related fields. In order to contribute to a growing BME Workforce, HBCUs need to react and offer more degree-programs relevant to BME. At the University of the District of Columbia (UDC), an HBCU and the District's only public institution for higher learning, we have recently established a new, degree program: Bachelor of Science in Biomedical Engineering (B.S. in BME) full-board approved in Fall 2014, with program activities initiated in Fall 2015. The educational goal of this program is to enhance the quality and diversity of the BME Workforce via student professional development, new and relevant BME courses, and BME scholarly activities (e.g., guest lectures and journal club sessions), ultimately to increase the number of ethnic minorities pursuing careers and degrees in BME. Through our program activities, we are aiming to meet the nation's demand to contribute to a diverse BME workforce, directed towards solving problems in human health. A secondary, but related goal, is to increase the diversity of STEM-related fields. This paper summarizes our initial, but encouraging, BME activity-related findings. However, this study will be longitudinal (on a multiple year time period) to observe the true outcomes of our initiative.

Knowledge and awareness regarding biomedical waste management in dental teaching institutions in India- A systematic review

PubMed Central

Kapoor, Daljit; Nirola, Ashutosh; Kapoor, Vinod

2014-01-01

Objectives: Proper handling, treatment and disposal of biomedical wastes are important elements in any health care setting. Not much attention has been paid to the management of Biomedical Waste (BMW) in recent years, in dental colleges and hospitals in India. The present systematic review was conducted to assess knowledge and awareness regarding BMW management among staff and students of dental teaching institutions in India. Material and Methods: A systematic review of relevant cross-sectional studies was conducted regarding BMW management in India in dental teaching institutions in India. Six studies were finally included in the present review after conducting both electronic and manual search like Pubmed, EMBASE etc. and after making necessary exclusions. Potential biases were addressed and relevant data was extracted by the concerned investigators. Results: Six studies were finally included in the review. Colour coding of wastes was not done by 67% of the subjects in one of the studies conducted in Haryana. Almost all the subjects agreed to the fact that exposure to hazardous health care waste can result in disease or infection in another study. According to another study reports, none of the respondents was able to list the legislative act regarding BMW when asked. Conclusions: The results of the present review showed that knowledge and awareness level of subjects was inadequate and there is considerable variation in practice and management regarding BMW. There is a great need for continuing education and training programmes to be conducted in dental teaching institutions in India. Key words:Biomedical waste, knowledge, awareness, dentists, institution. PMID:25593667

Knowledge and awareness regarding biomedical waste management in dental teaching institutions in India- A systematic review.

PubMed

Kapoor, Daljit; Nirola, Ashutosh; Kapoor, Vinod; Gambhir, Ramandeep-Singh

2014-10-01

Proper handling, treatment and disposal of biomedical wastes are important elements in any health care setting. Not much attention has been paid to the management of Biomedical Waste (BMW) in recent years, in dental colleges and hospitals in India. The present systematic review was conducted to assess knowledge and awareness regarding BMW management among staff and students of dental teaching institutions in India. A systematic review of relevant cross-sectional studies was conducted regarding BMW management in India in dental teaching institutions in India. Six studies were finally included in the present review after conducting both electronic and manual search like Pubmed, EMBASE etc. and after making necessary exclusions. Potential biases were addressed and relevant data was extracted by the concerned investigators. Six studies were finally included in the review. Colour coding of wastes was not done by 67% of the subjects in one of the studies conducted in Haryana. Almost all the subjects agreed to the fact that exposure to hazardous health care waste can result in disease or infection in another study. According to another study reports, none of the respondents was able to list the legislative act regarding BMW when asked. The results of the present review showed that knowledge and awareness level of subjects was inadequate and there is considerable variation in practice and management regarding BMW. There is a great need for continuing education and training programmes to be conducted in dental teaching institutions in India. Key words:Biomedical waste, knowledge, awareness, dentists, institution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larson, Richard; Branch, Darren; Edwards, Thayne

The acoustic wave biosensor is innovative device that is a handheld, battery-powered, portable detection system capable of multiplex identification of a wide range of medically relevant pathogens and their biomolecular signatures — viruses, bacteria, proteins, and DNA — at clinically relevant levels. This detection occurs within minutes — not hours — at the point of care, whether that care is in a physician's office, a hospital bed, or at the scene of a biodefense or biomedical emergency.

Do Public Involvement Activities in Biomedical Research and Innovation Recruit Representatively? A Systematic Qualitative Review.

PubMed

Lander, Jonas; Hainz, Tobias; Hirschberg, Irene; Bossert, Sabine; Strech, Daniel

2016-01-01

Public involvement activities (PIAs) may contribute to the governance of ethically challenging biomedical research and innovation by informing, consulting with and engaging the public in developments and decision-making processes. For PIAs to capture a population's preferences (e.g. on issues in whole genome sequencing, biobanks or genome editing), a central methodological requirement is to involve a sufficiently representative subgroup of the general public. While the existing literature focusses on theoretical and normative aspects of 'representation', this study assesses empirically how such considerations are implemented in practice. It evaluates how PIA reports describe representation objectives, the recruitment process and levels of representation achieved. PIA reports were included from a systematic literature search if they directly reported a PIA conducted in a relevant discipline such as genomics, biobanks, biotechnology or others. PIA reports were analyzed with thematic text analysis. The text analysis was guided by an assessment matrix based on PIA-specific guidelines and frameworks. We included 46 relevant reports, most focusing on issues in genomics. 27 reports (59%) explicitly described representation objectives, though mostly without adjusting eligibility criteria and recruiting methods to the specific objective. 11 reports (24%) explicitly reported to have achieved the intended representation; the rest either reported failure or were silent on this issue. Representation of study samples in PIAs in biomedical research and innovation is currently not reported systematically. Improved reporting on representation would not only improve the validity and value of PIAs, but could also contribute to PIA results being used more often in relevant policy and decision-making processes. © 2016 S. Karger AG, Basel.

Polymer-Based Electrospun Nanofibers for Biomedical Applications

PubMed Central

Al-Enizi, Abdullah M.; Zagho, Moustafa M.

2018-01-01

Electrospinning has been considered a promising and novel procedure to fabricate polymer nanofibers due to its simplicity, cost effectiveness, and high production rate, making this technique highly relevant for both industry and academia. It is used to fabricate non-woven fibers with unique characteristics such as high permeability, stability, porosity, surface area to volume ratio, ease of functionalization, and excellent mechanical performance. Nanofibers can be synthesized and tailored to suit a wide range of applications including energy, biotechnology, healthcare, and environmental engineering. A comprehensive outlook on the recent developments, and the influence of electrospinning on biomedical uses such as wound dressing, drug release, and tissue engineering, has been presented. Concerns regarding the procedural restrictions and research contests are addressed, in addition to providing insights about the future of this fabrication technique in the biomedical field. PMID:29677145

Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.

PubMed

Chen, Guocai; Zhao, Jieyi; Cohen, Trevor; Tao, Cui; Sun, Jingchun; Xu, Hua; Bernstam, Elmer V; Lawson, Andrew; Zeng, Jia; Johnson, Amber M; Holla, Vijaykumar; Bailey, Ann M; Lara-Guerra, Humberto; Litzenburger, Beate; Meric-Bernstam, Funda; Jim Zheng, W

2015-01-01

Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names. We obtained 93.6% precision for the test gene set and 80.4% for the area under a receiver-operating characteristics curve for gene and article association. The core algorithm was implemented using a graphics processing unit-based MapReduce framework to handle big data and to improve performance. We conclude that Ontology Fingerprints can help disambiguate gene names mentioned in text and analyse the association between genes and articles. Database URL: http://www.ontologyfingerprint.org © The Author(s) 2015. Published by Oxford University Press.

Manpower development for the biomedical industry space.

PubMed

Goh, James C H

2013-01-01

The Biomedical Sciences (BMS) Cluster is one of four key pillars of the Singapore economy. The Singapore Government has injected research funding for basic and translational research to attract companies to carry out their commercial R&D activities. To further intensify the R&D efforts, the National Research Foundation (NRF) was set up to coordinate the research activities of different agencies within the larger national framework and to fund strategic R&D initiatives. In recent years, funding agencies began to focus on support of translational and clinical research, particularly those with potential for commercialization. Translational research is beginning to have traction, in particular research funding for the development of innovation medical devices. Therefore, the Biomedical Sciences sector is projected to grow which means that there is a need to invest in human capital development to achieve sustainable growth. In support of this, education and training programs to strengthen the manpower capabilities for the Biomedical Sciences industry have been developed. In recent years, undergraduate and graduate degree courses in biomedical engineering/bioengineering have been developing at a rapid rate. The goal is to train students with skills to understand complex issues of biomedicine and to develop and implement of advanced technological applications to these problems. There are a variety of career opportunities open to graduates in biomedical engineering, however regardless of the type of career choices, students must not only focus on achieving good grades. They have to develop their marketability to employers through internships, overseas exchange programs, and involvement in leadership-type activities. Furthermore, curriculum has to be developed with biomedical innovation in mind and ensure relevance to the industry. The objective of this paper is to present the NUS Bioengineering undergraduate program in relation to manpower development for the biomedical industry in Singapore.

A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge

PubMed Central

Gururaj, Anupama E.; Chen, Xiaoling; Pournejati, Saeid; Alter, George; Hersh, William R.; Demner-Fushman, Dina; Ohno-Machado, Lucila

2017-01-01

Abstract The rapid proliferation of publicly available biomedical datasets has provided abundant resources that are potentially of value as a means to reproduce prior experiments, and to generate and explore novel hypotheses. However, there are a number of barriers to the re-use of such datasets, which are distributed across a broad array of dataset repositories, focusing on different data types and indexed using different terminologies. New methods are needed to enable biomedical researchers to locate datasets of interest within this rapidly expanding information ecosystem, and new resources are needed for the formal evaluation of these methods as they emerge. In this paper, we describe the design and generation of a benchmark for information retrieval of biomedical datasets, which was developed and used for the 2016 bioCADDIE Dataset Retrieval Challenge. In the tradition of the seminal Cranfield experiments, and as exemplified by the Text Retrieval Conference (TREC), this benchmark includes a corpus (biomedical datasets), a set of queries, and relevance judgments relating these queries to elements of the corpus. This paper describes the process through which each of these elements was derived, with a focus on those aspects that distinguish this benchmark from typical information retrieval reference sets. Specifically, we discuss the origin of our queries in the context of a larger collaborative effort, the biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium, and the distinguishing features of biomedical dataset retrieval as a task. The resulting benchmark set has been made publicly available to advance research in the area of biomedical dataset retrieval. Database URL: https://biocaddie.org/benchmark-data PMID:29220453

Recruiting intergenerational African American males for biomedical research Studies: a major research challenge.

PubMed

Byrd, Goldie S; Edwards, Christopher L; Kelkar, Vinaya A; Phillips, Ruth G; Byrd, Jennifer R; Pim-Pong, Dora Som; Starks, Takiyah D; Taylor, Ashleigh L; Mckinley, Raechel E; Li, Yi-Ju; Pericak-Vance, Margaret

2011-06-01

The health and well-being of all individuals, independent of race, ethnicity, or gender, is a significant public health concern. Despite many improvements in the status of minority health, African American males continue to have the highest age-adjusted mortality rate of any race-sex group in the United States. Such disparities are accounted for by deaths from a number of diseases such as diabetes, human immunodeficiency virus (HIV), cancer, and cardiovascular disease, as well as by many historical and present social and cultural constructs that present as obstacles to better health outcomes. Distrust of the medical community, inadequate education, low socioeconomic status, social deprivation, and underutilized primary health care services all contribute to disproportionate health and health care outcomes among African Americans compared to their Caucasian counterparts. Results of clinical research on diseases that disproportionately affect African American males are often limited in their reliability due to common sampling errors existing in the majority of biomedical research studies and clinical trials. There are many reasons for underrepresentation of African American males in clinical trials, including their common recollection and interpretation of relevant historical of biomedical events where minorities were abused or exposed to racial discrimination or racist provocation. In addition, African American males continue to be less educated and more disenfranchised from the majority in society than Caucasian males and females and their African American female counterparts. As such, understanding their perceptions, even in early developmental years, about health and obstacles to involvement in research is important. In an effort to understand perspectives about their level of participation, motivation for participation, impact of education, and engagement in research, this study was designed to explore factors that impact their willingness to participate. Our research suggests that: (1) African American males across all ages are willing to participate in several types of research studies, even those that require human samples; (2) their level of participation is significantly influenced by education level; and (3) their decision to participate in research studies is motivated by civic duty, monetary compensation, and whether they or a relative has had the disease of interest. However, African American males, across all age groups, continue to report a lack of trust as a primary reason for their unwillingness to participate in biomedical research. There is an ongoing need to continue to seek advice, improve communication, and design research studies that garner trust and improve participation among African American males as a targeted underrepresented population. Such communication and dialogues should occur at all age levels of research development to assess. current attitudes and behaviors of African American males around participation.

Pain Research Forum: application of scientific social media frameworks in neuroscience.

PubMed

Das, Sudeshna; McCaffrey, Patricia G; Talkington, Megan W T; Andrews, Neil A; Corlosquet, Stéphane; Ivinson, Adrian J; Clark, Tim

2014-01-01

Social media has the potential to accelerate the pace of biomedical research through online collaboration, discussions, and faster sharing of information. Focused web-based scientific social collaboratories such as the Alzheimer Research Forum have been successful in engaging scientists in open discussions of the latest research and identifying gaps in knowledge. However, until recently, tools to rapidly create such communities and provide high-bandwidth information exchange between collaboratories in related fields did not exist. We have addressed this need by constructing a reusable framework to build online biomedical communities, based on Drupal, an open-source content management system. The framework incorporates elements of Semantic Web technology combined with social media. Here we present, as an exemplar of a web community built on our framework, the Pain Research Forum (PRF) (http://painresearchforum.org). PRF is a community of chronic pain researchers, established with the goal of fostering collaboration and communication among pain researchers. Launched in 2011, PRF has over 1300 registered members with permission to submit content. It currently hosts over 150 topical news articles on research; more than 30 active or archived forum discussions and journal club features; a webinar series; an editor-curated weekly updated listing of relevant papers; and several other resources for the pain research community. All content is licensed for reuse under a Creative Commons license; the software is freely available. The framework was reused to develop other sites, notably the Multiple Sclerosis Discovery Forum (http://msdiscovery.org) and StemBook (http://stembook.org). Web-based collaboratories are a crucial integrative tool supporting rapid information transmission and translation in several important research areas. In this article, we discuss the success factors, lessons learned, and ongoing challenges in using PRF as a driving force to develop tools for online collaboration in neuroscience. We also indicate ways these tools can be applied to other areas and uses.

Pain Research Forum: application of scientific social media frameworks in neuroscience

PubMed Central

Das, Sudeshna; McCaffrey, Patricia G.; Talkington, Megan W. T.; Andrews, Neil A.; Corlosquet, Stéphane; Ivinson, Adrian J.; Clark, Tim

2014-01-01

Background: Social media has the potential to accelerate the pace of biomedical research through online collaboration, discussions, and faster sharing of information. Focused web-based scientific social collaboratories such as the Alzheimer Research Forum have been successful in engaging scientists in open discussions of the latest research and identifying gaps in knowledge. However, until recently, tools to rapidly create such communities and provide high-bandwidth information exchange between collaboratories in related fields did not exist. Methods: We have addressed this need by constructing a reusable framework to build online biomedical communities, based on Drupal, an open-source content management system. The framework incorporates elements of Semantic Web technology combined with social media. Here we present, as an exemplar of a web community built on our framework, the Pain Research Forum (PRF) (http://painresearchforum.org). PRF is a community of chronic pain researchers, established with the goal of fostering collaboration and communication among pain researchers. Results: Launched in 2011, PRF has over 1300 registered members with permission to submit content. It currently hosts over 150 topical news articles on research; more than 30 active or archived forum discussions and journal club features; a webinar series; an editor-curated weekly updated listing of relevant papers; and several other resources for the pain research community. All content is licensed for reuse under a Creative Commons license; the software is freely available. The framework was reused to develop other sites, notably the Multiple Sclerosis Discovery Forum (http://msdiscovery.org) and StemBook (http://stembook.org). Discussion: Web-based collaboratories are a crucial integrative tool supporting rapid information transmission and translation in several important research areas. In this article, we discuss the success factors, lessons learned, and ongoing challenges in using PRF as a driving force to develop tools for online collaboration in neuroscience. We also indicate ways these tools can be applied to other areas and uses. PMID:24653693

The Biomedical Ethics Ontology Proposal: Excellent Aims, Questionable Methods

PubMed Central

DuBois, James M.

2010-01-01

Koepsell et al. (2009) Describe an ideal biomedical ethics committee environment with efficiencies such as electronic and universal application forms and consent templates, automated decision-trees, and broad sharing of data. However, it is unclear that a biomedical ethics ontology (BMEO) is necessary or even helpful in establishing such environment. Two features of any applied ontology are particularly problematic in establishing a useful BMEO: (1) an ontology is a description of a domain of reality; and (2) the description is subject to ongoing revision as it is developed through open processes, e.g., the use of a wiki. A BMEO would need to address two main kinds of entities, regulatory definitions and ethical concepts, and is ill-suited to both. Regulatory definitions are fiats and ought to be adopted verbatim to ensure compliance, but in such cases we do not need the assistance of ontologists, and their modes of working (constant revision within open wiki-based communities) might even be counterproductive. Ethical concepts within pluralistic societies are social constructs, not a priori concepts or biological natural kinds, and the prospects of generating intuitive definitions that enjoy broad acceptance across cultures and institutional settings are slim. In making these arguments, I draw from the writings of leading applied ontologists and Koepsell et al.’s own proof of concept. PMID:19382878

Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems.

PubMed

Lam, Maggie P Y; Venkatraman, Vidya; Xing, Yi; Lau, Edward; Cao, Quan; Ng, Dominic C M; Su, Andrew I; Ge, Junbo; Van Eyk, Jennifer E; Ping, Peipei

2016-11-04

Amidst the proteomes of human tissues lie subsets of proteins that are closely involved in conserved pathophysiological processes. Much of biomedical research concerns interrogating disease signature proteins and defining their roles in disease mechanisms. With advances in proteomics technologies, it is now feasible to develop targeted proteomics assays that can accurately quantify protein abundance as well as their post-translational modifications; however, with rapidly accumulating number of studies implicating proteins in diseases, current resources are insufficient to target every protein without judiciously prioritizing the proteins with high significance and impact for assay development. We describe here a data science method to prioritize and expedite assay development on high-impact proteins across research fields by leveraging the biomedical literature record to rank and normalize proteins that are popularly and preferentially published by biomedical researchers. We demonstrate this method by finding priority proteins across six major physiological systems (cardiovascular, cerebral, hepatic, renal, pulmonary, and intestinal). The described method is data-driven and builds upon the collective knowledge of previous publications referenced on PubMed to lend objectivity to target selection. The method and resulting popular protein lists may also be useful for exploring biological processes associated with various physiological systems and research topics, in addition to benefiting ongoing efforts to facilitate the broad translation of proteomics technologies.

NASA Johnson Space Center Biomedical Research Resources

NASA Technical Reports Server (NTRS)

Paloski, W. H.

1999-01-01

Johnson Space Center (JSC) medical sciences laboratories constitute a national resource for support of medical operations and life sciences research enabling a human presence in space. They play a critical role in evaluating, defining, and mitigation the untoward effect of human adaption to space flight. Over the years they have developed the unique facilities and expertise required to perform: biomedical sample analysis and physiological performance tests supporting medical evaluations of space flight crew members and scientific investigations of the operationally relevant medical, physiological, cellular, and biochemical issues associated with human space flight. A general overview of these laboratories is presented in viewgraph form.

Design of Biomedical Robots for Phenotype Prediction Problems

PubMed Central

deAndrés-Galiana, Enrique J.; Sonis, Stephen T.

2016-01-01

Abstract Genomics has been used with varying degrees of success in the context of drug discovery and in defining mechanisms of action for diseases like cancer and neurodegenerative and rare diseases in the quest for orphan drugs. To improve its utility, accuracy, and cost-effectiveness optimization of analytical methods, especially those that translate to clinically relevant outcomes, is critical. Here we define a novel tool for genomic analysis termed a biomedical robot in order to improve phenotype prediction, identifying disease pathogenesis and significantly defining therapeutic targets. Biomedical robot analytics differ from historical methods in that they are based on melding feature selection methods and ensemble learning techniques. The biomedical robot mathematically exploits the structure of the uncertainty space of any classification problem conceived as an ill-posed optimization problem. Given a classifier, there exist different equivalent small-scale genetic signatures that provide similar predictive accuracies. We perform the sensitivity analysis to noise of the biomedical robot concept using synthetic microarrays perturbed by different kinds of noises in expression and class assignment. Finally, we show the application of this concept to the analysis of different diseases, inferring the pathways and the correlation networks. The final aim of a biomedical robot is to improve knowledge discovery and provide decision systems to optimize diagnosis, treatment, and prognosis. This analysis shows that the biomedical robots are robust against different kinds of noises and particularly to a wrong class assignment of the samples. Assessing the uncertainty that is inherent to any phenotype prediction problem is the right way to address this kind of problem. PMID:27347715

Design of Biomedical Robots for Phenotype Prediction Problems.

PubMed

deAndrés-Galiana, Enrique J; Fernández-Martínez, Juan Luis; Sonis, Stephen T

2016-08-01

Genomics has been used with varying degrees of success in the context of drug discovery and in defining mechanisms of action for diseases like cancer and neurodegenerative and rare diseases in the quest for orphan drugs. To improve its utility, accuracy, and cost-effectiveness optimization of analytical methods, especially those that translate to clinically relevant outcomes, is critical. Here we define a novel tool for genomic analysis termed a biomedical robot in order to improve phenotype prediction, identifying disease pathogenesis and significantly defining therapeutic targets. Biomedical robot analytics differ from historical methods in that they are based on melding feature selection methods and ensemble learning techniques. The biomedical robot mathematically exploits the structure of the uncertainty space of any classification problem conceived as an ill-posed optimization problem. Given a classifier, there exist different equivalent small-scale genetic signatures that provide similar predictive accuracies. We perform the sensitivity analysis to noise of the biomedical robot concept using synthetic microarrays perturbed by different kinds of noises in expression and class assignment. Finally, we show the application of this concept to the analysis of different diseases, inferring the pathways and the correlation networks. The final aim of a biomedical robot is to improve knowledge discovery and provide decision systems to optimize diagnosis, treatment, and prognosis. This analysis shows that the biomedical robots are robust against different kinds of noises and particularly to a wrong class assignment of the samples. Assessing the uncertainty that is inherent to any phenotype prediction problem is the right way to address this kind of problem.

A novel smart lighting clinical testbed.

PubMed

Gleason, Joseph D; Oishi, Meeko; Simkulet, Michelle; Tuzikas, Arunas; Brown, Lee K; Brueck, S R J; Karlicek, Robert F

2017-07-01

A real-time, feedback-capable, variable spectrum lighting system was recently installed at the University of New Mexico Hospital to facilitate biomedical research on the health impacts of lighting. The system consists of variable spectrum troffers, color sensors, occupancy sensors, and computing and communication infrastructure, and is the only such clinical facility in the US. The clinical environment posed special challenges for installation as well as for ongoing maintenance and operations. Pilot studies are currently underway to evaluate the effectiveness of the system to regulate circadian phase in subjects with delayed sleep-wake phase disorder.

A Novel Multi-Class Ensemble Model for Classifying Imbalanced Biomedical Datasets

NASA Astrophysics Data System (ADS)

Bikku, Thulasi; Sambasiva Rao, N., Dr; Rao, Akepogu Ananda, Dr

2017-08-01

This paper mainly focuseson developing aHadoop based framework for feature selection and classification models to classify high dimensionality data in heterogeneous biomedical databases. Wide research has been performing in the fields of Machine learning, Big data and Data mining for identifying patterns. The main challenge is extracting useful features generated from diverse biological systems. The proposed model can be used for predicting diseases in various applications and identifying the features relevant to particular diseases. There is an exponential growth of biomedical repositories such as PubMed and Medline, an accurate predictive model is essential for knowledge discovery in Hadoop environment. Extracting key features from unstructured documents often lead to uncertain results due to outliers and missing values. In this paper, we proposed a two phase map-reduce framework with text preprocessor and classification model. In the first phase, mapper based preprocessing method was designed to eliminate irrelevant features, missing values and outliers from the biomedical data. In the second phase, a Map-Reduce based multi-class ensemble decision tree model was designed and implemented in the preprocessed mapper data to improve the true positive rate and computational time. The experimental results on the complex biomedical datasets show that the performance of our proposed Hadoop based multi-class ensemble model significantly outperforms state-of-the-art baselines.

Graphene oxide based contacts as probes of biomedical signals

NASA Astrophysics Data System (ADS)

Hallfors, N. G.; Devarajan, A.; Farhat, I. A. H.; Abdurahman, A.; Liao, K.; Gater, D. L.; Elnaggar, M. I.; Isakovic, A. F.

We have developed a series of graphene oxide (GOx) on polymer contacts and have demonstrated these to be useful for collection of standard biomedically relevant signals, such as electrocardiogram (ECG). The process is wet solution-based and allows for control and tuning of the basic physical parameters of GOx, such as electrical and optical properties, simply by choosing the number of GOx layers. Our GOx characterization measurements show spectral (FTIR, XPS, IR absorbance) features most relevant to such performance, and point towards the likely explanations about the mechanisms for controlling the physical properties relevant for the contact performance. Structural (X-ray topography) and surface characterization (AFM, SEM) indicates to what degree these contacts can be considered homogeneous and therefore provide information on yield and repeatability. We compare the ECG signals recorded by standard commercial probes (Ag/AgCl) and GOx probes, displaying minor differences the solution to which may lead to a whole new way we perform ECG data collection, including wearable electronics and IoT friendly ECG monitoring. We acknowledge support from Mubadala-SRC AC4ES and from SRC 2011-KJ-2190. We thank J. B. Warren and G. L. Carr (BNL) for assistance.

Learning to rank-based gene summary extraction.

PubMed

Shang, Yue; Hao, Huihui; Wu, Jiajin; Lin, Hongfei

2014-01-01

In recent years, the biomedical literature has been growing rapidly. These articles provide a large amount of information about proteins, genes and their interactions. Reading such a huge amount of literature is a tedious task for researchers to gain knowledge about a gene. As a result, it is significant for biomedical researchers to have a quick understanding of the query concept by integrating its relevant resources. In the task of gene summary generation, we regard automatic summary as a ranking problem and apply the method of learning to rank to automatically solve this problem. This paper uses three features as a basis for sentence selection: gene ontology relevance, topic relevance and TextRank. From there, we obtain the feature weight vector using the learning to rank algorithm and predict the scores of candidate summary sentences and obtain top sentences to generate the summary. ROUGE (a toolkit for summarization of automatic evaluation) was used to evaluate the summarization result and the experimental results showed that our method outperforms the baseline techniques. According to the experimental result, the combination of three features can improve the performance of summary. The application of learning to rank can facilitate the further expansion of features for measuring the significance of sentences.

Analysis of Citations to Biomedical Articles Affected by Scientific Misconduct

PubMed Central

Dailey, Rhonda K.; Abrams, Judith

2014-01-01

We describe the ongoing citations to biomedical articles affected by scientific misconduct, and characterize the papers that cite these affected articles. The citations to 102 articles named in official findings of scientific misconduct during the period of 1993 and 2001 were identified through the Institute for Scientific Information Web of Science database. Using a stratified random sampling strategy, we performed a content analysis of 603 of the 5,393 citing papers to identify indications of awareness that the cited articles affected by scientific misconduct had validity issues, and to examine how the citing papers referred to the affected articles. Fewer than 5% of citing papers indicated any awareness that the cited article was retracted or named in a finding of misconduct. We also tested the hypothesis that affected articles would have fewer citations than a comparison sample; this was not supported. Most articles affected by misconduct were published in basic science journals, and we found little cause for concern that such articles may have affected clinical equipoise or clinical care. PMID:19597966

Zoonoses of occupational health importance in contemporary laboratory animal research.

PubMed

Hankenson, F Claire; Johnston, Nancy A; Weigler, Benjamin J; Di Giacomo, Ronald F

2003-12-01

In contemporary laboratory animal facilities, workplace exposure to zoonotic pathogens, agents transmitted to humans from vertebrate animals or their tissues, is an occupational hazard. The primary (e.g., macaques, pigs, dogs, rabbits, mice, and rats) and secondary species (e.g., sheep, goats, cats, ferrets, and pigeons) of animals commonly used in biomedical research, as classified by the American College of Laboratory Animal Medicine, are established or potential hosts for a large number of zoonotic agents. Diseases included in this review are principally those wherein a risk to biomedical facility personnel has been documented by published reports of human cases in laboratory animal research settings, or under reasonably similar circumstances. Diseases are listed alphabetically, and each section includes information about clinical disease, transmission, occurrence, and prevention in animal reservoir species and humans. Our goal is to provide a resource for veterinarians, health-care professionals, technical staff, and administrators that will assist in the design and on-going evaluation of institutional occupational health and safety programs.

Analysis of citations to biomedical articles affected by scientific misconduct.

PubMed

Neale, Anne Victoria; Dailey, Rhonda K; Abrams, Judith

2010-06-01

We describe the ongoing citations to biomedical articles affected by scientific misconduct, and characterize the papers that cite these affected articles. The citations to 102 articles named in official findings of scientific misconduct during the period of 1993 and 2001 were identified through the Institute for Scientific Information Web of Science database. Using a stratified random sampling strategy, we performed a content analysis of 603 of the 5,393 citing papers to identify indications of awareness that the cited articles affected by scientific misconduct had validity issues, and to examine how the citing papers referred to the affected articles. Fewer than 5% of citing papers indicated any awareness that the cited article was retracted or named in a finding of misconduct. We also tested the hypothesis that affected articles would have fewer citations than a comparison sample; this was not supported. Most articles affected by misconduct were published in basic science journals, and we found little cause for concern that such articles may have affected clinical equipoise or clinical care.

Chembank | Office of Cancer Genomics

Cancer.gov

Funded in large part by the Initiative for Chemical Genetics (ICG), Chembank is an interactive database for small molecules. It contains data from hundreds of biomedically relevant small molecule screens that involved hundreds-of-thousands of compounds. Chembank also provides analysis tools to facilitate data mining.

Development of an information retrieval tool for biomedical patents.

PubMed

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.

Can gamma irradiation during radiotherapy influence the metal release process for biomedical CoCrMo and 316L alloys?

PubMed

Wei, Zheng; Edin, Jonathan; Karlsson, Anna Emelie; Petrovic, Katarina; Soroka, Inna L; Odnevall Wallinder, Inger; Hedberg, Yolanda

2018-02-09

The extent of metal release from implant materials that are irradiated during radiotherapy may be influenced by irradiation-formed radicals. The influence of gamma irradiation, with a total dose of relevance for radiotherapy (e.g., for cancer treatments) on the extent of metal release from biomedical stainless steel AISI 316L and a cobalt-chromium alloy (CoCrMo) was investigated in physiological relevant solutions (phosphate buffered saline with and without 10 g/L bovine serum albumin) at pH 7.3. Directly after irradiation, the released amounts of metals were significantly higher for irradiated CoCrMo as compared to nonirradiated CoCrMo, resulting in an increased surface passivation (enhanced passive conditions) that hindered further release. A similar effect was observed for 316L showing lower nickel release after 1 h of initially irradiated samples as compared to nonirradiated samples. However, the effect of irradiation (total dose of 16.5 Gy) on metal release and surface oxide composition and thickness was generally small. Most metals were released initially (within seconds) upon immersion from CoCrMo but not from 316L. Albumin induced an increased amount of released metals from AISI 316L but not from CoCrMo. Albumin was not found to aggregate to any greater extent either upon gamma irradiation or in the presence of trace metal ions, as determined using different light scattering techniques. Further studies should elucidate the effect of repeated friction and fractionated low irradiation doses on the short- and long term metal release process of biomedical materials. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2018. © 2018 The Authors Journal of Biomedical Materials Research Part B: Applied Biomaterials Published by Wiley Periodicals, Inc.

Nanomaterials and nanofabrication for biomedical applications

NASA Astrophysics Data System (ADS)

Cheng, Chao-Min; Chia-Wen Wu, Kevin

2013-08-01

Traditional boundaries between materials science and engineering and life sciences are rapidly disintegrating as interdisciplinary research teams develop new materials-science-based tools for exploring fundamental issues in both medicine and biology. With recent technological advances in multiple research fields such as materials science, cell and molecular biology and micro-/nano-technology, much attention is shifting toward evaluating the functional advantages of nanomaterials and nanofabrication, at the cellular and molecular levels, for specific, biomedically relevant applications. The pursuit of this direction enhances the understanding of the mechanisms of, and therapeutic potentials for, some of the most lethal diseases, including cardiovascular diseases, organ fibrosis and cancers. This interdisciplinary approach has generated great interest among researchers working in a wide variety of communities including industry, universities and research laboratories. The purpose of this focus issue in Science and Technology of Advanced Materials is to bridge nanotechnology and biology with medicine, focusing more on the applications of nanomaterials and nanofabrication in biomedically relevant issues. This focus issue, we believe, will provide a more comprehensive understanding of (i) the preparation of nanomaterials and the underlying mechanisms of nanofabrication, and (ii) the linkage of nanomaterials and nanofabrication with biomedical applications. The multidisciplinary focus issue that we have attempted to organize is of interest to various research fields including biomaterials and tissue engineering, bioengineering, nanotechnology and nanomaterials, i.e. chemistry, physics and engineering. Nanomaterials and nanofabrication topics addressed in this focus issue include sensing and diagnosis (e.g. immunosensing and diagnostic devices for diseases), cellular and molecular biology (e.g. probing cellular behaviors and stem cell differentiation) and drug delivery carriers (e.g. polymers, gold nanoparticles, Prussian blue nanoparticles, mesoporous silica nanoparticles and carbon-based nanomaterials). Here, we would like to show our deep appreciation to all authors and reviewers. Without their great help and contributions, this focus issue, including the review and original papers, would not have been published on schedule. This focus issue may not cover all issues in this emerging scientific field; however, we believe that our efforts have great potential 'to hurl a boulder to draw a jade' and ignite innovation and challenging discussion in the relevant scientific communities.

on-course(®) portal: a tool for in-service training and career development for biomedical scientists.

PubMed

Payton, Antony; Janko, Christa; Renn, Oliver; Hardman, Michael

2013-09-01

Successfully navigating through the jungle of biomedical postgraduate courses in Europe has recently been made possible by the release of an Innovative Medicines Initiative (IMI) funded project called on-course(®) (http://www.on-course.eu). on-course(®) lists all master, continued professional development (CPD) and PhD courses in Europe and hosts advanced search options designed by the pharmaceutical industry, academia and regulatory bodies allowing the course seeker to find courses that are most relevant for them. In addition, an IMI cross education and training topic task force has developed a set of quality standards that have been applied to CPD courses. The comprehensive nature of on-course(®) offers a new level of transparency to biomedical course provision in Europe that will help steer future education and training. Copyright © 2013 Elsevier Ltd. All rights reserved.

Nuclear analytical techniques in medicine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cesareo, R.

1988-01-01

This book acquaints one with the fundamental principles and the instrumentation relevant to analytical technique based on atomic and nuclear physics, as well as present and future biomedical applications. Besides providing a theoretical description of the physical phenomena, a large part of the book is devoted to applications in the medical and biological field, particularly in hematology, forensic medicine and environmental science. This volume reviews methods such as the possibility of carrying out rapid multi-element analysis of trace elements on biomedical samples, in vitro and in vivo, by XRF-analysis; the ability of the PIXE-microprobe to analyze in detail and tomore » map trace elements in fragments of biomedical samples or inside the cells; the potentiality of in vivo nuclear activation analysis for diagnostic purposes. Finally, techniques are described such as radiation scattering (elastic and inelastic scattering) and attenuation measurements which will undoubtedly see great development in the immediate future.« less

Hypotheses generation as supervised link discovery with automated class labeling on large-scale biomedical concept networks

PubMed Central

2012-01-01

Computational approaches to generate hypotheses from biomedical literature have been studied intensively in recent years. Nevertheless, it still remains a challenge to automatically discover novel, cross-silo biomedical hypotheses from large-scale literature repositories. In order to address this challenge, we first model a biomedical literature repository as a comprehensive network of biomedical concepts and formulate hypotheses generation as a process of link discovery on the concept network. We extract the relevant information from the biomedical literature corpus and generate a concept network and concept-author map on a cluster using Map-Reduce frame-work. We extract a set of heterogeneous features such as random walk based features, neighborhood features and common author features. The potential number of links to consider for the possibility of link discovery is large in our concept network and to address the scalability problem, the features from a concept network are extracted using a cluster with Map-Reduce framework. We further model link discovery as a classification problem carried out on a training data set automatically extracted from two network snapshots taken in two consecutive time duration. A set of heterogeneous features, which cover both topological and semantic features derived from the concept network, have been studied with respect to their impacts on the accuracy of the proposed supervised link discovery process. A case study of hypotheses generation based on the proposed method has been presented in the paper. PMID:22759614

Clinical extracts of biomedical literature for patient-centered problem solving.

PubMed Central

Florance, V

1996-01-01

This paper reports on a four-part qualitative research project aimed at designing an online document surrogate tailored to the needs of physicians seeking biomedical literature for use in clinical problem solving. The clinical extract, designed in collaboration with three practicing physicians, combines traditional elements of the MEDLINE record (e.g., title, author, source, abstract) with new elements (e.g., table captions, text headings, case profiles) suggested by the physicians. Specifications for the prototype clinical extract were developed through a series of relevance-scoring exercises and semi-structured interviews. For six clinical questions, three physicians assessed the applicability of selected articles and their document surrogates, articulating relevance criteria and reasons for their judgments. A prototype clinical extract based on their suggestions was developed, tested, evaluated, and revised. The final version includes content and format aids to make the extract easy to use. The goals, methods, and outcomes of the research study are summarized, and a template of the final design is provided. PMID:8883986

Image acquisition context: procedure description attributes for clinically relevant indexing and selective retrieval of biomedical images.

PubMed

Bidgood, W D; Bray, B; Brown, N; Mori, A R; Spackman, K A; Golichowski, A; Jones, R H; Korman, L; Dove, B; Hildebrand, L; Berg, M

1999-01-01

To support clinically relevant indexing of biomedical images and image-related information based on the attributes of image acquisition procedures and the judgments (observations) expressed by observers in the process of image interpretation. The authors introduce the notion of "image acquisition context," the set of attributes that describe image acquisition procedures, and present a standards-based strategy for utilizing the attributes of image acquisition context as indexing and retrieval keys for digital image libraries. The authors' indexing strategy is based on an interdependent message/terminology architecture that combines the Digital Imaging and Communication in Medicine (DICOM) standard, the SNOMED (Systematized Nomenclature of Human and Veterinary Medicine) vocabulary, and the SNOMED DICOM microglossary. The SNOMED DICOM microglossary provides context-dependent mapping of terminology to DICOM data elements. The capability of embedding standard coded descriptors in DICOM image headers and image-interpretation reports improves the potential for selective retrieval of image-related information. This favorably affects information management in digital libraries.

Patterning of polymer nanofiber meshes by electrospinning for biomedical applications

PubMed Central

Neves, Nuno M; Campos, Rui; Pedro, Adriano; Cunha, José; Macedo, Francisco; Reis, Rui L

2007-01-01

The end-product of the electrospinning process is typically a randomly aligned fiber mesh or membrane. This is a result of the electric field generated between the drop of polymer solution at the needle and the collector. The developed electric field causes the stretching of the fibers and their random deposition. By judicious selection of the collector architecture, it is thus possible to develop other morphologies on the nanofiber meshes. The aim of this work is to prepare fiber meshes using various patterned collectors with specific dimensions and designs and to evaluate how those patterns can affect the properties of the meshes relevant to biomedical applications. This study aims at verifying whether it is possible to control the architecture of the fiber meshes by tailoring the geometry of the collector. Three different metallic collector topographies are used to test this hypothesis. Electrospun nonwoven patterned meshes of polyethylene oxide (PEO) and poly(ε-capro-lactone) (PCL) were successfully prepared. Those fiber meshes were analyzed by scanning electron microscopy (SEM). Both mechanical properties of the meshes and cell contacting experiments were performed to test the effect of the produced patterns over the properties of the meshes relevant for biomedical applications. The present study will evaluate cell adhesion sensitivity to the patterns generated and the effect of those patterns on the tensile properties of the fiber meshes. PMID:18019842

[The relevance of the International Committee of Medical Journal Editors (ICMJE) for medical publishing and research].

PubMed

Reyes, Humberto B

2014-01-01

The International Committee of Medical Journal Editors is a leading independent institution providing guidance for the report of biomedical research and health related topics in medical journals. Established in 1978, it is currently constituted by editors of fourteen general medical journals from different countries, plus one representative for the US National Library of Medicine and one representative for the World Association of Biomedical Journal Editors. Since 1978 the Committee provides a document, originally named "Uniform Requirements…", "to help authors, editors, and others involved in peer review and biomedical publishing create and distribute accurate, clear, unbiased medical journal articles". This document has been updated several times and the last version was released in August 2013, now renamed "Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals", available in www.icmje.org and citable as "ICMJE Recommendations". A vast proportion of medical journals, worldwide, have adopted these recommendations as rules. The ICMJE discusses and provides guidance on several relevant aspects including criteria on authorship, peer review, scientific misconduct, conflicts of interest, clinical trials registration, good editorial practices, the relations between editors and journal owners, the protection of individuals subject to medical research, the solvency of electronic publications, among others. The 2013 ICMJE Annual Meeting took place in Santiago, Chile, in November 4 and 5. The photograph shows attendants to the final session.

A research education program model to prepare a highly qualified workforce in biomedical and health-related research and increase diversity.

PubMed

Crockett, Elahé T

2014-09-24

The National Institutes of Health has recognized a compelling need to train highly qualified individuals and promote diversity in the biomedical/clinical sciences research workforce. In response, we have developed a research-training program known as REPID (Research Education Program to Increase Diversity among Health Researchers) to prepare students/learners to pursue research careers in these fields and address the lack of diversity and health disparities. By inclusion of students/learners from minority and diverse backgrounds, the REPID program aims to provide a research training and enrichment experience through team mentoring to inspire students/learners to pursue research careers in biomedical and health-related fields. Students/learners are recruited from the University campus from a diverse population of undergraduates, graduates, health professionals, and lifelong learners. Our recruits first enroll into an innovative on-line introductory course in Basics and Methods in Biomedical Research that uses a laboratory Tool-Kit (a lab in a box called the My Dr. ET Lab Tool-Kit) to receive the standard basics of research education, e.g., research skills, and lab techniques. The students/learners will also learn about the responsible conduct of research, research concept/design, data recording/analysis, and scientific writing/presentation. The course is followed by a 12-week hands-on research experience during the summer. The students/learners also attend workshops and seminars/conferences. The students/learners receive scholarship to cover stipends, research related expenses, and to attend a scientific conference. The scholarship allows the students/learners to gain knowledge and seize opportunities in biomedical and health-related careers. This is an ongoing program, and during the first three years of the program, fifty-one (51) students/learners have been recruited. Thirty-six (36) have completed their research training, and eighty percent (80%) of them have continued their research experiences beyond the program. The combination of carefully providing standard basics of research education and mentorship has been successful and instrumental for training these students/learners and their success in finding biomedical/health-related jobs and/or pursuing graduate/medical studies. All experiences have been positive and highly promoted. This approach has the potential to train a highly qualified workforce, change lives, enhance biomedical research, and by extension, improve national health-care.

[Biomedical publications in Spain on debate (II): the on-going 'revolutions' and their application to neurological journals].

PubMed

González de Dios, J; Sempere, A P; Aleixandre-Benavent, R

To debate about the application of on-going 'revolutions' in medical knowledge to Spanish neurological journals in the 21st century. This article reviews the current status of five revolutions in the field of health sciences, in general, and in neurological sciences, in particular: 1) the knowledge revolution: to translate the scientific investigation to the patient, with knowledge needs-driven research agenda with founder commissioning research to answer questions posed by clinicians, managers and patients, and systematic and critical appraisal reviews as the creator of quality improved knowledge; 2) the evidence based medicine revolution: the pyramid information of '4S', with systems (guidelines and computerized decision support systems), synopses (secondary journals), syntheses (systematic reviews and meta-analysis) and studies (original studies published in journals); 3) the web revolution: the possibility of dissemination of biomedical documentation by means of the Internet network are producing changes in the traditional way of conceiving scientific publication; the Internet represents a great advantage for investigation and also for clinical practice, since it permits free, universal access to databases and the interchange of texts, images and videos; 4) the open access revolution: to take full control over all operations related to the process of publish (to create, publish, communicate, distribute, reproduce and transform) with no need of any intermediaries, and to transform fundamental aspects concerning the circulation of knowledge, its use and availability; and 5) the librarian revolution: the project of a Virtual Health Library in Spain as a tool to access and disseminate scientific and technical knowledge on health through the Internet.

Biomedical text mining for research rigor and integrity: tasks, challenges, directions.

PubMed

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.

Teaching ethical aptitude to graduate student researchers.

PubMed

Weyrich, Laura S; Harvill, Eric T

2013-01-01

Limited time dedicated to each training areas, irrelevant case-studies, and ethics "checklists" have resulted in bare-bones Responsible Conduct of Research (RCR) training for present biomedical graduate student researchers. Here, we argue that science graduate students be taught classical ethical theory, such as virtue ethics, consequentialist theory, and deontological theory, to provide a basic framework to guide researchers through ethically complex situations and examine the applicability, implications, and societal ramifications of their research. Using a relevant biomedical research example to illustrate this point, we argue that proper ethics training for graduate student researchers not only will enhance current RCR training, but train more creative, responsible scientists.

Reflections on relevance: the fields of psychosomatics and psychotherapy in 2006.

PubMed

Balon, Richard

2007-01-01

This article reviews several areas of new and interesting development in the fields of psychosomatics and psychotherapy published in the literature during 2006. These areas are: (1) cardiovascular illness and its interplay with depression; (2) risks and predisposing factors in the areas of mental illness and physical illness; (3) new developments in chronic fatigue syndrome, and (4) new or newly explored/modified (psycho)therapies, especially cognitive-behavioral therapy. In addition, an important area of conflict of interest in psychiatry in particular and in biomedical science in general is discussed, as this issue has reached prominence in the biomedical literature. Copyright 2007 S. Karger AG, Basel.

Systems Biology of the Vervet Monkey

PubMed Central

Jasinska, Anna J.; Schmitt, Christopher A.; Service, Susan K.; Cantor, Rita M.; Dewar, Ken; Jentsch, James D.; Kaplan, Jay R.; Turner, Trudy R.; Warren, Wesley C.; Weinstock, George M.; Woods, Roger P.; Freimer, Nelson B.

2013-01-01

Nonhuman primates (NHP) provide crucial biomedical model systems intermediate between rodents and humans. The vervet monkey (also called the African green monkey) is a widely used NHP model that has unique value for genetic and genomic investigations of traits relevant to human diseases. This article describes the phylogeny and population history of the vervet monkey and summarizes the use of both captive and wild vervet monkeys in biomedical research. It also discusses the effort of an international collaboration to develop the vervet monkey as the most comprehensively phenotypically and genomically characterized NHP, a process that will enable the scientific community to employ this model for systems biology investigations. PMID:24174437

New directions in biomedical text annotation: definitions, guidelines and corpus construction

PubMed Central

Wilbur, W John; Rzhetsky, Andrey; Shatkay, Hagit

2006-01-01

Background While biomedical text mining is emerging as an important research area, practical results have proven difficult to achieve. We believe that an important first step towards more accurate text-mining lies in the ability to identify and characterize text that satisfies various types of information needs. We report here the results of our inquiry into properties of scientific text that have sufficient generality to transcend the confines of a narrow subject area, while supporting practical mining of text for factual information. Our ultimate goal is to annotate a significant corpus of biomedical text and train machine learning methods to automatically categorize such text along certain dimensions that we have defined. Results We have identified five qualitative dimensions that we believe characterize a broad range of scientific sentences, and are therefore useful for supporting a general approach to text-mining: focus, polarity, certainty, evidence, and directionality. We define these dimensions and describe the guidelines we have developed for annotating text with regard to them. To examine the effectiveness of the guidelines, twelve annotators independently annotated the same set of 101 sentences that were randomly selected from current biomedical periodicals. Analysis of these annotations shows 70–80% inter-annotator agreement, suggesting that our guidelines indeed present a well-defined, executable and reproducible task. Conclusion We present our guidelines defining a text annotation task, along with annotation results from multiple independently produced annotations, demonstrating the feasibility of the task. The annotation of a very large corpus of documents along these guidelines is currently ongoing. These annotations form the basis for the categorization of text along multiple dimensions, to support viable text mining for experimental results, methodology statements, and other forms of information. We are currently developing machine learning methods, to be trained and tested on the annotated corpus, that would allow for the automatic categorization of biomedical text along the general dimensions that we have presented. The guidelines in full detail, along with annotated examples, are publicly available. PMID:16867190

ALA Guide to Medical & Health Sciences Reference

ERIC Educational Resources Information Center

ALA Editions, 2011

2011-01-01

This resource provides an annotated list of print and electronic biomedical and health-related reference sources, including Internet resources and digital image collections. Readers will find relevant research, clinical, and consumer health information resources. The emphasis is on resources within the United States, with a few representative…

Commentary on domestic animals in agricultural and biomedical research: An endangered enterprise

USDA-ARS?s Scientific Manuscript database

Despite the long and successful history of research on agriculturally relevant domestic animals, basic and translational research using domestic species is becoming increasingly threatened due to budgetary erosion. This funding decline is well documented in a recent article by Ireland et al., publis...

R&D 100 Winner 2010: Acoustic Wave Biosensors

ScienceCinema

Larson, Richard; Branch, Darren; Edwards, Thayne

2018-01-16

The acoustic wave biosensor is innovative device that is a handheld, battery-powered, portable detection system capable of multiplex identification of a wide range of medically relevant pathogens and their biomolecular signatures — viruses, bacteria, proteins, and DNA — at clinically relevant levels. This detection occurs within minutes — not hours — at the point of care, whether that care is in a physician's office, a hospital bed, or at the scene of a biodefense or biomedical emergency.

[Scientometrics and bibliometrics of biomedical engineering periodicals and papers].

PubMed

Zhao, Ping; Xu, Ping; Li, Bingyan; Wang, Zhengrong

2003-09-01

This investigation was made to reveal the current status, research trend and research level of biomedical engineering in Chinese mainland by means of scientometrics and to assess the quality of the four domestic publications by bibliometrics. We identified all articles of four related publications by searching Chinese and foreign databases from 1997 to 2001. All articles collected or cited by these databases were searched and statistically analyzed for finding out the relevant distributions, including databases, years, authors, institutions, subject headings and subheadings. The source of sustentation funds and the related articles were analyzed too. The results showed that two journals were cited by two foreign databases and five Chinese databases simultaneously. The output of Journal of Biomedical Engineering was the highest. Its quantity of original papers cited by EI, CA and the totality of papers sponsored by funds were higher than those of the others, but the quantity and percentage per year of biomedical articles cited by EI were decreased in all. Inland core authors and institutions had come into being in the field of biomedical engineering. Their research topics were mainly concentrated on ten subject headings which included biocompatible materials, computer-assisted signal processing, electrocardiography, computer-assisted image processing, biomechanics, algorithms, electroencephalography, automatic data processing, mechanical stress, hemodynamics, mathematical computing, microcomputers, theoretical models, etc. The main subheadings were concentrated on instrumentation, physiopathology, diagnosis, therapy, ultrasonography, physiology, analysis, surgery, pathology, method, etc.

The diversity and disparity in biomedical informatics (DDBI) workshop.

PubMed

Southerland, William M; Swamidass, S Joshua; Payne, Philip R O; Wiley, Laura; Williams-DeVane, ClarLynda

2018-01-01

The Diversity and Disparity in Biomedical Informatics (DDBI) workshop will be focused on complementary and critical issues concerned with enhancing diversity in the informatics workforce as well as diversity in patient cohorts. According to the National Institute of Minority Health and Health Disparities (NIMHD) at the NIH, diversity refers to the inclusion of the following traditionally underrepresented groups: African Americans/Blacks, Asians (>30 countries), American Indian or Alaska Native, Native Hawaiian or Other Pacific Islander, Latino or Hispanic (20 countries). Gender, culture, and socioeconomic status are also important dimensions of diversity, which may define some underrepresented groups. The under-representation of specific groups in both the biomedical informatics workforce as well as in the patient-derived data that is being used for research purposes has contributed to an ongoing disparity; these groups have not experienced equity in contributing to or benefiting from advancements in informatics research. This workshop will highlight innovative efforts to increase the pool of minority informaticians and discuss examples of informatics research that addresses the health concerns that impact minority populations. This workshop topics will provide insight into overcoming pipeline issues in the development of minority informaticians while emphasizing the importance of minority participation in health related research. The DDBI workshop will occur in two parts. Part I will discuss specific minority health & health disparities research topics and Part II will cover discussions related to overcoming pipeline issues in the training of minority informaticians.

Using the Emanuel et al. framework to assess ethical issues raised by a biomedical research ethics committee in South Africa.

PubMed

Tsoka-Gwegweni, Joyce M; Wassenaar, Douglas R

2014-12-01

The Emanuel, Wendler, and Grady framework was designed as a universal tool for use in many settings including developing countries. However, it is not known whether the work of African health research ethics committees (RECs) is compatible with this framework. The absence of any normative or empirical weighting of the eight principles within this framework suggests that different health RECs may raise some ethical issues more frequently than others when reviewing protocols. We used the Emanuel et al. framework to assess, code, and rank the most frequent ethical issues considered by a biomedical REC during review of research protocols for the years 2008 to 2012. We extracted data from the recorded minutes of a South African biomedical REC for the years 2008 to 2012, designed the data collection sheet according to the Emanuel et al. framework, and removed all identifiers during data processing and analysis. From the 98 protocols that we assessed, the most frequent issues that emerged were the informed consent, scientific validity, fair participant selection, and ongoing respect for participants. This study represents the first known attempt to analyze REC responses/minutes using the Emanuel et al. framework, and suggests that this framework may be useful in describing and categorizing the core activities of an REC. © The Author(s) 2014.

Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics.

PubMed

Ganapathiraju, Madhavi K; Orii, Naoki

2013-08-30

Advances in biotechnology have created "big-data" situations in molecular and cellular biology. Several sophisticated algorithms have been developed that process big data to generate hundreds of biomedical hypotheses (or predictions). The bottleneck to translating this large number of biological hypotheses is that each of them needs to be studied by experimentation for interpreting its functional significance. Even when the predictions are estimated to be very accurate, from a biologist's perspective, the choice of which of these predictions is to be studied further is made based on factors like availability of reagents and resources and the possibility of formulating some reasonable hypothesis about its biological relevance. When viewed from a global perspective, say from that of a federal funding agency, ideally the choice of which prediction should be studied would be made based on which of them can make the most translational impact. We propose that algorithms be developed to identify which of the computationally generated hypotheses have potential for high translational impact; this way, funding agencies and scientific community can invest resources and drive the research based on a global view of biomedical impact without being deterred by local view of feasibility. In short, data-analytic algorithms analyze big-data and generate hypotheses; in contrast, the proposed inference-analytic algorithms analyze these hypotheses and rank them by predicted biological impact. We demonstrate this through the development of an algorithm to predict biomedical impact of protein-protein interactions (PPIs) which is estimated by the number of future publications that cite the paper which originally reported the PPI. This position paper describes a new computational problem that is relevant in the era of big-data and discusses the challenges that exist in studying this problem, highlighting the need for the scientific community to engage in this line of research. The proposed class of algorithms, namely inference-analytic algorithms, is necessary to ensure that resources are invested in translating those computational outcomes that promise maximum biological impact. Application of this concept to predict biomedical impact of PPIs illustrates not only the concept, but also the challenges in designing these algorithms.

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses

PubMed Central

Torre, Denis; Krawczuk, Patrycja; Jagodnik, Kathleen M.; Lachmann, Alexander; Wang, Zichen; Wang, Lily; Kuleshov, Maxim V.; Ma’ayan, Avi

2018-01-01

Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools, index bioinformatics tools that can extract knowledge from these digital data objects. However, systematic access to pre-generated ‘canned’ analyses applied by bioinformatics tools to biomedical digital data objects is currently not available. Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets. The Datasets2Tools repository also contains the indexing of 4,901 published bioinformatics software tools, and all the analyzed datasets. Datasets2Tools enables users to rapidly find datasets, tools, and canned analyses through an intuitive web interface, a Google Chrome extension, and an API. Furthermore, Datasets2Tools provides a platform for contributing canned analyses, datasets, and tools, as well as evaluating these digital objects according to their compliance with the findable, accessible, interoperable, and reusable (FAIR) principles. By incorporating community engagement, Datasets2Tools promotes sharing of digital resources to stimulate the extraction of knowledge from biomedical research data. Datasets2Tools is freely available from: http://amp.pharm.mssm.edu/datasets2tools. PMID:29485625

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses.

PubMed

Torre, Denis; Krawczuk, Patrycja; Jagodnik, Kathleen M; Lachmann, Alexander; Wang, Zichen; Wang, Lily; Kuleshov, Maxim V; Ma'ayan, Avi

2018-02-27

Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools, index bioinformatics tools that can extract knowledge from these digital data objects. However, systematic access to pre-generated 'canned' analyses applied by bioinformatics tools to biomedical digital data objects is currently not available. Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets. The Datasets2Tools repository also contains the indexing of 4,901 published bioinformatics software tools, and all the analyzed datasets. Datasets2Tools enables users to rapidly find datasets, tools, and canned analyses through an intuitive web interface, a Google Chrome extension, and an API. Furthermore, Datasets2Tools provides a platform for contributing canned analyses, datasets, and tools, as well as evaluating these digital objects according to their compliance with the findable, accessible, interoperable, and reusable (FAIR) principles. By incorporating community engagement, Datasets2Tools promotes sharing of digital resources to stimulate the extraction of knowledge from biomedical research data. Datasets2Tools is freely available from: http://amp.pharm.mssm.edu/datasets2tools.

Effective use of latent semantic indexing and computational linguistics in biological and biomedical applications.

PubMed

Chen, Hongyu; Martin, Bronwen; Daimon, Caitlin M; Maudsley, Stuart

2013-01-01

Text mining is rapidly becoming an essential technique for the annotation and analysis of large biological data sets. Biomedical literature currently increases at a rate of several thousand papers per week, making automated information retrieval methods the only feasible method of managing this expanding corpus. With the increasing prevalence of open-access journals and constant growth of publicly-available repositories of biomedical literature, literature mining has become much more effective with respect to the extraction of biomedically-relevant data. In recent years, text mining of popular databases such as MEDLINE has evolved from basic term-searches to more sophisticated natural language processing techniques, indexing and retrieval methods, structural analysis and integration of literature with associated metadata. In this review, we will focus on Latent Semantic Indexing (LSI), a computational linguistics technique increasingly used for a variety of biological purposes. It is noted for its ability to consistently outperform benchmark Boolean text searches and co-occurrence models at information retrieval and its power to extract indirect relationships within a data set. LSI has been used successfully to formulate new hypotheses, generate novel connections from existing data, and validate empirical data.

Annotating image ROIs with text descriptions for multimodal biomedical document retrieval

NASA Astrophysics Data System (ADS)

You, Daekeun; Simpson, Matthew; Antani, Sameer; Demner-Fushman, Dina; Thoma, George R.

2013-01-01

Regions of interest (ROIs) that are pointed to by overlaid markers (arrows, asterisks, etc.) in biomedical images are expected to contain more important and relevant information than other regions for biomedical article indexing and retrieval. We have developed several algorithms that localize and extract the ROIs by recognizing markers on images. Cropped ROIs then need to be annotated with contents describing them best. In most cases accurate textual descriptions of the ROIs can be found from figure captions, and these need to be combined with image ROIs for annotation. The annotated ROIs can then be used to, for example, train classifiers that separate ROIs into known categories (medical concepts), or to build visual ontologies, for indexing and retrieval of biomedical articles. We propose an algorithm that pairs visual and textual ROIs that are extracted from images and figure captions, respectively. This algorithm based on dynamic time warping (DTW) clusters recognized pointers into groups, each of which contains pointers with identical visual properties (shape, size, color, etc.). Then a rule-based matching algorithm finds the best matching group for each textual ROI mention. Our method yields a precision and recall of 96% and 79%, respectively, when ground truth textual ROI data is used.

A resource facility for kinetic analysis: modeling using the SAAM computer programs.

PubMed

Foster, D M; Boston, R C; Jacquez, J A; Zech, L

1989-01-01

Kinetic analysis and integrated system modeling have contributed significantly to understanding the physiology and pathophysiology of metabolic systems in humans and animals. Many experimental biologists are aware of the usefulness of these techniques and recognize that kinetic modeling requires special expertise. The Resource Facility for Kinetic Analysis (RFKA) provides this expertise through: (1) development and application of modeling technology for biomedical problems, and (2) development of computer-based kinetic modeling methodologies concentrating on the computer program Simulation, Analysis, and Modeling (SAAM) and its conversational version, CONversational SAAM (CONSAM). The RFKA offers consultation to the biomedical community in the use of modeling to analyze kinetic data and trains individuals in using this technology for biomedical research. Early versions of SAAM were widely applied in solving dosimetry problems; many users, however, are not familiar with recent improvements to the software. The purpose of this paper is to acquaint biomedical researchers in the dosimetry field with RFKA, which, together with the joint National Cancer Institute-National Heart, Lung and Blood Institute project, is overseeing SAAM development and applications. In addition, RFKA provides many service activities to the SAAM user community that are relevant to solving dosimetry problems.

100 Metrics to Assess and Communicate the Value of Biomedical Research: An Ideas Book.

PubMed

Guthrie, Susan; Krapels, Joachim; Lichten, Catherine A; Wooding, Steven

2017-01-01

Biomedical research affects society in many ways. It has been shown to improve health, create jobs, add to our knowledge, and foster new collaborations. Despite the complexity of modern research, many of the metrics used to evaluate the impacts of research still focus on the traditional, often academic, part of the research pathway, covering areas such as the amount of grant funding received and the number of peer-reviewed publications. In response to increasing expectations of accountability and transparency, the Association of American Medical Colleges (AAMC), in collaboration with RAND Europe, undertook a project to help communicate the wider value of biomedical research. The initiative developed resources to support academic medical centers in evaluating the outcomes and impacts of their research using approaches relevant to various stakeholders, including patients, providers, administrators, and legislators. This study presents 100 ideas for metrics that can be used to assess and communicate the value of biomedical research. The list is not comprehensive, and the metrics are not fully developed, but they should serve to stimulate and broaden thinking about how academic medical centers can communicate the value of their research to a broad range of stakeholders.

100 Metrics to Assess and Communicate the Value of Biomedical Research

PubMed Central

Guthrie, Susan; Krapels, Joachim; Lichten, Catherine A.; Wooding, Steven

2017-01-01

Abstract Biomedical research affects society in many ways. It has been shown to improve health, create jobs, add to our knowledge, and foster new collaborations. Despite the complexity of modern research, many of the metrics used to evaluate the impacts of research still focus on the traditional, often academic, part of the research pathway, covering areas such as the amount of grant funding received and the number of peer-reviewed publications. In response to increasing expectations of accountability and transparency, the Association of American Medical Colleges (AAMC), in collaboration with RAND Europe, undertook a project to help communicate the wider value of biomedical research. The initiative developed resources to support academic medical centers in evaluating the outcomes and impacts of their research using approaches relevant to various stakeholders, including patients, providers, administrators, and legislators. This study presents 100 ideas for metrics that can be used to assess and communicate the value of biomedical research. The list is not comprehensive, and the metrics are not fully developed, but they should serve to stimulate and broaden thinking about how academic medical centers can communicate the value of their research to a broad range of stakeholders. PMID:28983437

Medically unexplained physical symptoms, misunderstood and wrongly treated? A semiotic perspective on chronic pain.

PubMed

Busvold, Kari Irene H; Bondevik, Hilde

2018-06-01

Medically unexplained physical symptoms (MUPS) are a significant and increasing health issue in the western world. Chronic pain constitutes a considerable element of these symptoms, and the lack of a biomedical explanation of their cause challenges the clinical encounter. The limitations of biomedicine become evident in these encounters and expose the need for an expanded understanding of body and symptom. Semiotics, as an anti-dualistic meta-theory, closes the gap between natural science and the humanities and views the human body in an evolutionary and existential perspective. By focusing on interpretation and communication of signs as ongoing processes at all levels of life, biology and experience, the subjective and the measurable will be integrated. A special type of sign, the self-referential, is part of the body's internal communication. These signs may be viewed as the body's warnings to itself, for instance when the individual's consciousness, thought and action run counter to the organism's physiological and psychological needs. In a semiotic perspective, existential conditions may also activate the body's defense systems. In this context, the unexplained pain may be understood as a functional warning sign. The enhanced understanding of body and symptom that a semiotic approach calls for is relevant for the work of physiotherapists and may lead to more constructive clinical encounters with patients with unexplained chronic pain.

Intraperitoneal adhesions--an ongoing challenge between biomedical engineering and the life sciences.

PubMed

Brochhausen, Christoph; Schmitt, Volker H; Rajab, Taufiek K; Planck, Constanze N E; Krämer, Bernhard; Wallwiener, Markus; Hierlemann, Helmut; Kirkpatrick, C James

2011-07-01

Peritoneal adhesions remain a relevant clinical problem despite the currently available prophylactic barrier materials. So far, the physical separation of traumatized serosa areas using barriers represents the most important clinical strategy for adhesion prevention. However, the optimal material has not yet been found. Further optimization or pharmacological functionalization of these barriers could give an innovative input for peritoneal adhesion prevention. Therefore, a more complete understanding of pathogenesis is required. On the basis of the pathophysiology of adhesion formation the main barriers currently in clinical practice as well as new innovations are discussed in the present review. Physiologically, mesothelial cells play a decisive role in providing a frictionless gliding surface on the serosa. Adhesion formation results from a cascade of events and is regulated by a variety of cellular and humoral factors. The main clinically applied strategy for adhesion prevention is based on the use of liquid or solid adhesion barriers to separate physically any denuded tissue. Both animal and human trials have not yet been able to identify the optimal barrier to prevent adhesion formation in a sustainable way. Therefore, further developments are required for effective prevention of postoperative adhesion formation. To reach this goal the combination of structural modification and pharmacological functionalization of barrier materials should be addressed. Achieving this aim requires the interaction between basic research, materials science and clinical expertise. Copyright © 2011 Wiley Periodicals, Inc.

God in the brain: Experiencing psychosis in the postsecular United States.

PubMed

Jones, Nev; Kelly, Timothy; Shattell, Mona

2016-08-01

There is a growing literature on what contemporary cultural theorists have broadly termed the "postsecular": the abandonment of clear-cut boundaries between the secular and nonsecular in the industrialized West and an embrace of a complex understanding of what is real that neither accepts nor rejects the supernatural. These new cultural currents may affect not only philosophers and theologians, but also the ways in which individuals with psychosis make sense of their experiences. This paper reports on the key findings of an in-depth qualitative analysis of 19 interviews of individuals diagnosed with psychotic disorders. The majority of participants described ongoing and self-conscious struggles to demarcate their experiences as the products of the real world or a "crazy" mind. With equal frequency, participants weighed and debated competing secular and supernatural explanations, often juxtaposing and blending different explanatory frameworks. We found that this syncretic process affected not only the content of psychotic experiences-what delusions or hallucinations are about-but also the type of arguments or logics used to justify particular interpretations. We discuss the implications of these observations with respect to clinical practice and the broader phenomenology of psychosis, challenging often oversimplified discourse on "insight" and suggesting that polarization(s) between "biomedical" and "psychosocial" explanations may be of less relevance to patients' real-world experiences than is often assumed. © The Author(s) 2016.

"And now for the good news..." the impact of negative and positive messages in self-management education for people with Type 2 diabetes: A qualitative study in an ethnically diverse population.

PubMed

Eborall, Helen C; Virdee, Satnam K; Patel, Naina; Redwood, Sabi; Greenfield, Sheila M; Stone, Margaret A

2016-03-01

To explore the impact of Diabetes Education and Self Management for Ongoing and Newly Diagnosed (DESMOND) Foundation education, particularly from interviewees' narratives regarding recall of good and bad news messages and behaviour changes. In-depth, semi-structured interviews were conducted with a purposive sample (n=19) of people who had attended education sessions as part of a randomised controlled trial in two UK sites with ethnically diverse populations. Data collection and analysis were informed by the constant comparative approach and facilitated through charting. Findings were similar in people from different ethnic backgrounds. Exploration of levels of recall of the sessions suggested that this was variable and sometimes very limited, but that interviewees had all assimilated some relevant learning. Key themes emerged relating to the way in which interviewees recalled and had been influenced by positive (good news) and negative (bad news) messages within the education sessions, including biomedical explanations. Both types of message appeared to have an important role in terms of motivation to change behaviour, but a notable observation was that none of the interviewees recalled receiving bad news messages when diagnosed. Our findings have highlighted the importance of providing and combining both negative and positive messages within education designed to promote self-management behaviour change. © The Author(s) 2015.

Should MD-PhD programs encourage graduate training in disciplines beyond conventional biomedical or clinical sciences?

PubMed

O'Mara, Ryan J; Hsu, Stephen I; Wilson, Daniel R

2015-02-01

The goal of MD-PhD training programs is to produce physician-scientists with unique capacities to lead the future biomedical research workforce. The current dearth of physician-scientists with expertise outside conventional biomedical or clinical sciences raises the question of whether MD-PhD training programs should allow or even encourage scholars to pursue doctoral studies in disciplines that are deemed nontraditional, yet are intrinsically germane to major influences on health. This question is especially relevant because the central value and ultimate goal of the academic medicine community is to help attain the highest level of health and health equity for all people. Advances in medical science and practice, along with improvements in health care access and delivery, are steps toward health equity, but alone they will not come close to eliminating health inequalities. Addressing the complex health issues in our communities and society as a whole requires a biomedical research workforce with knowledge, practice, and research skills well beyond conventional biomedical or clinical sciences. To make real progress in advancing health equity, educational pathways must prepare physician-scientists to treat both micro and macro determinants of health. The authors argue that MD-PhD programs should allow and encourage their scholars to cross boundaries into less traditional disciplines such as epidemiology, statistics, anthropology, sociology, ethics, public policy, management, economics, education, social work, informatics, communications, and marketing. To fulfill current and coming health care needs, nontraditional MD-PhD students should be welcomed and supported as valuable members of our biomedical research workforce.

Reaching Consensus on Essential Biomedical Science Learning Objectives in a Dental Curriculum.

PubMed

Best, Leandra; Walton, Joanne N; Walker, Judith; von Bergmann, HsingChi

2016-04-01

This article describes how the University of British Columbia Faculty of Dentistry reached consensus on essential basic biomedical science objectives for DMD students and applied the information to the renewal of its DMD curriculum. The Delphi Method was used to build consensus among dental faculty members and students regarding the relevance of over 1,500 existing biomedical science objectives. Volunteer panels of at least three faculty members (a basic scientist, a general dentist, and a dental specialist) and a fourth-year dental student were formed for each of 13 biomedical courses in the first two years of the program. Panel members worked independently and anonymously, rating each course objective as "need to know," "nice to know," "irrelevant," or "don't know." Panel members were advised after each round which objectives had not yet achieved a 75% consensus and were asked to reconsider their ratings. After a maximum of three rounds to reach consensus, a second group of faculty experts reviewed and refined the results to establish the biomedical science objectives for the renewed curriculum. There was consensus on 46% of the learning objectives after round one, 80% after round two, and 95% after round three. The second expert group addressed any remaining objectives as part of its review process. Only 47% of previous biomedical science course objectives were judged to be essential or "need to know" for the general dentist. The consensus reached by participants in the Delphi Method panels and a second group of faculty experts led to a streamlined, better integrated DMD curriculum to prepare graduates for future practice.

Learning through projects in the training of biomedical engineers: an application experience

NASA Astrophysics Data System (ADS)

Gambi, José Antonio Li; Peme, Carmen

2011-09-01

Learning through Projects in the curriculum consists of both the identification and analysis of a problem, and the design of solution, execution and evaluation strategies, with teams of students. The project is conceived as the creation of a set of strategies articulated and developed during a certain amount of time to solve a problem contextualized in situations continually changing, where the constant evaluation provides feedback to make adjustments. In 2009, Learning through Projects was applied on the subject Hospital Facilities and three intervention projects were developed in health centers. This first stage is restricted to the analysis of the aspects that are considered to be basic to the professional training: a) Context knowledge: The future biomedical engineers must be familiarized with the complex health system where they will develop their profession; b) Team work: This is one of the essential skills in the training of students, since Biomedical Engineering connects the knowledge of sciences of life with the knowledge of exact sciences and technology; c) Regulations: The activities related to the profession require the implementation of regulations; therefore, to be aware of and to apply these regulations is a fundamental aspect to be analyzed in this stage; d) Project evaluation: It refers to the elaboration and studying of co-evaluation reports, which helps to find out if Learning through Projects contributes to the training. This new line of investigation has the purpose of discovering if the application of this learning strategy makes changes in the training of students in relation to their future professional career. The findings of this ongoing investigation will allow for the analysis of the possibility of extending its application. Key words: engineering, biomedical, learning, projects, strategies.

Intelligent biomedical clothing for personal health and disease management: state of the art and future vision.

PubMed

Lymberis, Andreas; Olsson, Silas

2003-01-01

Telemedicine has been introduced to overcome distance in order to get prompt access to medical knowledge and appropriate health care. More recently, work in telemedicine has aimed at developing solutions to support the management of chronic diseases such as diabetes, and lung and heart diseases, as well as to provide support for home care services. Telemedicine is also entering the fields of health promotion/prevention disease, life style management, and well-being. The evolution and broadening of telemedicine gives birth to a nomenclature that includes "e-health," "telehealth," and "telecare." The latest developments in microsystems and nanotechnologies as well as in information processing and communication technologies allow miniaturization and non-invasive smart monitoring of physiological and physical data. Ongoing cutting-edge multidisciplinary research in textile fibers, biomedical sensors, and wireless and mobile telecommunications integrated with telemedicine, aims at developing intelligent biomedical clothing (IBC) that could pave the way to support personalized management of health and diseases at the point of need and at any time. In this study, we aim to describe the current status of multidisciplinary research and development of IBC, based on bibliographic research and reports from seminars, workshops, conferences, and working groups. A further aim is to inform the developers, the decision makers, and users in the health and healthcare sector regarding future solutions to support personalized health care and disease management. Both the textile sector and healthcare sector are looking with great interest at the innovative products and applications that could result from the integration of microsystems, nanotechnologies, biomedical sensors, textiles, and mobile telecommunications. For health monitoring, disease prevention and management, rehabilitation, and sport medicine, IBC may offer, in the mid-term future, a unique, wearable non-obtrusive telemedicine platform for individualized services that is readily accessible and of good quality.

Neurofeedback for autistic spectrum disorder: a review of the literature.

PubMed

Coben, Robert; Linden, Michael; Myers, Thomas E

2010-03-01

There is a need for effective interventions to address the core symptoms and problems associated with autistic spectrum disorder (ASD). Behavior therapy improves communication and behavioral functioning. Additional treatment options include psychopharmacological and biomedical interventions. Although these approaches help children with autistic problems, they may be associated with side effects, risks or require ongoing or long-term treatment. Neurofeedback is a noninvasive approach shown to enhance neuroregulation and metabolic function in ASD. We present a review of the literature on the application of Neurofeedback to the multiple problems associated with ASD. Directions for future research are discussed.

Creating Simulated Microgravity Patient Models

NASA Technical Reports Server (NTRS)

Hurst, Victor; Doerr, Harold K.; Bacal, Kira

2004-01-01

The Medical Operational Support Team (MOST) has been tasked by the Space and Life Sciences Directorate (SLSD) at the NASA Johnson Space Center (JSC) to integrate medical simulation into 1) medical training for ground and flight crews and into 2) evaluations of medical procedures and equipment for the International Space Station (ISS). To do this, the MOST requires patient models that represent the physiological changes observed during spaceflight. Despite the presence of physiological data collected during spaceflight, there is no defined set of parameters that illustrate or mimic a 'space normal' patient. Methods: The MOST culled space-relevant medical literature and data from clinical studies performed in microgravity environments. The areas of focus for data collection were in the fields of cardiovascular, respiratory and renal physiology. Results: The MOST developed evidence-based patient models that mimic the physiology believed to be induced by human exposure to a microgravity environment. These models have been integrated into space-relevant scenarios using a human patient simulator and ISS medical resources. Discussion: Despite the lack of a set of physiological parameters representing 'space normal,' the MOST developed space-relevant patient models that mimic microgravity-induced changes in terrestrial physiology. These models are used in clinical scenarios that will medically train flight surgeons, biomedical flight controllers (biomedical engineers; BME) and, eventually, astronaut-crew medical officers (CMO).

SOCIAL, HISTORICAL AND CULTURAL DIMENSIONS OF TUBERCULOSIS.

PubMed

Mason, Paul H; Roy, Anupom; Spillane, Jayden; Singh, Puneet

2016-03-01

Tuberculosis (TB) researchers and clinicians, by virtue of the social disease they study, are drawn into an engagement with ways of understanding illness that extend beyond the strictly biomedical model. Primers on social science concepts directly relevant to TB, however, are lacking. The particularities of TB disease mean that certain social science concepts are more relevant than others. Concepts such as structural violence can seem complicated and off-putting. Other concepts, such as gender, can seem so familiar that they are left relatively unexplored. An intimate familiarity with the social dimensions of disease is valuable, particularly for infectious diseases, because the social model is an important complement to the biomedical model. This review article offers an important introduction to a selection of concepts directly relevant to TB from health sociology, medical anthropology and social cognitive theory. The article has pedagogical utility and also serves as a useful refresher for those researchers already engaged in this genre of work. The conceptual tools of health sociology, medical anthropology and social cognitive theory offer insightful ways to examine the social, historical and cultural dimensions of public health. By recognizing cultural experience as a central force shaping human interactions with the world, TB researchers and clinicians develop a more nuanced consideration of how health, illness and medical treatment are understood, interpreted and confronted.

Semantic biomedical resource discovery: a Natural Language Processing framework.

PubMed

Sfakianaki, Pepi; Koumakis, Lefteris; Sfakianakis, Stelios; Iatraki, Galatia; Zacharioudakis, Giorgos; Graf, Norbert; Marias, Kostas; Tsiknakis, Manolis

2015-09-30

A plethora of publicly available biomedical resources do currently exist and are constantly increasing at a fast rate. In parallel, specialized repositories are been developed, indexing numerous clinical and biomedical tools. The main drawback of such repositories is the difficulty in locating appropriate resources for a clinical or biomedical decision task, especially for non-Information Technology expert users. In parallel, although NLP research in the clinical domain has been active since the 1960s, progress in the development of NLP applications has been slow and lags behind progress in the general NLP domain. The aim of the present study is to investigate the use of semantics for biomedical resources annotation with domain specific ontologies and exploit Natural Language Processing methods in empowering the non-Information Technology expert users to efficiently search for biomedical resources using natural language. A Natural Language Processing engine which can "translate" free text into targeted queries, automatically transforming a clinical research question into a request description that contains only terms of ontologies, has been implemented. The implementation is based on information extraction techniques for text in natural language, guided by integrated ontologies. Furthermore, knowledge from robust text mining methods has been incorporated to map descriptions into suitable domain ontologies in order to ensure that the biomedical resources descriptions are domain oriented and enhance the accuracy of services discovery. The framework is freely available as a web application at ( http://calchas.ics.forth.gr/ ). For our experiments, a range of clinical questions were established based on descriptions of clinical trials from the ClinicalTrials.gov registry as well as recommendations from clinicians. Domain experts manually identified the available tools in a tools repository which are suitable for addressing the clinical questions at hand, either individually or as a set of tools forming a computational pipeline. The results were compared with those obtained from an automated discovery of candidate biomedical tools. For the evaluation of the results, precision and recall measurements were used. Our results indicate that the proposed framework has a high precision and low recall, implying that the system returns essentially more relevant results than irrelevant. There are adequate biomedical ontologies already available, sufficiency of existing NLP tools and quality of biomedical annotation systems for the implementation of a biomedical resources discovery framework, based on the semantic annotation of resources and the use on NLP techniques. The results of the present study demonstrate the clinical utility of the application of the proposed framework which aims to bridge the gap between clinical question in natural language and efficient dynamic biomedical resources discovery.

Task Effects in the Interpretation of Pronouns

ERIC Educational Resources Information Center

Sanoudaki, Eirini; Varlokosta, Spyridoula

2015-01-01

Children acquiring a range of languages have difficulties in the interpretation of personal pronouns. Ongoing debates in the relevant literature concern the extent to which different pronoun types are subject to this phenomenon, as well as the role of methodology in relevant research. In this study, we use two different experimental tasks to…

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

PubMed

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.

Prioritising lexical patterns to increase axiomatisation in biomedical ontologies. The role of localisation and modularity.

PubMed

Quesada-Martínez, M; Fernández-Breis, J T; Stevens, R; Mikroyannidi, E

2015-01-01

This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". In previous work, we have defined methods for the extraction of lexical patterns from labels as an initial step towards semi-automatic ontology enrichment methods. Our previous findings revealed that many biomedical ontologies could benefit from enrichment methods using lexical patterns as a starting point.Here, we aim to identify which lexical patterns are appropriate for ontology enrichment, driving its analysis by metrics to prioritised the patterns. We propose metrics for suggesting which lexical regularities should be the starting point to enrich complex ontologies. Our method determines the relevance of a lexical pattern by measuring its locality in the ontology, that is, the distance between the classes associated with the pattern, and the distribution of the pattern in a certain module of the ontology. The methods have been applied to four significant biomedical ontologies including the Gene Ontology and SNOMED CT. The metrics provide information about the engineering of the ontologies and the relevance of the patterns. Our method enables the suggestion of links between classes that are not made explicit in the ontology. We propose a prioritisation of the lexical patterns found in the analysed ontologies. The locality and distribution of lexical patterns offer insights into the further engineering of the ontology. Developers can use this information to improve the axiomatisation of their ontologies.

Magnetic hydroxyapatite: a promising multifunctional platform for nanomedicine application

PubMed Central

Mondal, Sudip; Manivasagan, Panchanathan; Bharathiraja, Subramaniyan; Santha Moorthy, Madhappan; Kim, Hye Hyun; Seo, Hansu; Lee, Kang Dae; Oh, Junghwan

2017-01-01

In this review, specific attention is paid to the development of nanostructured magnetic hydroxyapatite (MHAp) and its potential application in controlled drug/gene delivery, tissue engineering, magnetic hyperthermia treatment, and the development of contrast agents for magnetic resonance imaging. Both magnetite and hydroxyapatite materials have excellent prospects in nanomedicine with multifunctional therapeutic approaches. To date, many research articles have focused on biomedical applications of nanomaterials because of which it is very difficult to focus on any particular type of nanomaterial. This study is possibly the first effort to emphasize on the comprehensive assessment of MHAp nanostructures for biomedical applications supported with very recent experimental studies. From basic concepts to the real-life applications, the relevant characteristics of magnetic biomaterials are patented which are briefly discussed. The potential therapeutic and diagnostic ability of MHAp-nanostructured materials make them an ideal platform for future nanomedicine. We hope that this advanced review will provide a better understanding of MHAp and its important features to utilize it as a promising material for multifunctional biomedical applications. PMID:29200851

Art and science of authorship for biomedical research publication.

PubMed

Harsoor, S S

2016-09-01

Completion of research is logically followed by process of submission of the outcomes for publication. The objective of this article is to sensitise the young potential authors to improve their skill of writing so that the acceptance rate of publication is improved without significant comments and efforts of the editors of the journal. The article is based on the available literature combined with the experience of the author himself as reviewer and editor of biomedical journals. The treatment patterns of clinicians are moving towards evidence-based medical practice. Hence, a clinically relevant research question based on the contemporary knowledge gap is studied using appropriate research methodology. The writers are informed about the criteria to be fulfilled to claim authorship. Finally, emphasis is laid on the essentials of good medical writing necessary for publication. The writing for submission to biomedical journal is both an art and science in itself. A scientifically well-conducted study along with a sound knowledge of the mechanics of writing will enable the novices to achieve better acceptance rate for publication.

RECOPE: How to succeed in bringing ideas from academia to market without compromising ingenuity.

PubMed

Gaymalov, Zagit; Kabanov, Alexander

2017-04-01

Translation of biomedical technology originated in academia to the market is hindered by lack of consideration of market needs and commercialization pathways that leads academic research away from the market, leaving the public without long-awaited cures. Here we describe Reverse Conceptual Product Engineering (RECOPE), an approach applied in academic setting early in the course of the research project to facilitate biomedical research translation from bench to bedside. By using expertise of diverse set of biomedical professionals and trainees to solve a problem, RECOPE helps to make research goals more relevant to the society needs and translatable in a long-term perspective. Through the use of RECOPE one can critically reassess research design and translational potential and identify new market opportunities. RECOPE also provides for considerable educational opportunities to pre- and post-doctoral trainees. Adoption of RECOPE as a basic to for research design education will have a noticeable impact on academic research. Copyright © 2016 Elsevier Inc. All rights reserved.

Sensor Fusion and Smart Sensor in Sports and Biomedical Applications.

PubMed

Mendes, José Jair Alves; Vieira, Mário Elias Marinho; Pires, Marcelo Bissi; Stevan, Sergio Luiz

2016-09-23

The following work presents an overview of smart sensors and sensor fusion targeted at biomedical applications and sports areas. In this work, the integration of these areas is demonstrated, promoting a reflection about techniques and applications to collect, quantify and qualify some physical variables associated with the human body. These techniques are presented in various biomedical and sports applications, which cover areas related to diagnostics, rehabilitation, physical monitoring, and the development of performance in athletes, among others. Although some applications are described in only one of two fields of study (biomedicine and sports), it is very likely that the same application fits in both, with small peculiarities or adaptations. To illustrate the contemporaneity of applications, an analysis of specialized papers published in the last six years has been made. In this context, the main characteristic of this review is to present the largest quantity of relevant examples of sensor fusion and smart sensors focusing on their utilization and proposals, without deeply addressing one specific system or technique, to the detriment of the others.

Biomedical Research Ethics Committees in sub-Saharan Africa: a collective review of their structure, functioning, and outcomes.

PubMed

Silaigwana, Blessing; Wassenaar, Douglas

2015-04-01

Research Ethics Committees (RECs) are mandated to protect human participants by conducting ethical reviews of biomedical research. To date, there is a dearth of information on the structure, functioning, and outcomes of RECs in Africa. This article reviews empirical studies investigating African RECs, with the aim of providing an overview of what is known and identifying gaps in our knowledge. We conducted a literature search of the EBSCO, PubMed, and Google Scholar electronic databases. Twenty-three empirical studies reporting on the structure, functions, and outcomes of African RECs were included in our analysis. The review yielded limited systematic data on RECs in Africa. Available empirical evidence suggests that challenges hampering the effective functioning of RECs included lack of membership diversity, scarcity of resources, insufficient training of members, inadequate capacity to review and monitor studies, and lack of national ethics guidelines and accreditation. Relatively little data on the review outcomes of African RECs were described. There is an ongoing need for concerted efforts from various stakeholders to support capacity development and enhancement of African RECs. © The Author(s) 2015.

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.

PubMed

Haque, Ashraful; Engel, Jessica; Teichmann, Sarah A; Lönnberg, Tapio

2017-08-18

RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled much discovery and innovation in medicine over recent years. For practical reasons, the technique is usually conducted on samples comprising thousands to millions of cells. However, this has hindered direct assessment of the fundamental unit of biology-the cell. Since the first single-cell RNA-sequencing (scRNA-seq) study was published in 2009, many more have been conducted, mostly by specialist laboratories with unique skills in wet-lab single-cell genomics, bioinformatics, and computation. However, with the increasing commercial availability of scRNA-seq platforms, and the rapid ongoing maturation of bioinformatics approaches, a point has been reached where any biomedical researcher or clinician can use scRNA-seq to make exciting discoveries. In this review, we present a practical guide to help researchers design their first scRNA-seq studies, including introductory information on experimental hardware, protocol choice, quality control, data analysis and biological interpretation.

Intimacy motivations and pre-exposure prophylaxis (PrEP) adoption intentions among HIV-negative men who have sex with men (MSM) in romantic relationships

PubMed Central

Gamarel, Kristi E.; Golub, Sarit A.

2014-01-01

Background In the United States, men who have sex with men (MSM) in primary partnerships are at elevated risk for human immunodeficiency virus (HIV) infection. Pre-exposure prophylaxis (PrEP), a new biomedical prevention strategy, has potential to reduce HIV transmission. This study examined predictors of PrEP adoption intentions among HIV-negative MSM in primary partnerships. Methods The sample included HIV-negative MSM (n = 164) who participated in an ongoing cross-sectional study with an in-person interview examining PrEP adoption intentions. Results Higher HIV risk perception, intimacy motivations for condomless sex, recent condomless anal sex with outside partners, education, and age were each independently associated with PrEP adoption intentions. In a multivariate model, only age, education, and intimacy motivations for condomless sex were significantly associated with PrEP adoption intentions. Conclusions Intimacy motivations may play a central role in PrEP adoption for MSM couples. Incorporating relationship dynamics into biomedical strategies is a promising avenue for research and intervention. PMID:25124457

Impact of Overt and Subclinical Hypothyroidism on Exercise Tolerance: A Systematic Review

ERIC Educational Resources Information Center

Lankhaar, Jeannette A. C.; de Vries, Wouter R.; Jansen, Jaap A. C. G.; Zelissen, Pierre M. J.; Backx, Frank J. G.

2014-01-01

Purpose: This systematic review describes the state of the art of the impact of hypothyroidism on exercise tolerance and physical performance capacity in untreated and treated patients with hypothyroidism. Method: A systematic computer-aided search was conducted using biomedical databases. Relevant studies in English, German, and Dutch, published…

Headline Bioethics: Engagement with Bioethics in the News

ERIC Educational Resources Information Center

Willmott, Chris

2013-01-01

An exercise is described in which second year undergraduate bioscientists write a reflective commentary on the ethical implications of a recent biological/biomedical news story of their own choosing. As well as being of more real-world relevance than writing in a traditional essay format, the commentaries also have potential utility in helping the…

A Historical Reflection on Research Evaluation Studies, Their Recurrent Themes and Challenges. Technical Report

ERIC Educational Resources Information Center

Marjanovic, Sonja; Hanney, Stephen; Wooding, Steven

2009-01-01

This report critically examines studies of how scientific research drives innovation which is then translated into socio-economic benefits. It focuses on research evaluation insights that are relevant not only to the academic community, but also to policymakers and evaluation practitioners--and particularly to biomedical and health research…

Using a Popular Science Nonfiction Book to Introduce Biomedical Research Ethics in a Biology Majors Course †

PubMed Central

Walton, Kristen L. W.

2014-01-01

Although bioethics is an important topic in modern society, it is not a required part of the curriculum for many biology degree programs in the United States. Students in our program are exposed to biologically relevant ethical issues informally in many classes, but we do not have a requirement for a separate bioethics course. The Immortal Life of Henrietta Lacks is a recent nonfiction book that describes the life of the woman whose cervical cancer biopsy gave rise to the HeLa cell line, as well as discussing relevant medical, societal, and ethical issues surrounding human tissue use for research. Weekly reading assignments from the book with discussion questions and a final paper were used to engage students in learning about the ethics of human subjects and human tissues research. Students were surveyed for qualitative feedback on the usefulness of including this book as part of the course. This book has been a successful platform for increasing student knowledge and interest in ethics related to biomedical and biological research. PMID:25574289

Using a popular science nonfiction book to introduce biomedical research ethics in a biology majors course.

PubMed

Walton, Kristen L W

2014-12-01

Although bioethics is an important topic in modern society, it is not a required part of the curriculum for many biology degree programs in the United States. Students in our program are exposed to biologically relevant ethical issues informally in many classes, but we do not have a requirement for a separate bioethics course. The Immortal Life of Henrietta Lacks is a recent nonfiction book that describes the life of the woman whose cervical cancer biopsy gave rise to the HeLa cell line, as well as discussing relevant medical, societal, and ethical issues surrounding human tissue use for research. Weekly reading assignments from the book with discussion questions and a final paper were used to engage students in learning about the ethics of human subjects and human tissues research. Students were surveyed for qualitative feedback on the usefulness of including this book as part of the course. This book has been a successful platform for increasing student knowledge and interest in ethics related to biomedical and biological research.

The effect of public disclosure laws on biomedical research.

PubMed

Cardon, Andrew D; Bailey, Matthew R; Bennett, B Taylor

2012-05-01

The Freedom of Information Act (FOIA) and state 'open-records' laws govern access to records in the possession of federal agencies and state entities, such as public universities. Although these laws are intended to promote 'open government' and to assure the existence of an informed citizenry capable of holding government officials accountable for their decisions, an inherent tension exists between the public's access to information and biomedical research institutions' need to ensure the confidentiality of proprietary records and to protect the personal safety of employees. Recognizing these and other conflicts, the federal FOIA and state public-disclosure laws contain express exemptions to protect sensitive information from disclosure. Although some state open-records laws are modeled after the federal FOIA, important differences exist based on the language used by the state law, court interpretations, and exemptions. Two specific types of exemptions are particularly relevant to research facilities: exemptions for research information and exemptions for personal information. Responding to FOIA and state open-records requests requires knowledge of relevant laws and the involvement of all interested parties to facilitate a coordinated and orderly response.

Biomedical coatings on magnesium alloys - a review.

PubMed

Hornberger, H; Virtanen, S; Boccaccini, A R

2012-07-01

This review comprehensively covers research carried out in the field of degradable coatings on Mg and Mg alloys for biomedical applications. Several coating methods are discussed, which can be divided, based on the specific processing techniques used, into conversion and deposition coatings. The literature review revealed that in most cases coatings increase the corrosion resistance of Mg and Mg alloys. The critical factors determining coating performance, such as corrosion rate, surface chemistry, adhesion and coating morphology, are identified and discussed. The analysis of the literature showed that many studies have focused on calcium phosphate coatings produced either using conversion or deposition methods which were developed for orthopaedic applications. However, the control of phases and the formation of cracks still appear unsatisfactory. More research and development is needed in the case of biodegradable organic based coatings to generate reproducible and relevant data. In addition to biocompatibility, the mechanical properties of the coatings are also relevant, and the development of appropriate methods to study the corrosion process in detail and in the long term remains an important area of research. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Translating orthopaedic basic science into clinical relevance.

PubMed

Madry, Henning

2014-12-01

In orthopaedic and trauma surgery, the rapid evolution of biomedical research has fundamentally changed the perception of the musculoskeletal system. Here, the rigor of basic science and the art of musculoskeletal surgery have come together to create a new discipline -experimental orthopaedics- that holds great promise for the causative cure of many orthopaedic conditions. The Journal of Experimental Orthopaedics intends to bridge the gap between orthopaedic basic science and clinical relevance, to allow for a fruitful clinical translation of excellent and important investigations in the field of the entire musculoskeletal system.

[The long pilgrimage of Spanish biomedical journals toward excellence. Who helps? Quality, impact and research merit].

PubMed

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.

Catalyzing Interdisciplinary Research and Training: Initial Outcomes and Evolution of the Affinity Research Collaboratives Model.

PubMed

Ravid, Katya; Seta, Francesca; Center, David; Waters, Gloria; Coleman, David

2017-10-01

Team science has been recognized as critical to solving increasingly complex biomedical problems and advancing discoveries in the prevention, diagnosis, and treatment of human disease. In 2009, the Evans Center for Interdisciplinary Biomedical Research (ECIBR) was established in the Department of Medicine at Boston University School of Medicine as a new organizational paradigm to promote interdisciplinary team science. The ECIBR is made up of affinity research collaboratives (ARCs), consisting of investigators from different departments and disciplines who come together to study biomedical problems that are relevant to human disease and not under interdisciplinary investigation at the university. Importantly, research areas are identified by investigators according to their shared interests. ARC proposals are evaluated by a peer review process, and collaboratives are funded annually for up to three years.Initial outcomes of the first 12 ARCs show the value of this model in fostering successful biomedical collaborations that lead to publications, extramural grants, research networking, and training. The most successful ARCs have been developed into more sustainable organizational entities, including centers, research cores, translational research projects, and training programs.To further expand team science at Boston University, the Interdisciplinary Biomedical Research Office was established in 2015 to more fully engage the entire university, not just the medical campus, in interdisciplinary research using the ARC mechanism. This approach to promoting team science may be useful to other academic organizations seeking to expand interdisciplinary research at their institutions.

Recent development and biomedical applications of self-healing hydrogels.

PubMed

Wang, Yinan; Adokoh, Christian K; Narain, Ravin

2018-01-01

Hydrogels are of special importance, owing to their high-water content and various applications in biomedical and bio-engineering research. Self-healing properties is a common phenomenon in living organisms. Their endowed property of being able to self-repair after physical/chemical/mechanical damage to fully or partially its original properties demonstrates their prospective therapeutic applications. Due to complicated preparation and selection of suitable materials, the application of many host-guest supramolecular polymeric hydrogels are so limited. Thus, the design and construction of self-repairing material are highly desirable for effectively increase in the lifetime of a functional material. However, recent advances in the field of materials science and bioengineering and nanotechnology have led to the design of biologically relevant self-healing hydrogels for therapeutic applications. This review focuses on the recent development of self-healing hydrogels for biomedical application. Areas covered: The strategies of making self-healing hydrogels and their healing mechanisms are discussed. The significance of self-healing hydrogel for biomedical application is also highlighted in areas such as 3D/4D printing, cell/drug delivery, as well as soft actuators. Expert opinion: Materials that have the ability to self-repair damage and regain the desired mechanical properties, have been found to be excellent candidate materials for a range of biomedical uses especially if their unique characteristics are similar to that of soft-tissues. Self-healing hydrogels have been synthesized and shown to exhibit similar characteristics as human tissues, however, significant improvement is required in the fabrication process from inexpensive and nontoxic/non-hazardous materials and techniques, and, in addition, further fine-tuning of the self-healing properties are needed for specific biomedical uses.

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

PubMed

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

Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach.

PubMed

Rinaldi, Fabio; Schneider, Gerold; Kaljurand, Kaarel; Hess, Michael; Andronis, Christos; Konstandi, Ourania; Persidis, Andreas

2007-02-01

The amount of new discoveries (as published in the scientific literature) in the biomedical area is growing at an exponential rate. This growth makes it very difficult to filter the most relevant results, and thus the extraction of the core information becomes very expensive. Therefore, there is a growing interest in text processing approaches that can deliver selected information from scientific publications, which can limit the amount of human intervention normally needed to gather those results. This paper presents and evaluates an approach aimed at automating the process of extracting functional relations (e.g. interactions between genes and proteins) from scientific literature in the biomedical domain. The approach, using a novel dependency-based parser, is based on a complete syntactic analysis of the corpus. We have implemented a state-of-the-art text mining system for biomedical literature, based on a deep-linguistic, full-parsing approach. The results are validated on two different corpora: the manually annotated genomics information access (GENIA) corpus and the automatically annotated arabidopsis thaliana circadian rhythms (ATCR) corpus. We show how a deep-linguistic approach (contrary to common belief) can be used in a real world text mining application, offering high-precision relation extraction, while at the same time retaining a sufficient recall.

Knowledge of the Nigerian Code of Health Research Ethics Among Biomedical Researchers in Southern Nigeria.

PubMed

Ogunrin, Olubunmi A; Daniel, Folasade; Ansa, Victor

2016-12-01

Responsibility for protection of research participants from harm and exploitation rests on Research Ethics Committees and principal investigators. The Nigerian National Code of Health Research Ethics defines responsibilities of stakeholders in research so its knowledge among researchers will likely aid ethical conduct of research. The levels of awareness and knowledge of the Code among biomedical researchers in southern Nigerian research institutions was assessed. Four institutions were selected using a stratified random sampling technique. Research participants were selected by purposive sampling and completed a pre-tested structured questionnaire. A total of 102 biomedical researchers completed the questionnaires. Thirty percent of the participants were aware of the National Code though 64% had attended at least one training seminar in research ethics. Twenty-five percent had a fairly acceptable knowledge (scores 50%-74%) and 10% had excellent knowledge of the code (score ≥75%). Ninety-five percent expressed intentions to learn more about the National Code and agreed that it is highly relevant to the ethical conduct of research. Awareness and knowledge of the Code were found to be very limited among biomedical researchers in southern Nigeria. There is need to improve awareness and knowledge through ethics seminars and training. Use of existing Nigeria-specific online training resources is also encouraged.

Zinc Oxide Nanomaterials for Biomedical Fluorescence Detection

PubMed Central

Hahm, Jong-in

2014-01-01

One-dimensional zinc oxide nanomaterials have been recently developed into novel, extremely effective, optical signal-enhancing bioplatforms. Their usefulness has been demonstrated in various biomedical fluorescence assays. Fluorescence is extensively used in biology and medicine as a sensitive and noninvasive detection method for tracking and analyzing biological molecules. Achieving high sensitivity via improving signal-to-noise ratio is of paramount importance in fluorescence-based, trace-level detection. Recent advances in the development of optically superior one-dimensional materials have contributed to this important biomedical area of detection. This review article will discuss major research developments that have so far been made in this emerging and exciting topical field. The discussion will cover a broad range of subjects including synthesis of zinc oxide nanorods (ZnO NRs), various properties differentiating them as suitable optical biodetection platforms, their demonstrated applicability in DNA and protein detection, and the nanomaterial characteristics relevant for biomolecular fluorescence enhancement. This review will then summarize the current status of ZnO NR-based biodetection and further elaborate future utility of ZnO NR platforms for advanced biomedical assays, based on their proven advantages. Lastly, present challenges experienced in this topical area will be identified and focal subject areas for future research will be suggested as well. PMID:24730276

Strengthening research capacity through the medical education partnership initiative: the Mozambique experience

PubMed Central

2013-01-01

Background Since Mozambique’s independence, the major emphasis of its higher educational institutions has been on didactic education. Because of fiscal and human resource constraints, basic and applied research activities have been relatively modest in scope, and priorities have often been set primarily by external collaborators. These factors have compromised the scope and the relevance of locally conducted research and have limited the impact of Mozambique’s universities as major catalysts for national development. Case description We developed a multi-institutional partnership to undertake a comprehensive analysis of the research environment at Mozambique’s major public universities to identify factors that have served as barriers to the development of a robust research enterprise. Based on this analysis, we developed a multifaceted plan to reduce the impact of these barriers and to enhance research capacity within Mozambique. Interventions On the basis of our needs assessment, we have implemented a number of major initiatives within participating institutions to facilitate basic and applied research activities. These have included specialized training programmes, a reorganization of the research administration infrastructure, the development of multiple collaborative research projects that have emphasized local research priorities and a substantial investment in bioinformatics. We have established a research support centre that provides grant development and management services to Mozambique’s public universities and have developed an independent Institutional Review Board for the review of research involving human research subjects. Multiple research projects involving both communicable and non-communicable diseases have been developed and substantial external research support has been obtained to undertake these projects. A sizable investment in biomedical informatics has enhanced both connectivity and access to digital reference material. Active engagement with relevant entities within the Government of Mozambique has aligned institutional development with national priorities. Conclusions Although multiple challenges remain, over the past 3 years significant progress has been made towards establishing conditions within which a broad range of basic, translational and clinical and public health research can be undertaken. Ongoing development of this research enterprise will enhance capacity to address critical locally relevant research questions and will leverage resources to accelerate the development of Mozambique’s national universities. PMID:24304706

Transitions from biomedical to recovery-oriented practices in mental health: a scoping review to explore the role of Internet-based interventions.

PubMed

Strand, Monica; Gammon, Deede; Ruland, Cornelia M

2017-04-07

The Internet is transforming mental health care services by increasing access to, and potentially improving the quality of, care. Internet-based interventions in mental health can potentially play a role in transitions from biomedical to recovery-oriented research and practices, but an overview of what this may entail, current work, and issues that need addressing, is lacking. The objective of this study is to describe Internet-based recovery-oriented interventions (referred to as e-recovery) and current research, and to identify gaps and issues relevant to advancing recovery research and practices through opportunities provided by the Internet. Five iterative stages of a scoping review framework were followed in searching and analyzing the literature. A recovery framework with four domains and 16 themes was used to deductively code intervention characteristics according to their support for recovery-oriented practices. Only Internet-based interventions used in conjunction with ongoing care were included. Twenty studies describing six e-recovery interventions were identified and originated in Australia, Finland, the Netherlands, Norway and USA. The domain supporting personal recovery was most clearly reflected in interventions, whereas the last three domains, i.e., promoting citizenship, organizational commitment and working relationship were less evident. Support for the formulation and follow-up of personal goals and preferences, and in accessing peer-support, were the characteristics shared by most interventions. Three of the six studies that employed a comparison group used randomization, and none presented definitive findings. None used recovery-oriented frameworks or specific recovery outcome measures. Four of the interventions were specific to a diagnosis. Research about how technologies might aid in illuminating and shaping recovery processes is in its formative stages. We recommend that future e-recovery research and innovation attend to four dimensions: evidence-supported interventions, new knowledge about personal recovery, values-based approaches and Internet as a facilitator for organizational transformation. The incremental changes facilitated by e-recovery may help propel a shift in mental health care toward recovery-oriented practices.

Strengthening Biostatistics Resources in Sub-Saharan Africa: Research Collaborations through U.S. partnerships

PubMed Central

Gezmu, Misrak; DeGruttola, Victor; Dixon, Dennis; Essex, Max; Halloran, Elizabeth; Hogan, Joseph; Grobler, Anneke; Kim, Soyeon; McDermott, Jeanne; McKaig, Rosemary; Neaton, James D

2015-01-01

SUMMARY On September 30, 2009, the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) conducted a workshop on strengthening biostatistics resources in sub-Saharan Africa (SSA). An increase in global spending on health research over the last decade has boosted funds available to conduct biomedical research in low to mid income countries. The HIV/AIDS pandemic, the reemergence of malaria and tuberculosis, and other emerging infectious agents are major driving forces behind the increase in biomedical research and clinical care programs (clinical trials, observational studies and other public health programs) in SSA [1]. In addition, the increased engagement of the United States (US) government through the Global Health Initiative, which expands the traditional focus beyond infectious diseases to other causes of poor health and to the recognition of need to strengthen health systems for a sustainable response, only increases the need for in-depth in-country expertise in all aspects of biomedical research [2]. In this workshop, researchers both from the US and SSA were invited to discuss their collaborative work, to discuss ways in which biostatistical activities are carried out within their research projects, and to identify both general and specific needs for capacity building in biostatistics. Capacity building discussions highlighted the critical need to increase the number of well-trained in-country biostatisticians, both to participate in ongoing studies and to contribute to an infrastructure that can produce the next generation of biostatistical researchers. PMID:21394746

A scoping review of competencies for scientific editors of biomedical journals.

PubMed

Galipeau, James; Barbour, Virginia; Baskin, Patricia; Bell-Syer, Sally; Cobey, Kelly; Cumpston, Miranda; Deeks, Jon; Garner, Paul; MacLehose, Harriet; Shamseer, Larissa; Straus, Sharon; Tugwell, Peter; Wager, Elizabeth; Winker, Margaret; Moher, David

2016-02-02

Biomedical journals are the main route for disseminating the results of health-related research. Despite this, their editors operate largely without formal training or certification. To our knowledge, no body of literature systematically identifying core competencies for scientific editors of biomedical journals exists. Therefore, we aimed to conduct a scoping review to determine what is known on the competency requirements for scientific editors of biomedical journals. We searched the MEDLINE®, Cochrane Library, Embase®, CINAHL, PsycINFO, and ERIC databases (from inception to November 2014) and conducted a grey literature search for research and non-research articles with competency-related statements (i.e. competencies, knowledge, skills, behaviors, and tasks) pertaining to the role of scientific editors of peer-reviewed health-related journals. We also conducted an environmental scan, searched the results of a previous environmental scan, and searched the websites of existing networks, major biomedical journal publishers, and organizations that offer resources for editors. A total of 225 full-text publications were included, 25 of which were research articles. We extracted a total of 1,566 statements possibly related to core competencies for scientific editors of biomedical journals from these publications. We then collated overlapping or duplicate statements which produced a list of 203 unique statements. Finally, we grouped these statements into seven emergent themes: (1) dealing with authors, (2) dealing with peer reviewers, (3) journal publishing, (4) journal promotion, (5) editing, (6) ethics and integrity, and (7) qualities and characteristics of editors. To our knowledge, this scoping review is the first attempt to systematically identify possible competencies of editors. Limitations are that (1) we may not have captured all aspects of a biomedical editor's work in our searches, (2) removing redundant and overlapping items may have led to the elimination of some nuances between items, (3) restricting to certain databases, and only French and English publications, may have excluded relevant publications, and (4) some statements may not necessarily be competencies. This scoping review is the first step of a program to develop a minimum set of core competencies for scientific editors of biomedical journals which will be followed by a training needs assessment, a Delphi exercise, and a consensus meeting.

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

PubMed

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

2016-07-01

Text mining and semantic analysis approaches can be applied to the construction of biomedical domain-specific search engines and provide an attractive alternative to create personalized and enhanced search experiences. Therefore, this work introduces the new open-source BIOMedical Search Engine Framework for the fast and lightweight development of domain-specific search engines. The rationale behind this framework is to incorporate core features typically available in search engine frameworks with flexible and extensible technologies to retrieve biomedical documents, annotate meaningful domain concepts, and develop highly customized Web search interfaces. The BIOMedical Search Engine Framework integrates taggers for major biomedical concepts, such as diseases, drugs, genes, proteins, compounds and organisms, and enables the use of domain-specific controlled vocabulary. Technologies from the Typesafe Reactive Platform, the AngularJS JavaScript framework and the Bootstrap HTML/CSS framework support the customization of the domain-oriented search application. Moreover, the RESTful API of the BIOMedical Search Engine Framework allows the integration of the search engine into existing systems or a complete web interface personalization. The construction of the Smart Drug Search is described as proof-of-concept of the BIOMedical Search Engine Framework. This public search engine catalogs scientific literature about antimicrobial resistance, microbial virulence and topics alike. The keyword-based queries of the users are transformed into concepts and search results are presented and ranked accordingly. The semantic graph view portraits all the concepts found in the results, and the researcher may look into the relevance of different concepts, the strength of direct relations, and non-trivial, indirect relations. The number of occurrences of the concept shows its importance to the query, and the frequency of concept co-occurrence is indicative of biological relations 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.

Centralized mouse repositories.

PubMed

Donahue, Leah Rae; Hrabe de Angelis, Martin; Hagn, Michael; Franklin, Craig; Lloyd, K C Kent; Magnuson, Terry; McKerlie, Colin; Nakagata, Naomi; Obata, Yuichi; Read, Stuart; Wurst, Wolfgang; Hörlein, Andreas; Davisson, Muriel T

2012-10-01

Because the mouse is used so widely for biomedical research and the number of mouse models being generated is increasing rapidly, centralized repositories are essential if the valuable mouse strains and models that have been developed are to be securely preserved and fully exploited. Ensuring the ongoing availability of these mouse strains preserves the investment made in creating and characterizing them and creates a global resource of enormous value. The establishment of centralized mouse repositories around the world for distributing and archiving these resources has provided critical access to and preservation of these strains. This article describes the common and specialized activities provided by major mouse repositories around the world.

Centralized Mouse Repositories

PubMed Central

Donahue, Leah Rae; de Angelis, Martin Hrabe; Hagn, Michael; Franklin, Craig; Lloyd, K. C. Kent; Magnuson, Terry; McKerlie, Colin; Nakagata, Naomi; Obata, Yuichi; Read, Stuart; Wurst, Wolfgang; Hörlein, Andreas; Davisson, Muriel T.

2013-01-01

Because the mouse is used so widely for biomedical research and the number of mouse models being generated is increasing rapidly, centralized repositories are essential if the valuable mouse strains and models that have been developed are to be securely preserved and fully exploited. Ensuring the ongoing availability of these mouse strains preserves the investment made in creating and characterizing them and creates a global resource of enormous value. The establishment of centralized mouse repositories around the world for distributing and archiving these resources has provided critical access to and preservation of these strains. This article describes the common and specialized activities provided by major mouse repositories around the world. PMID:22945696

Silk-polypyrrole biocompatible actuator performance under biologically relevant conditions

NASA Astrophysics Data System (ADS)

Hagler, Jo'elen; Peterson, Ben; Murphy, Amanda; Leger, Janelle

Biocompatible actuators that are capable of controlled movement and can function under biologically relevant conditions are of significant interest in biomedical fields. Previously, we have demonstrated that a composite material of silk biopolymer and the conducting polymer polypyrrole (PPy) can be formed into a bilayer device that can bend under applied voltage. Further, these silk-PPy composites can generate forces comparable to human muscle (>0.1 MPa) making them ideal candidates for interfacing with biological tissues. Here silk-PPy composite films are tested for performance under biologically relevant conditions including exposure to a complex protein serum and biologically relevant temperatures. Free-end bending actuation performance, current response, force generation and, mass degradation were investigated . Preliminary results show that when exposed to proteins and biologically relevant temperatures, these silk-PPy composites show minimal degradation and are able to generate forces and conduct currents comparable to devices tested under standard conditions. NSF.

Learning Terminology in Order to Become an Active Agent in the Development of Basque Biomedical Registers

ERIC Educational Resources Information Center

Zabala Unzalu, Igone; San Martin Egia, Itziar; Lersundi Ayestaran, Mikel

2016-01-01

The aim of this article is to describe some theoretical and methodological bases underpinning the design of the course Health Communication in Basque (HCB) at the University of the Basque Country (UPV/EHU). Based on some relevant theoretical tenets of the socioterminologic and communicative approaches to Terminology, the authors assume that…

77 FR 23810 - Joint Biomedical Laboratory Research and Development and Clinical Science Research and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-20

....... Sheraton Suites--Old Town Alexandria. Neurobiology-C June 14-15, 2012.... L'Enfant Plaza Hotel. Oncology-A... addresses of the hotel and VA Central Office are: L'Enfant Plaza Hotel, 480 L'Enfant Plaza SW., Washington... Board is to provide advice on the scientific quality, budget, safety and mission relevance of...

77 FR 20489 - Joint Biomedical Laboratory Research and Development and Clinical Science Research and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-04

..., 2012. L'Enfant Plaza Hotel. Oncology-A June 14-15, 2012. Sheraton Suites--Old Town Alexandria... Suites--Old Town Alexandria. The addresses of the hotel and VA Central Office are: L'Enfant Plaza Hotel... purpose of the Board is to provide advice on the scientific quality, budget, safety and mission relevance...

An Approach toward the Development of Core Syllabuses for the Anatomical Sciences

ERIC Educational Resources Information Center

Moxham, Bernard John; Plaisant, Odile; Smith, Claire F.; Pawlina, Wojciech; McHanwell, Stephen

2014-01-01

There is increasingly a call for clinical relevance in the teaching of the biomedical sciences within all health care programs. This presupposes that there is an understanding of what is "core" material within the curriculum. To date, the anatomical sciences have been poorly served by the development of core syllabuses, although there…

Can Basic Research on Children and Families Be Useful for the Policy Process?

ERIC Educational Resources Information Center

Moore, Kristin A.

Based on the assumption that basic science is the crucial building block for technological and biomedical progress, this paper examines the relevance for public policy of basic demographic and behavioral sciences research on children and families. The characteristics of basic research as they apply to policy making are explored. First, basic…

From Systems Understanding to Personalized Medicine: Lessons and Recommendations Based on a Multidisciplinary and Translational Analysis of COPD.

PubMed

Roca, Josep; Cano, Isaac; Gomez-Cabrero, David; Tegnér, Jesper

2016-01-01

Systems medicine, using and adapting methods and approaches as developed within systems biology, promises to be essential in ongoing efforts of realizing and implementing personalized medicine in clinical practice and research. Here we review and critically assess these opportunities and challenges using our work on COPD as a case study. We find that there are significant unresolved biomedical challenges in how to unravel complex multifactorial components in disease initiation and progression producing different clinical phenotypes. Yet, while such a systems understanding of COPD is necessary, there are other auxiliary challenges that need to be addressed in concert with a systems analysis of COPD. These include information and communication technology (ICT)-related issues such as data harmonization, systematic handling of knowledge, computational modeling, and importantly their translation and support of clinical practice. For example, clinical decision-support systems need a seamless integration with new models and knowledge as systems analysis of COPD continues to develop. Our experience with clinical implementation of systems medicine targeting COPD highlights the need for a change of management including design of appropriate business models and adoption of ICT providing and supporting organizational interoperability among professional teams across healthcare tiers, working around the patient. In conclusion, in our hands the scope and efforts of systems medicine need to concurrently consider these aspects of clinical implementation, which inherently drives the selection of the most relevant and urgent issues and methods that need further development in a systems analysis of disease.

Population health and status of epidemiology: WHO European Region I.

PubMed

Rahu, Mati; Vlassov, Vasiliy V; Pega, Frank; Andreeva, Tatiana; Ay, Pinar; Baburin, Aleksei; Bencko, Vladimír; Csépe, Péter; Gebska-Kuczerowska, Anita; Ondrusová, Martina; Ribak, Joseph

2013-06-01

This article of the International Epidemiological Association commissioned paper series stocktakes the population health and status of epidemiology in 21 of the 53 countries of the WHO European Region. By United Nations geographical classification, these countries belong to Eastern Europe, Western Asia and South-Central Asia. Published data were used to describe population health indicators and risk factors. Epidemiological training and research was assessed based on author knowledge, information searches and E-mail survey of experts. Bibliometric analyses determined epidemiological publication outputs. Between-country differences in life expectancy, amount and profile of disease burden and prevalence of risk factors are marked. Epidemiological training is affected by ongoing structural reforms of educational systems. Training is advanced in Israel and several Eastern European countries. Epidemiological research is mainly university-based in most countries, but predominantly conducted by governmental research institutes in several countries of the former Soviet Union. Funding is generally external and limited, partially due to competition from and prioritization of biomedical research. Multiple relevant professional societies exist, especially in Poland, the Czech Republic and Hungary. Few of the region's 39 epidemiological academic journals have international currency. The number of epidemiological publications per population is highest for Israel and lowest for South-Central Asian countries. Epidemiological capacity will continue to be heterogeneous across the region and depend more on countries' individual historical, social, political and economic conditions and contexts than their epidemiologists' successive efforts. National and international research funding, and within- and between-country collaborations should be enhanced, especially for South-Central Asian countries.

Passage relevance models for genomics search.

PubMed

Urbain, Jay; Frieder, Ophir; Goharian, Nazli

2009-03-19

We present a passage relevance model for integrating syntactic and semantic evidence of biomedical concepts and topics using a probabilistic graphical model. Component models of topics, concepts, terms, and document are represented as potential functions within a Markov Random Field. The probability of a passage being relevant to a biologist's information need is represented as the joint distribution across all potential functions. Relevance model feedback of top ranked passages is used to improve distributional estimates of query concepts and topics in context, and a dimensional indexing strategy is used for efficient aggregation of concept and term statistics. By integrating multiple sources of evidence including dependencies between topics, concepts, and terms, we seek to improve genomics literature passage retrieval precision. Using this model, we are able to demonstrate statistically significant improvements in retrieval precision using a large genomics literature corpus.

Research in intelligent biomedical clothing vs. realities in the European textile business.

PubMed

Walter, Lutz

2004-01-01

In order to make intelligent biomedical clothing a market reality, a critical mass of scientific, technical and industrial capacities from various disciplines and industries must be successfully brought together. The textiles and clothing sector, i.e. the industry that transform natural or man-made fibres into yarns then with a myriad of processing options into complex tissues and finally into clothing, is undoubtedly a crucial element in such development. With Europe disposing of the world's most diverse, productive and innovative textiles and clothing industry, in addition to relevant expertise and resources in other scientific disciplines and industrial sectors, it could play a leading role in the advancement of the concept of intelligent biomedical clothing. In this process, a great number of challenges--firstly scientific and technical in nature--still need to be overcome and support from public funding programmes could constitute the necessary trigger for research and industrial efforts to be seriously undertaken. In view of the great benefits of such new products for the individual consumer, national health care systems and the society as a whole, a concerted effort in private-public partnership seems merited.

Exploring environment-dependent effects of Pd nanostructures on reactive oxygen species (ROS) using electron spin resonance (ESR) technique: implications for biomedical applications.

PubMed

Wen, Tao; He, Weiwei; Chong, Yu; Liu, Yi; Yin, Jun-Jie; Wu, Xiaochun

2015-10-14

Recently, because of the great advances in tailoring their shape and structure, palladium nanoparticles (Pd NPs) have been receiving increasing attention in biomedical fields apart from their traditional application as industrial catalysts. When considering the potential uses of Pd NPs in biomedicine, their catalytic properties need to be evaluated under physiologically relevant conditions. In this article, we demonstrate that Pd nanostructures (NSs, both commercial Pd NPs and in-house-prepared Au@Pd nanorods) can induce O2 or ˙OH production depending on pH values in the presence of H2O2. We observed that O2 is produced under neutral and alkaline conditions but ˙OH under acidic conditions. We also found that Pd NSs can scavenge superoxide and singlet oxygen, which may provide protection in biological systems. On the other hand, their oxidase-like activity may accelerate the oxidation of ascorbic acid and thus may produce negative biological effects. The presented study will provide useful guidance for designing noble metal nanostructures with desired catalytic and biological properties in biomedical applications.

[Presence of the biomedical periodicals of Hungarian editions in international databases].

PubMed

Vasas, Lívia; Hercsel, Imréné

2006-01-15

Presence of the biomedical periodicals of Hungarian editions in international databases. The majority of Hungarian scientific results in medical and related sciences are published in scientific periodicals of foreign edition with high impact factor (IF) values, and they appear in international scientific literature in foreign languages. In this study the authors dealt with the presence and registered citation in international databases of those periodicals only, which had been published in Hungary and/or in cooperation with foreign publishing companies. The examination went back to year 1980 and covered a 25-year long period. 110 periodicals were selected for more detailed examination. The authors analyzed the situation of the current periodicals in the three most often visited databases (MEDLINE, EMBASE, Web of Science), and discovered, that the biomedical scientific periodicals of Hungarian interests were not represented with reasonable emphasis in the relevant international bibliographic databases. Because of the great number of data the scientific literature of medicine and related sciences could not be represented in its entirety, this publication, however, might give useful information for the inquirers, and call the attention of the competent people.

Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

PubMed

Gilad, Assaf A; Shapiro, Mikhail G

2017-06-01

Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

Sensor Fusion and Smart Sensor in Sports and Biomedical Applications

PubMed Central

Mendes, José Jair Alves; Vieira, Mário Elias Marinho; Pires, Marcelo Bissi; Stevan, Sergio Luiz

2016-01-01

The following work presents an overview of smart sensors and sensor fusion targeted at biomedical applications and sports areas. In this work, the integration of these areas is demonstrated, promoting a reflection about techniques and applications to collect, quantify and qualify some physical variables associated with the human body. These techniques are presented in various biomedical and sports applications, which cover areas related to diagnostics, rehabilitation, physical monitoring, and the development of performance in athletes, among others. Although some applications are described in only one of two fields of study (biomedicine and sports), it is very likely that the same application fits in both, with small peculiarities or adaptations. To illustrate the contemporaneity of applications, an analysis of specialized papers published in the last six years has been made. In this context, the main characteristic of this review is to present the largest quantity of relevant examples of sensor fusion and smart sensors focusing on their utilization and proposals, without deeply addressing one specific system or technique, to the detriment of the others. PMID:27669260

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

PubMed Central

Dugan, Vivien G.; Emrich, Scott J.; Giraldo-Calderón, Gloria I.; Harb, Omar S.; Newman, Ruchi M.; Pickett, Brett E.; Schriml, Lynn M.; Stockwell, Timothy B.; Stoeckert, Christian J.; Sullivan, Dan E.; Singh, Indresh; Ward, Doyle V.; Yao, Alison; Zheng, Jie; Barrett, Tanya; Birren, Bruce; Brinkac, Lauren; Bruno, Vincent M.; Caler, Elizabet; Chapman, Sinéad; Collins, Frank H.; Cuomo, Christina A.; Di Francesco, Valentina; Durkin, Scott; Eppinger, Mark; Feldgarden, Michael; Fraser, Claire; Fricke, W. Florian; Giovanni, Maria; Henn, Matthew R.; Hine, Erin; Hotopp, Julie Dunning; Karsch-Mizrachi, Ilene; Kissinger, Jessica C.; Lee, Eun Mi; Mathur, Punam; Mongodin, Emmanuel F.; Murphy, Cheryl I.; Myers, Garry; Neafsey, Daniel E.; Nelson, Karen E.; Nierman, William C.; Puzak, Julia; Rasko, David; Roos, David S.; Sadzewicz, Lisa; Silva, Joana C.; Sobral, Bruno; Squires, R. Burke; Stevens, Rick L.; Tallon, Luke; Tettelin, Herve; Wentworth, David; White, Owen; Will, Rebecca; Wortman, Jennifer; Zhang, Yun; Scheuermann, Richard H.

2014-01-01

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium’s minimal information (MIxS) and NCBI’s BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant. PMID:24936976

Standardized metadata for human pathogen/vector genomic sequences.

PubMed

Dugan, Vivien G; Emrich, Scott J; Giraldo-Calderón, Gloria I; Harb, Omar S; Newman, Ruchi M; Pickett, Brett E; Schriml, Lynn M; Stockwell, Timothy B; Stoeckert, Christian J; Sullivan, Dan E; Singh, Indresh; Ward, Doyle V; Yao, Alison; Zheng, Jie; Barrett, Tanya; Birren, Bruce; Brinkac, Lauren; Bruno, Vincent M; Caler, Elizabet; Chapman, Sinéad; Collins, Frank H; Cuomo, Christina A; Di Francesco, Valentina; Durkin, Scott; Eppinger, Mark; Feldgarden, Michael; Fraser, Claire; Fricke, W Florian; Giovanni, Maria; Henn, Matthew R; Hine, Erin; Hotopp, Julie Dunning; Karsch-Mizrachi, Ilene; Kissinger, Jessica C; Lee, Eun Mi; Mathur, Punam; Mongodin, Emmanuel F; Murphy, Cheryl I; Myers, Garry; Neafsey, Daniel E; Nelson, Karen E; Nierman, William C; Puzak, Julia; Rasko, David; Roos, David S; Sadzewicz, Lisa; Silva, Joana C; Sobral, Bruno; Squires, R Burke; Stevens, Rick L; Tallon, Luke; Tettelin, Herve; Wentworth, David; White, Owen; Will, Rebecca; Wortman, Jennifer; Zhang, Yun; Scheuermann, Richard H

2014-01-01

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.

ChemBank: a small-molecule screening and cheminformatics resource database.

PubMed

Seiler, Kathleen Petri; George, Gregory A; Happ, Mary Pat; Bodycombe, Nicole E; Carrinski, Hyman A; Norton, Stephanie; Brudz, Steve; Sullivan, John P; Muhlich, Jeremy; Serrano, Martin; Ferraiolo, Paul; Tolliday, Nicola J; Schreiber, Stuart L; Clemons, Paul A

2008-01-01

ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

European and US publications in the 50 highest ranking pathology journals from 2000 to 2006.

PubMed

Fritzsche, F R; Oelrich, B; Dietel, M; Jung, K; Kristiansen, G

2008-04-01

To analyse the contributions of the 15 primary member states of the European Union and selected non-European countries to pathological research between 2000 and 2006. Pathological journals were screened using ISI Web of Knowledge database. The number of publications and related impact factors were determined for each country. Relevant socioeconomic indicators were related to the scientific output. Subsequently, results were compared to publications in 10 of the leading biomedical journals. The research output remained generally stable. In Europe, the UK, Germany, France, Italy and Spain ranked top concerning contributions to publications and impact factors in the pathological and leading general biomedical journals. With regard to socioeconomic data, smaller, mainly northern European countries showed a relatively higher efficiency. Of the lager countries, the UK is the most efficient in that respect. The rising economic powers of China and India were consistently in the rear. Results mirror the leading role of the USA in pathology research but also show the relevance of European scientists. The scientometric approach in this study provides a new fundamental and comparative overview of pathology research in the European Union and the USA which could help to benchmark scientific output among countries.

Caldora penicillata gen. nov., comb. nov. (Cyanobacteria), a pantropical marine species with biomedical relevance

PubMed Central

Engene, Niclas; Tronholm, Ana; Salvador-Reyes, Lilibeth A.; Luesch, Hendrik; Paul, Valerie J.

2015-01-01

Many tropical marine cyanobacteria are prolific producers of bioactive secondary metabolites with ecological relevance and promising pharmaceutical applications. One species of chemically rich, tropical marine cyanobacteria that was previously identified as Symploca hydnoides or Symploca sp. corresponds to the traditional taxonomic definition of Phormidium penicillatum. In this study, we clarified the taxonomy of this biomedically and ecologically important cyanobacterium by comparing recently collected specimens with the original type material and the taxonomic description of P. penicillatum. Molecular phylogenetic analyses of the 16S rRNA gene and the 16S-23S ITS regions showed that P. penicillatum formed an independent clade sister to the genus Symploca, and distantly related to Phormidium and Lyngbya. We propose the new genus Caldora for this clade, with Caldora penicillata comb. nov. as the type species and designate as the epitype the recently collected strain FK13-1. Furthermore, the production of bioactive secondary metabolites among various geographically dispersed collections of C. penicillata showed that this species consistently produced the metabolite dolastatin 10 and/or the related compound symplostatin 1, which appear to be robust autapomorphic characters and chemotaxonomic markers for this taxon. PMID:26327714

Biomedical signal and image processing.

PubMed

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.

An active visual search interface for Medline.

PubMed

Xuan, Weijian; Dai, Manhong; Mirel, Barbara; Wilson, Justin; Athey, Brian; Watson, Stanley J; Meng, Fan

2007-01-01

Searching the Medline database is almost a daily necessity for many biomedical researchers. However, available Medline search solutions are mainly designed for the quick retrieval of a small set of most relevant documents. Because of this search model, they are not suitable for the large-scale exploration of literature and the underlying biomedical conceptual relationships, which are common tasks in the age of high throughput experimental data analysis and cross-discipline research. We try to develop a new Medline exploration approach by incorporating interactive visualization together with powerful grouping, summary, sorting and active external content retrieval functions. Our solution, PubViz, is based on the FLEX platform designed for interactive web applications and its prototype is publicly available at: http://brainarray.mbni.med.umich.edu/Brainarray/DataMining/PubViz.

The Challenging Road towards a Unified Animal Research Network in Europe

PubMed Central

Martinez-Sanchez, Emma; Leech, Kirk

2015-01-01

Animal models are key in biomedical research as a proof of concept to study complex processes in a physiological context. Despite the small yet crucial role animals play in fundamental and applied research, the value of animal research is recurrently undermined. Lack of openness and transparency encourages misconceptions, which can have a dramatic negative impact on science and medicine. Research centres should use all available resources to ensure that relevant details about their use of animals in research are readily accessible. More concerted efforts by professional advocacy groups devoted to informing about the benefits of biomedical animal research are also crucial. The European Animal Research Association acts as an umbrella organisation providing support to national advocacy groups and coordinating actions in countries in which no advocacy group exists. PMID:26018997

Imaging Mass Spectrometry in Neuroscience

PubMed Central

2013-01-01

Imaging mass spectrometry is an emerging technique of great potential for investigating the chemical architecture in biological matrices. Although the potential for studying neurobiological systems is evident, the relevance of the technique for application in neuroscience is still in its infancy. In the present Review, a principal overview of the different approaches, including matrix assisted laser desorption ionization and secondary ion mass spectrometry, is provided with particular focus on their strengths and limitations for studying different neurochemical species in situ and in vitro. The potential of the various approaches is discussed based on both fundamental and biomedical neuroscience research. This Review aims to serve as a general guide to familiarize the neuroscience community and other biomedical researchers with the technique, highlighting its great potential and suitability for comprehensive and specific chemical imaging. PMID:23530951

Scientific Approach for Optimising Performance, Health and Safety in High-Altitude Observatories

NASA Astrophysics Data System (ADS)

Böcker, Michael; Vogy, Joachim; Nolle-Gösser, Tanja

2008-09-01

The ESO coordinated study “Optimising Performance, Health and Safety in High-Altitude Observatories” is based on a psychological approach using a questionnaire for data collection and assessment of high-altitude effects. During 2007 and 2008, data from 28 staff and visitors involved in APEX and ALMA were collected and analysed and the first results of the study are summarised. While there is a lot of information about biomedical changes at high altitude, relatively few studies have focussed on psychological changes, for example with respect to performance of mental tasks, safety consciousness and emotions. Both, biomedical and psychological changes are relevant factors in occupational safety and health. The results of the questionnaire on safety, health and performance issues demonstrate that the working conditions at high altitude are less detrimental than expected.

Male and female genital cutting among Southern Thailand's Muslims: rituals, biomedical practice and local discourses.

PubMed

Merli, Claudia

2010-10-01

This paper explores how local people in a province in southern Thailand perceive the practice of male and female genital cutting. In order to understand the importance placed on these practices, a comparison is drawn between the two and also between the male circumcision and the Buddhist ordination of monks as rites of passage. Discourses on the exposure or concealment of male and female bodies, respectively, witness to the relevance of both the local political-historical context and biomedical hegemony to gendered bodies. The comparisons evince the need to reflect upon the theoretical and ethical implications of studying genital cutting and focusing exclusively on one of the two practices rather than, as this paper claims to be necessary, considering them as inextricably connected.

Elemental and isotopic imaging of biological samples using NanoSIMS.

PubMed

Kilburn, Matt R; Clode, Peta L

2014-01-01

With its low detection limits and the ability to analyze most of the elements in the periodic table, secondary ion mass spectrometry (SIMS) represents one of the most versatile in situ analytical techniques available, and recent developments have resulted in significant advantages for the use of imaging mass spectrometry in biological and biomedical research. Increases in spatial resolution and sensitivity allow detailed interrogation of samples at relevant scales and chemical concentrations. Advances in dynamic SIMS, specifically with the advent of NanoSIMS, now allow the tracking of stable isotopes within biological systems at subcellular length scales, while static SIMS combines subcellular imaging with molecular identification. In this chapter, we present an introduction to the SIMS technique, with particular reference to NanoSIMS, and discuss its application in biological and biomedical research.

Shaping the Future of Nanomedicine: Anisotropy in Polymeric Nanoparticle Design

PubMed Central

Meyer, Randall A.; Green, Jordan J.

2015-01-01

Nanofabrication and biomedical applications of polymeric nanoparticles have become important areas of research. Biocompatible polymeric nanoparticles have been investigated for their use as delivery vehicles for therapeutic and diagnostic agents. Although polymeric nanoconstructs have traditionally been fabricated as isotropic spheres, anisotropic, non-spherical nanoparticles have gained interest in the biomaterials community due to their unique interactions with biological systems. Polymeric nanoparticles with different forms of anisotropy have been manufactured utilizing a variety of novel methods in recent years. In addition, they have enhanced physical, chemical, and biological properties compared to spherical nanoparticles, including increased targeting avidity and decreased non-specific in vivo clearance. With these desirable properties, anisotropic nanoparticles have been successfully utilized in many biomedical settings and have performed superiorly to analogous spherical nanoparticles. We summarize the current state-of-the-art fabrication methods for anisotropic polymeric nanoparticles including top-down, bottom-up, and microfluidic design approaches. We also summarize the current and potential future applications of these nanoparticles, including drug delivery, biological targeting, immunoengineering, and tissue engineering. Ongoing research into the properties and utility of anisotropic polymeric nanoparticles will prove critical to realizing their potential in nanomedicine. PMID:25981390

@Note: a workbench for biomedical text mining.

PubMed

Lourenço, Anália; Carreira, Rafael; Carneiro, Sónia; Maia, Paulo; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Ferreira, Eugénio C; Rocha, Isabel; Rocha, Miguel

2009-08-01

Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. However, most efforts have addressed the benchmarking of new algorithms rather than user operational needs. Bridging the gap between BioTM researchers and biologists' needs is crucial to solve real-world problems and promote further research. We present @Note, a platform for BioTM that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers. Its main functional contributions are the ability to process abstracts and full-texts; an information retrieval module enabling PubMed search and journal crawling; a pre-processing module with PDF-to-text conversion, tokenisation and stopword removal; a semantic annotation schema; a lexicon-based annotator; a user-friendly annotation view that allows to correct annotations and a Text Mining Module supporting dataset preparation and algorithm evaluation. @Note improves the interoperability, modularity and flexibility when integrating in-home and open-source third-party components. Its component-based architecture allows the rapid development of new applications, emphasizing the principles of transparency and simplicity of use. Although it is still on-going, it has already allowed the development of applications that are currently being used.

Messy entanglements: research assemblages in heart transplantation discourses and practices

PubMed Central

Shildrick, Margrit; Carnie, Andrew; Wright, Alexa; McKeever, Patricia; Jan, Emily Huan-Ching; De Luca, Enza; Bachmann, Ingrid; Abbey, Susan; Dal Bo, Dana; Poole, Jennifer; El-Sheikh, Tammer; Ross, Heather

2018-01-01

The paper engages with a variety of data around a supposedly single biomedical event, that of heart transplantation. In conventional discourse, organ transplantation constitutes an unproblematised form of spare part surgery in which failing biological components are replaced by more efficient and enduring ones, but once that simple picture is complicated by employing a radically interdisciplinary approach, any biomedical certainty is profoundly disrupted. Our aim, as a cross-sectorial partnership, has been to explore the complexities of heart transplantation by explicitly entangling research from the arts, biosciences and humanities without privileging any one discourse. It has been no easy enterprise yet it has been highly productive of new insights. We draw on our own ongoing funded research with both heart donor families and recipients to explore our different perceptions of what constitutes data and to demonstrate how the dynamic entangling of multiple data produces a constitutive assemblage of elements in which no one can claim priority. Our claim is that the use of such research assemblages and the collaborations that we bring to our project breaks through disciplinary silos to enable a fuller comprehension of the significance and experience of heart transplantation in both theory and practice. PMID:28972037

Informatics for Peru in the new millennium.

PubMed

Karras, B T; Kimball, A M; Gonzales, V; Pautler, N A; Alarcón, J; Garcia, P J; Fuller, S

2001-01-01

As efforts continue to narrow the digital divide between the North and South, a new biomedical and health informatics training effort has been launched in Peru. This report describes the first year of work on this collaborative effort between the University of Washington (Seattle) Universidad Peruana Cayetano Heredia and Universidad Nacional de San Marcos (Peru) To describe activities in the first year of a new International Research and Training Program in Biomedical and Health Informatics. Descriptive analysis of key activities including an assessment of electronic environment through observation and survey, an in country short course with quantitative evaluation, and first round of recruitment of Peruvian scholars for long-term training in Seattle. A two-week short course on informatics was held in the country. Participants' success in learning was demonstrated through pretest/posttest. A systematic assessment of electronic environment in Peru was carried out and two scholars for long-term training were enrolled at the University of Washington, Seattle. Initial activity in the collaborative training effort has been high. Of particular importance in this environment is orchestration of efforts among interested parties with similar goals in Peru, and integration of informatics skills into ongoing large-scale research projects in country.

Effects of acupuncture on rates of pregnancy and live birth among women undergoing in vitro fertilisation: systematic review and meta-analysis.

PubMed

Manheimer, Eric; Zhang, Grant; Udoff, Laurence; Haramati, Aviad; Langenberg, Patricia; Berman, Brian M; Bouter, Lex M

2008-03-08

To evaluate whether acupuncture improves rates of pregnancy and live birth when used as an adjuvant treatment to embryo transfer in women undergoing in vitro fertilisation. Systematic review and meta-analysis. Medline, Cochrane Central, Embase, Chinese Biomedical Database, hand searched abstracts, and reference lists. Review methods Eligible studies were randomised controlled trials that compared needle acupuncture administered within one day of embryo transfer with sham acupuncture or no adjuvant treatment, with reported outcomes of at least one of clinical pregnancy, ongoing pregnancy, or live birth. Two reviewers independently agreed on eligibility; assessed methodological quality; and extracted outcome data. For all trials, investigators contributed additional data not included in the original publication (such as live births). Meta-analyses included all randomised patients. Seven trials with 1366 women undergoing in vitro fertilisation were included in the meta-analyses. There was little clinical heterogeneity. Trials with sham acupuncture and no adjuvant treatment as controls were pooled for the primary analysis. Complementing the embryo transfer process with acupuncture was associated with significant and clinically relevant improvements in clinical pregnancy (odds ratio 1.65, 95% confidence interval 1.27 to 2.14; number needed to treat (NNT) 10 (7 to 17); seven trials), ongoing pregnancy (1.87, 1.40 to 2.49; NNT 9 (6 to 15); five trials), and live birth (1.91, 1.39 to 2.64; NNT 9 (6 to 17); four trials). Because we were unable to obtain outcome data on live births for three of the included trials, the pooled odds ratio for clinical pregnancy more accurately represents the true combined effect from these trials rather than the odds ratio for live birth. The results were robust to sensitivity analyses on study validity variables. A prespecified subgroup analysis restricted to the three trials with the higher rates of clinical pregnancy in the control group, however, suggested a smaller non-significant benefit of acupuncture (odds ratio 1.24, 0.86 to 1.77). Current preliminary evidence suggests that acupuncture given with embryo transfer improves rates of pregnancy and live birth among women undergoing in vitro fertilisation.

Will biomedical innovation change the future of healthcare?

PubMed

Schmid, Esther F; Ashkenazy, Rebecca; Merson, James; Smith, Dennis A

2009-11-01

Healthcare costs in all industrial nations have increased and payors are starting to look at new ways to contain costs and at new funding models. The business model of pharmaceutical companies is also undergoing rapid changes - potentially disruptive new modalities, such as RNAi, therapeutic vaccines, and cell therapy are emerging, R&D costs have increased year on year, pressures on drug pricing and the efficacy and safety of medicines are mounting. Change is therefore inevitable and already ongoing in healthcare systems and pharmaceutical companies alike. This paper presents several major forces which could drive different future scenarios including: R&D costs, the source of payments for medicines and the emergence of new modalities.

Misconduct accounts for the majority of retracted scientific publications

PubMed Central

Fang, Ferric C.; Steen, R. Grant; Casadevall, Arturo

2012-01-01

A detailed review of all 2,047 biomedical and life-science research articles indexed by PubMed as retracted on May 3, 2012 revealed that only 21.3% of retractions were attributable to error. In contrast, 67.4% of retractions were attributable to misconduct, including fraud or suspected fraud (43.4%), duplicate publication (14.2%), and plagiarism (9.8%). Incomplete, uninformative or misleading retraction announcements have led to a previous underestimation of the role of fraud in the ongoing retraction epidemic. The percentage of scientific articles retracted because of fraud has increased ∼10-fold since 1975. Retractions exhibit distinctive temporal and geographic patterns that may reveal underlying causes. PMID:23027971

From competencies to human interests: ways of knowing and understanding in medical education.

PubMed

Kumagai, Arno K

2014-07-01

When considering the teaching and learning of topics of social relevance in medicine, such as professionalism, medical ethics, the doctor-patient relationship, and issues of diversity and social justice, one is tempted to ask, are the ways of knowing in these fields different from that in the biomedical and clinical sciences? Furthermore, given that the competency approach is dominant in medical education, one might also ask, is the competency model truly appropriate for all of the types of knowledge necessary to become a good physician? These questions are not merely academic, for they are at the core of how these subjects are taught, learned, and assessed.The goal of this article is threefold: first, to explore the nature of knowing and the educational goals in different areas of medicine and, in particular, those areas that have social relevance; second, to critically review the concept of competencies when applied to education in these areas; and third, to explore alternative strategies for teaching, learning, and assessment. This discussion reflects a view that the goal of education in areas of social relevance in medicine should be the enhancement of an understanding of-a deep and abiding connection with-the social responsibilities of the physician. Moving beyond competencies, this approach aspires toward the development of practical wisdom (phronesis) which, when embodied in the physician, links the knowledge and skills of the biomedical and clinical sciences with a moral orientation and call to action that addresses human interests in the practice of medicine.

OBO to UML: Support for the development of conceptual models in the biomedical domain.

PubMed

Waldemarin, Ricardo C; de Farias, Cléver R G

2018-04-01

A conceptual model abstractly defines a number of concepts and their relationships for the purposes of understanding and communication. Once a conceptual model is available, it can also be used as a starting point for the development of a software system. The development of conceptual models using the Unified Modeling Language (UML) facilitates the representation of modeled concepts and allows software developers to directly reuse these concepts in the design of a software system. The OBO Foundry represents the most relevant collaborative effort towards the development of ontologies in the biomedical domain. The development of UML conceptual models in the biomedical domain may benefit from the use of domain-specific semantics and notation. Further, the development of these models may also benefit from the reuse of knowledge contained in OBO ontologies. This paper investigates the support for the development of conceptual models in the biomedical domain using UML as a conceptual modeling language and using the support provided by the OBO Foundry for the development of biomedical ontologies, namely entity kind and relationship types definitions provided by the Basic Formal Ontology (BFO) and the OBO Core Relations Ontology (OBO Core), respectively. Further, the paper investigates the support for the reuse of biomedical knowledge currently available in OBOFFF ontologies in the development these conceptual models. The paper describes a UML profile for the OBO Core Relations Ontology, which basically defines a number of stereotypes to represent BFO entity kinds and OBO Core relationship types definitions. The paper also presents a support toolset consisting of a graphical editor named OBO-RO Editor, which directly supports the development of UML models using the extensions defined by our profile, and a command-line tool named OBO2UML, which directly converts an OBOFFF ontology into a UML model. Copyright © 2018 Elsevier Inc. All rights reserved.

The BioLexicon: a large-scale terminological resource for biomedical text mining

PubMed Central

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 Markup Framework, an ISO standard. Conclusions The BioLexicon contains over 2.2 M lexical entries and over 1.8 M terminological variants, as well as over 3.3 M semantic relations, including over 2 M synonymy relations. Its exploitation can benefit both application developers and users. We demonstrate some such benefits by describing integration of the resource into a number of different tools, and evaluating improvements in performance that this can bring. PMID:21992002

The BioLexicon: a large-scale terminological resource for biomedical text mining.

PubMed

Thompson, Paul; McNaught, John; Montemagni, Simonetta; Calzolari, Nicoletta; del Gratta, Riccardo; Lee, Vivian; Marchi, Simone; Monachini, Monica; Pezik, Piotr; Quochi, Valeria; Rupp, C J; Sasaki, Yutaka; Venturi, Giulia; Rebholz-Schuhmann, Dietrich; Ananiadou, Sophia

2011-10-12

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. 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 Markup Framework, an ISO standard. The BioLexicon contains over 2.2 M lexical entries and over 1.8 M terminological variants, as well as over 3.3 M semantic relations, including over 2 M synonymy relations. Its exploitation can benefit both application developers and users. We demonstrate some such benefits by describing integration of the resource into a number of different tools, and evaluating improvements in performance that this can bring.

ReRouting biomedical innovation: observations from a mapping of the alternative research and development (R&D) landscape.

PubMed

Greenberg, Alexandra; Kiddell-Monroe, Rachel

2016-09-14

In recent years, the world has witnessed the tragic outcomes of multiple global health crises. From Ebola to high prices to antibiotic resistance, these events highlight the fundamental constraints of the current biomedical research and development (R&D) system in responding to patient needs globally.To mitigate this lack of responsiveness, over 100 self-identified "alternative" R&D initiatives, have emerged in the past 15 years. To begin to make sense of this panoply of initiatives working to overcome the constraints of the current system, UAEM began an extensive, though not comprehensive, mapping of the alternative biomedical R&D landscape. We developed a two phase approach: (1) an investigation, via the RE:Route Mapping, of both existing and proposed initiatives that claim to offer an alternative approach to R&D, and (2) evaluation of those initiatives to determine which are in fact achieving increased access to and innovation in medicines. Through phase 1, the RE:Route Mapping, we examined 81 initiatives that claim to redress the inequity perpetuated by the current system via one of five commonly recognized mechanisms necessary for truly alternative R&D.Preliminary analysis of phase 1 provides the following conclusions: 1. No initiative presents a completely alternative model of biomedical R&D. 2. The majority of initiatives focus on developing incentives for drug discovery. 3. The majority of initiatives focus on rare diseases or diseases of the poor and marginalized. 4. There is an increasing emphasis on the use of push, pull, pool, collaboration and open mechanisms alongside the concept of delinkage in alternative R&D. 5. There is a trend towards public funding and launching of initiatives by the Global South. Given the RE:Route Mapping's inevitable limitations and the assumptions made in its methodology, it is not intended to be the final word on a constantly evolving and complex field; however, its findings are significant. The Mapping's value lies in its timely and unique insight into the importance of ongoing efforts to develop a new global framework for biomedical R&D. As we progress to phase 2, an evaluation tool for initiatives focused on identifying which approaches have truly achieved increased innovation and access for patients, we aim to demonstrate that there are a handful of initiatives which represent some, but not all, of the building blocks for a new approach to R&D.Through this mapping and our forthcoming evaluation, UAEM aims to initiate an evidence-based conversation around a truly alternative biomedical R&D model that serves people rather than profits.

Guns, society, and medicine.

PubMed

Kassirer, Jerome P

2015-02-26

Given the 96 incidents of firearm violence on school campuses since Sandy Hook and the ongoing toll on lives and health, the lack of relevant data and a research pipeline in this area should be anathema to all physicians.

Maritime trade & transportation 2007

DOT National Transportation Integrated Search

2005-01-10

This latest edition of Maritime Trade and Transportation follows two prior reports released in 1999 and 2002. These reports refl ect an ongoing effort by the Maritime Data Working Group to provide quality, timely, comprehensive, and relevant maritime...

Communicable Diseases Prioritized According to Their Public Health Relevance, Sweden, 2013

PubMed Central

Dahl, Viktor; Tegnell, Anders; Wallensten, Anders

2015-01-01

To establish strategic priorities for the Public Health Agency of Sweden we prioritized pathogens according to their public health relevance in Sweden in order to guide resource allocation. We then compared the outcome to ongoing surveillance. We used a modified prioritization method developed at the Robert Koch Institute in Germany. In a Delphi process experts scored pathogens according to ten variables. We ranked the pathogens according to the total score and divided them into four priority groups. We then compared the priority groups to self-reported time spent on surveillance by epidemiologists and ongoing programmes for surveillance through mandatory and/or voluntary notifications and for surveillance of typing results. 106 pathogens were scored. The result of the prioritization process was similar to the outcome of the prioritization in Germany. Common pathogens such as calicivirus and Influenza virus as well as blood-borne pathogens such as human immunodeficiency virus, hepatitis B and C virus, gastro-intestinal infections such as Campylobacter and Salmonella and vector-borne pathogens such as Borrelia were all in the highest priority group. 63% of time spent by epidemiologists on surveillance was spent on pathogens in the highest priority group and all pathogens in the highest priority group, except for Borrelia and varicella-zoster virus, were under surveillance through notifications. Ten pathogens in the highest priority group (Borrelia, calicivirus, Campylobacter, Echinococcus multilocularis, hepatitis C virus, HIV, respiratory syncytial virus, SARS- and MERS coronavirus, tick-borne encephalitis virus and varicella-zoster virus) did not have any surveillance of typing results. We will evaluate the possibilities of surveillance for the pathogens in the highest priority group where we currently do not have any ongoing surveillance and evaluate the need of surveillance for the pathogens from the low priority group where there is ongoing surveillance in order to focus our work on the pathogens with the highest relevance. PMID:26397699

Human Emotional State and its Relevance for Military VR Training

DTIC Science & Technology

2005-07-01

buckwalt@usc.edu Abstract Combat environments by their nature can produce a dramatic range of emotional responses in military personnel. When...paper will present the rationale and status of two ongoing VR research programs at the ICT that address sharply contrasting ends of the emotional ...spectrum relevant to the military: 1. The Sensory Environments Evaluation (SEE) Project is examining basic factors that underlie emotion as it occurs

State of reporting of primary biomedical research: a scoping review protocol

PubMed Central

Mbuagbaw, Lawrence; Samaan, Zainab; Jin, Yanling; Nwosu, Ikunna; Levine, Mitchell A H; Adachi, Jonathan D; Thabane, Lehana

2017-01-01

Introduction Incomplete or inconsistent reporting remains a major concern in the biomedical literature. Incomplete or inconsistent reporting may yield the published findings unreliable, irreproducible or sometimes misleading. In this study based on evidence from systematic reviews and surveys that have evaluated the reporting issues in primary biomedical studies, we aim to conduct a scoping review with focuses on (1) the state-of-the-art extent of adherence to the emerging reporting guidelines in primary biomedical research, (2) the inconsistency between protocols or registrations and full reports and (3) the disagreement between abstracts and full-text articles. Methods and analyses We will use a comprehensive search strategy to retrieve all available and eligible systematic reviews and surveys in the literature. We will search the following electronic databases: Web of Science, Excerpta Medica Database (EMBASE), MEDLINE and Cumulative Index to Nursing and Allied Health Literature (CINAHL). Our outcomes are levels of adherence to reporting guidelines, levels of consistency between protocols or registrations and full reports and the agreement between abstracts and full reports, all of which will be expressed as percentages, quality scores or categorised rating (such as high, medium and low). No pooled analyses will be performed quantitatively given the heterogeneity of the included systematic reviews and surveys. Likewise, factors associated with improved completeness and consistency of reporting will be summarised qualitatively. The quality of the included systematic reviews will be evaluated using AMSTAR (a measurement tool to assess systematic reviews). Ethics and dissemination All findings will be published in peer-reviewed journals and relevant conferences. These results may advance our understanding of the extent of incomplete and inconsistent reporting, factors related to improved completeness and consistency of reporting and potential recommendations for various stakeholders in the biomedical community. PMID:28360252

Misconduct Policies in High-Impact Biomedical Journals

PubMed Central

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 increase public trust in the integrity of the published record in biomedicine. PMID:23284820

Misconduct policies in high-impact biomedical journals.

PubMed

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

2012-01-01

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 integrity of the published record in biomedicine.

Biomedical literature classification using encyclopedic knowledge: a Wikipedia-based bag-of-concepts approach.

PubMed

Mouriño García, Marcos Antonio; Pérez Rodríguez, Roberto; Anido Rifón, Luis E

2015-01-01

Automatic classification of text documents into a set of categories has a lot of applications. Among those applications, the automatic classification of biomedical literature stands out as an important application for automatic document classification strategies. Biomedical staff and researchers have to deal with a lot of literature in their daily activities, so it would be useful a system that allows for accessing to documents of interest in a simple and effective way; thus, it is necessary that these documents are sorted based on some criteria-that is to say, they have to be classified. Documents to classify are usually represented following the bag-of-words (BoW) paradigm. Features are words in the text-thus suffering from synonymy and polysemy-and their weights are just based on their frequency of occurrence. This paper presents an empirical study of the efficiency of a classifier that leverages encyclopedic background knowledge-concretely Wikipedia-in order to create bag-of-concepts (BoC) representations of documents, understanding concept as "unit of meaning", and thus tackling synonymy and polysemy. Besides, the weighting of concepts is based on their semantic relevance in the text. For the evaluation of the proposal, empirical experiments have been conducted with one of the commonly used corpora for evaluating classification and retrieval of biomedical information, OHSUMED, and also with a purpose-built corpus of MEDLINE biomedical abstracts, UVigoMED. Results obtained show that the Wikipedia-based bag-of-concepts representation outperforms the classical bag-of-words representation up to 157% in the single-label classification problem and up to 100% in the multi-label problem for OHSUMED corpus, and up to 122% in the single-label classification problem and up to 155% in the multi-label problem for UVigoMED corpus.

Biomedical literature classification using encyclopedic knowledge: a Wikipedia-based bag-of-concepts approach

PubMed Central

Pérez Rodríguez, Roberto; Anido Rifón, Luis E.

2015-01-01

Automatic classification of text documents into a set of categories has a lot of applications. Among those applications, the automatic classification of biomedical literature stands out as an important application for automatic document classification strategies. Biomedical staff and researchers have to deal with a lot of literature in their daily activities, so it would be useful a system that allows for accessing to documents of interest in a simple and effective way; thus, it is necessary that these documents are sorted based on some criteria—that is to say, they have to be classified. Documents to classify are usually represented following the bag-of-words (BoW) paradigm. Features are words in the text—thus suffering from synonymy and polysemy—and their weights are just based on their frequency of occurrence. This paper presents an empirical study of the efficiency of a classifier that leverages encyclopedic background knowledge—concretely Wikipedia—in order to create bag-of-concepts (BoC) representations of documents, understanding concept as “unit of meaning”, and thus tackling synonymy and polysemy. Besides, the weighting of concepts is based on their semantic relevance in the text. For the evaluation of the proposal, empirical experiments have been conducted with one of the commonly used corpora for evaluating classification and retrieval of biomedical information, OHSUMED, and also with a purpose-built corpus of MEDLINE biomedical abstracts, UVigoMED. Results obtained show that the Wikipedia-based bag-of-concepts representation outperforms the classical bag-of-words representation up to 157% in the single-label classification problem and up to 100% in the multi-label problem for OHSUMED corpus, and up to 122% in the single-label classification problem and up to 155% in the multi-label problem for UVigoMED corpus. PMID:26468436

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

PubMed

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

Controlling complexity: the clinical relevance of mouse complex genetics

PubMed Central

Schughart, Klaus; Libert, Claude; Kas, Martien J

2013-01-01

Experimental animal models are essential to obtain basic knowledge of the underlying biological mechanisms in human diseases. Here, we review major contributions to biomedical research and discoveries that were obtained in the mouse model by using forward genetics approaches and that provided key insights into the biology of human diseases and paved the way for the development of novel therapeutic approaches. PMID:23632795

Decarboxylative Fluorination Strategies for Accessing Medicinally-relevant Products

PubMed Central

Qiao, Yupu; Zhu, Lingui; Ambler, Brett R.

2014-01-01

Fluorinated organic compounds have a long history in medicinal chemistry, and synthetic methods to access target fluorinated compounds are undergoing a revolution. One powerful strategy for the installation of fluorine-containing functional groups includes decarboxylative reactions. Benefits of decarboxylative approaches potentially include: 1) readily available substrates or reagents 2) mild reaction conditions; 3) simplified purification. This focus review highlights the applications of decarboxylation strategies for fluorination reactions to access compounds with biomedical potential. The manuscript highlights on two general strategies, fluorination by decarboxylative reagents and by decarboxylation of substrates. Where relevant, examples of medicinally useful compounds that can be accessed using these strategies are highlighted. PMID:24484421

Habilitation Services for Developmentally Disabled Persons.

ERIC Educational Resources Information Center

Flexer, Robert W.

1983-01-01

Developmental disabilities are reviewed from the standpoint of definition, service systems, and interventions. Definitions from relevant laws outline population characteristics and required services. Intensive, comprehensive, coordinated ongoing delivery mechanisms are emphasized, including vocational, residential, and generic services. General…

Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts.

PubMed

Sharma, Vivekanand; Law, Wayne; Balick, Michael J; Sarkar, Indra Neil

2017-01-01

The growing amount of data describing historical medicinal uses of plants from digitization efforts provides the opportunity to develop systematic approaches for identifying potential plant-based therapies. However, the task of cataloguing plant use information from natural language text is a challenging task for ethnobotanists. To date, there have been only limited adoption of informatics approaches used for supporting the identification of ethnobotanical information associated with medicinal uses. This study explored the feasibility of using biomedical terminologies and natural language processing approaches for extracting relevant plant-associated therapeutic use information from historical biodiversity literature collection available from the Biodiversity Heritage Library. The results from this preliminary study suggest that there is potential utility of informatics methods to identify medicinal plant knowledge from digitized resources as well as highlight opportunities for improvement.

Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts

PubMed Central

Sharma, Vivekanand; Law, Wayne; Balick, Michael J.; Sarkar, Indra Neil

2017-01-01

The growing amount of data describing historical medicinal uses of plants from digitization efforts provides the opportunity to develop systematic approaches for identifying potential plant-based therapies. However, the task of cataloguing plant use information from natural language text is a challenging task for ethnobotanists. To date, there have been only limited adoption of informatics approaches used for supporting the identification of ethnobotanical information associated with medicinal uses. This study explored the feasibility of using biomedical terminologies and natural language processing approaches for extracting relevant plant-associated therapeutic use information from historical biodiversity literature collection available from the Biodiversity Heritage Library. The results from this preliminary study suggest that there is potential utility of informatics methods to identify medicinal plant knowledge from digitized resources as well as highlight opportunities for improvement. PMID:29854223

Respect for persons, respect for integrity: remarks for the conceptualization of integrity in social ethics.

PubMed

Fjellstrom, Roger

2005-01-01

Even though respect for integrity is hailed in several authoritative legal and ethical documents, and is typically presented as a complement to respect for autonomy, it is largely neglected in many leading works in ethics. Is such neglect warranted, or does it express a prejudice? This article argues that the latter is the case, and that this is due to misplaced conceptual concerns. It offers some proposals as regards the conceptualization of integrity in social ethics in general and in biomedical ethics in particular. Five main directions of interpretation of "integrity" are discerned and shown to be relevant for different areas of biomedical ethics. The defense of respect for integrity is served by a softening of principlism and by greater attention to context among the initial critics of this principle.

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.

PubMed

Wimalaratne, Sarala M; Grenon, Pierre; Hoehndorf, Robert; Gkoutos, Georgios V; de Bono, Bernard

2012-02-01

The article presents an infrastructure for supporting the semantic interoperability of biomedical resources based on the management (storing and inference-based querying) of their ontology-based annotations. This infrastructure consists of: (i) a repository to store and query ontology-based annotations; (ii) a knowledge base server with an inference engine to support the storage of and reasoning over ontologies used in the annotation of resources; (iii) a set of applications and services allowing interaction with the integrated repository and knowledge base. The infrastructure is being prototyped and developed and evaluated by the RICORDO project in support of the knowledge management of biomedical resources, including physiology and pharmacology models and associated clinical data. The RICORDO toolkit and its source code are freely available from http://ricordo.eu/relevant-resources. sarala@ebi.ac.uk.

Treatment options after sorafenib failure in patients with hepatocellular carcinoma

PubMed Central

Dika, Imane El

2017-01-01

Second line therapy after failure of sorafenib continues to be under study. Prognosis of hepatocellular carcinoma is measured in months, with median overall survival reaching 10.7 months with sorafenib. Because of the modest net benefit sorafenib has contributed, and rising incidence of hepatocellular carcinoma in the world, continued efforts are ongoing to look for efficient upfront, second line, or combination therapies. Herein we review the most relevant to date published literature on treatment options beyond sorafenib, reported studies, ongoing investigational efforts, and possibilities for future studies in advanced hepatocellular carcinoma. PMID:29151326

Effects of technical editing in biomedical journals: a systematic review.

PubMed

Wager, Elizabeth; Middleton, Philippa

2002-06-05

Technical editing supposedly improves the accuracy and clarity of journal articles. We examined evidence of its effects on research reports in biomedical journals. Subset of a systematic review using Cochrane methods, searching MEDLINE, EMBASE, and other databases from earliest entries to February 2000 by using inclusive search terms; hand searching relevant journals. We selected comparative studies of the effects of editorial processes on original research articles between acceptance and publication in biomedical journals. Two reviewers assessed each study and performed independent data extraction. The 11 studies on technical editing indicate that it improves the readability of articles slightly (as measured by Gunning Fog and Flesch reading ease scores), may improve other aspects of their quality, can increase the accuracy of references and quotations, and raises the quality of abstracts. Supplying authors with abstract preparation instructions had no discernible effect. Considering the time and resources devoted to technical editing, remarkably little is know about its effects or the effects of imposing different house styles. Studies performed at 3 journals employing relatively large numbers of professional technical editors suggest that their editorial processes are associated with increases in readability and quality of articles, but these findings may not be generalizable to other journals.

Biologically Relevant Heterogeneity: Metrics and Practical Insights.

PubMed

Gough, Albert; Stern, Andrew M; Maier, John; Lezon, Timothy; Shun, Tong-Ying; Chennubhotla, Chakra; Schurdak, Mark E; Haney, Steven A; Taylor, D Lansing

2017-03-01

Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high-throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell-level data, as well as the need for standard metrics of the spatial, temporal, and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high-throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics, and the design of optimal therapeutic strategies for individual patients.

Electrophoretic deposition of biomaterials

PubMed Central

Boccaccini, A. R.; Keim, S.; Ma, R.; Li, Y.; Zhitomirsky, I.

2010-01-01

Electrophoretic deposition (EPD) is attracting increasing attention as an effective technique for the processing of biomaterials, specifically bioactive coatings and biomedical nanostructures. The well-known advantages of EPD for the production of a wide range of microstructures and nanostructures as well as unique and complex material combinations are being exploited, starting from well-dispersed suspensions of biomaterials in particulate form (microsized and nanoscale particles, nanotubes, nanoplatelets). EPD of biological entities such as enzymes, bacteria and cells is also being investigated. The review presents a comprehensive summary and discussion of relevant recent work on EPD describing the specific application of the technique in the processing of several biomaterials, focusing on (i) conventional bioactive (inorganic) coatings, e.g. hydroxyapatite or bioactive glass coatings on orthopaedic implants, and (ii) biomedical nanostructures, including biopolymer–ceramic nanocomposites, carbon nanotube coatings, tissue engineering scaffolds, deposition of proteins and other biological entities for sensors and advanced functional coatings. It is the intention to inform the reader on how EPD has become an important tool in advanced biomaterials processing, as a convenient alternative to conventional methods, and to present the potential of the technique to manipulate and control the deposition of a range of nanomaterials of interest in the biomedical and biotechnology fields. PMID:20504802

An automated procedure to identify biomedical articles that contain cancer-associated gene variants.

PubMed

McDonald, Ryan; Scott Winters, R; Ankuda, Claire K; Murphy, Joan A; Rogers, Amy E; Pereira, Fernando; Greenblatt, Marc S; White, Peter S

2006-09-01

The proliferation of biomedical literature makes it increasingly difficult for researchers to find and manage relevant information. However, identifying research articles containing mutation data, a requisite first step in integrating large and complex mutation data sets, is currently tedious, time-consuming and imprecise. More effective mechanisms for identifying articles containing mutation information would be beneficial both for the curation of mutation databases and for individual researchers. We developed an automated method that uses information extraction, classifier, and relevance ranking techniques to determine the likelihood of MEDLINE abstracts containing information regarding genomic variation data suitable for inclusion in mutation databases. We targeted the CDKN2A (p16) gene and the procedure for document identification currently used by CDKN2A Database curators as a measure of feasibility. A set of abstracts was manually identified from a MEDLINE search as potentially containing specific CDKN2A mutation events. A subset of these abstracts was used as a training set for a maximum entropy classifier to identify text features distinguishing "relevant" from "not relevant" abstracts. Each document was represented as a set of indicative word, word pair, and entity tagger-derived genomic variation features. When applied to a test set of 200 candidate abstracts, the classifier predicted 88 articles as being relevant; of these, 29 of 32 manuscripts in which manual curation found CDKN2A sequence variants were positively predicted. Thus, the set of potentially useful articles that a manual curator would have to review was reduced by 56%, maintaining 91% recall (sensitivity) and more than doubling precision (positive predictive value). Subsequent expansion of the training set to 494 articles yielded similar precision and recall rates, and comparison of the original and expanded trials demonstrated that the average precision improved with the larger data set. Our results show that automated systems can effectively identify article subsets relevant to a given task and may prove to be powerful tools for the broader research community. This procedure can be readily adapted to any or all genes, organisms, or sets of documents. Published 2006 Wiley-Liss, Inc.

Determining the relative importance of figures in journal articles to find representative images

NASA Astrophysics Data System (ADS)

Müller, Henning; Foncubierta-Rodríguez, Antonio; Lin, Chang; Eggel, Ivan

2013-03-01

When physicians are searching for articles in the medical literature, images of the articles can help determining relevance of the article content for a specific information need. The visual image representation can be an advantage in effectiveness (quality of found articles) and also in efficiency (speed of determining relevance or irrelevance) as many articles can likely be excluded much quicker by looking at a few representative images. In domains such as medical information retrieval, allowing to determine relevance quickly and accurately is an important criterion. This becomes even more important when small interfaces are used as it is frequently the case on mobile phones and tablets to access scientific data whenever information needs arise. In scientific articles many figures are used and particularly in the biomedical literature only a subset may be relevant for determining the relevance of a specific article to an information need. In many cases clinical images can be seen as more important for visual appearance than graphs or histograms that require looking at the context for interpretation. To get a clearer idea of image relevance in articles, a user test with a physician was performed who classified images of biomedical research articles into categories of importance that can subsequently be used to evaluate algorithms that automatically select images as representative examples. The manual sorting of images of 50 journal articles of BioMedCentral with each containing more than 8 figures by importance also allows to derive several rules that determine how to choose images and how to develop algorithms for choosing the most representative images of specific texts. This article describes the user tests and can be a first important step to evaluate automatic tools to select representative images for representing articles and potentially also images in other contexts, for example when representing patient records or other medical concepts when selecting images to represent RadLex terms in tutorials or interactive interfaces for example. This can help to make the image retrieval process more efficient and effective for physicians.

Chronic Diseases in North-West Tanzania and Southern Uganda. Public Perceptions of Terminologies, Aetiologies, Symptoms and Preferred Management.

PubMed

Nnko, Soori; Bukenya, Dominic; Kavishe, Bazil Balthazar; Biraro, Samuel; Peck, Robert; Kapiga, Saidi; Grosskurth, Heiner; Seeley, Janet

2015-01-01

Research has shown that health system utilization is low for chronic diseases (CDs) other than HIV. We describe the knowledge and perceptions of CDs identified from rural and urban communities in north-west Tanzania and southern Uganda. Data were collected through a quantitative population survey, a quantitative health facility survey and focus group discussions (FGDs) and in-depth interviews (IDIs) in subgroups of population survey participants. The main focus of this paper is the findings from the FGDs and IDIs. We conducted 24 FGDs, involving approximately 180 adult participants and IDIs with 116 participants (≥18 years). CDs studied included: asthma/chronic obstructive lung disease (COPD), diabetes, epilepsy, hypertension, cardiac failure and HIV- related disease. The understanding of most chronic conditions involved a combination of biomedical information, gleaned from health facility visits, local people who had suffered from a complaint or knew others who had and beliefs drawn from information shared in the community. The biomedical contribution shows some understanding of the aetiology of a condition and the management of that condition. However, local beliefs for certain conditions (such as epilepsy) suggest that biomedical treatment may be futile and therefore work counter to biomedical prescriptions for management. Current perceptions of selected CDs may represent a barrier that prevents people from adopting efficacious health and treatment seeking behaviours. Interventions to improve this situation must include efforts to improve the quality of existing health services, so that people can access relevant, reliable and trustworthy services.

Electroactive polymers for healthcare and biomedical applications

NASA Astrophysics Data System (ADS)

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.

Department of Defense In-House RDT&E Activities. Management Analysis Report

DTIC Science & Technology

1988-10-30

Surveying 621 Nurse Assistant Technician 622 Medical Supply Aid 818 Engineering 625 Autopsy Attendant Drafting 636 Rehabilitation Therapy Asst 856...IMPORTANT PROGRAMS AVIATOR PERFORMANCE EFFECTS OF CHEMICAL AGENT ANTIDOTE THERAPIES . INDIVIDUAL AND CREW STRESS/WORKLOAD/PERFORMANCE. BIOMEDICAL HAZARDS...MIL.RELEVANT INFECT.DISEASES IN S.W.ASIA AND AFRICA. THERAPY OF INFECT. DISEASE IN S.W.ASIA AND AFRICA RAPID & EARLY DIAG. OF INFECT.DISEASES OF

Text mining resources for the life sciences.

PubMed

Przybyła, Piotr; Shardlow, Matthew; Aubin, Sophie; Bossy, Robert; Eckart de Castilho, Richard; Piperidis, Stelios; McNaught, John; Ananiadou, Sophia

2016-01-01

Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work. We categorize the various resources under three sections: Content Discovery looks at where and how to find biomedical publications for text mining; Knowledge Encoding describes the formats used to represent the different levels of information associated with content that enable text mining, including those formats used to carry such information between processes; Tools and Services gives an overview of workflow management systems that can be used to rapidly configure and compare domain- and task-specific processes, via access to a wide range of pre-built tools. We also provide links to relevant repositories in each section to enable the reader to find resources relevant to their own area of interest. Throughout this work we give a special focus to resources that are interoperable-those that have the crucial ability to share information, enabling smooth integration and reusability. © The Author(s) 2016. Published by Oxford University Press.

Text mining resources for the life sciences

PubMed Central

Shardlow, Matthew; Aubin, Sophie; Bossy, Robert; Eckart de Castilho, Richard; Piperidis, Stelios; McNaught, John; Ananiadou, Sophia

2016-01-01

Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work. We categorize the various resources under three sections: Content Discovery looks at where and how to find biomedical publications for text mining; Knowledge Encoding describes the formats used to represent the different levels of information associated with content that enable text mining, including those formats used to carry such information between processes; Tools and Services gives an overview of workflow management systems that can be used to rapidly configure and compare domain- and task-specific processes, via access to a wide range of pre-built tools. We also provide links to relevant repositories in each section to enable the reader to find resources relevant to their own area of interest. Throughout this work we give a special focus to resources that are interoperable—those that have the crucial ability to share information, enabling smooth integration and reusability. PMID:27888231

SKIMMR: facilitating knowledge discovery in life sciences by machine-aided skim reading

PubMed Central

Burns, Gully A.P.C.

2014-01-01

Background. Unlike full reading, ‘skim-reading’ involves the process of looking quickly over information in an attempt to cover more material whilst still being able to retain a superficial view of the underlying content. Within this work, we specifically emulate this natural human activity by providing a dynamic graph-based view of entities automatically extracted from text. For the extraction, we use shallow parsing, co-occurrence analysis and semantic similarity computation techniques. Our main motivation is to assist biomedical researchers and clinicians in coping with increasingly large amounts of potentially relevant articles that are being published ongoingly in life sciences. Methods. To construct the high-level network overview of articles, we extract weighted binary statements from the text. We consider two types of these statements, co-occurrence and similarity, both organised in the same distributional representation (i.e., in a vector-space model). For the co-occurrence weights, we use point-wise mutual information that indicates the degree of non-random association between two co-occurring entities. For computing the similarity statement weights, we use cosine distance based on the relevant co-occurrence vectors. These statements are used to build fuzzy indices of terms, statements and provenance article identifiers, which support fuzzy querying and subsequent result ranking. These indexing and querying processes are then used to construct a graph-based interface for searching and browsing entity networks extracted from articles, as well as articles relevant to the networks being browsed. Last but not least, we describe a methodology for automated experimental evaluation of the presented approach. The method uses formal comparison of the graphs generated by our tool to relevant gold standards based on manually curated PubMed, TREC challenge and MeSH data. Results. We provide a web-based prototype (called ‘SKIMMR’) that generates a network of inter-related entities from a set of documents which a user may explore through our interface. When a particular area of the entity network looks interesting to a user, the tool displays the documents that are the most relevant to those entities of interest currently shown in the network. We present this as a methodology for browsing a collection of research articles. To illustrate the practical applicability of SKIMMR, we present examples of its use in the domains of Spinal Muscular Atrophy and Parkinson’s Disease. Finally, we report on the results of experimental evaluation using the two domains and one additional dataset based on the TREC challenge. The results show how the presented method for machine-aided skim reading outperforms tools like PubMed regarding focused browsing and informativeness of the browsing context. PMID:25097821

Development of polypyrrole based solid-state on-chip microactuators using photolithography

NASA Astrophysics Data System (ADS)

Zhong, Yong; Lundemo, Staffan; Jager, Edwin W. H.

2018-07-01

There is a need for soft microactuators, especially for biomedical applications. We have developed a microfabrication process to create such soft, on-chip polymer based microactuators that can operate in air. The on-chip microactuators were fabricated using standard photolithographic techniques and wet etching, combined with special designed process to micropattern the electroactive polymer polypyrrole that drives the microactuators. By immobilizing a UV-patternable gel containing a liquid electrolyte on top of the electroactive polypyrrole layer, actuation in air was achieved although with reduced movement. Further optimization of the processing is currently on-going. The result shows the possibility to batch fabricate complex microsystems such as microrobotics and micromanipulators based on these solid-state on-chip microactuators using microfabrication methods including standard photolithographic processes.

The persuasive appeal of alternative medicine.

PubMed

Kaptchuk, T J; Eisenberg, D M

1998-12-15

Alternative medicine has a major presence and persuasive attraction in the industrialized western world. The extent to which these practices have clinical efficacy according to biomedical criteria is a matter of ongoing research and debate. It may be that independent of any such efficacy, the attraction of alternative medicine is related to the power of its underlying shared beliefs and cultural assumptions. The fundamental premises are an advocacy of nature, vitalism, "science," and spirituality. These themes offer patients a participatory experience of empowerment, authenticity, and enlarged self-identity when illness threatens their sense of intactness and connection to the world. A discussion of these themes may enable conventionally trained clinicians to better understand their patients' attraction to and acceptance of alternative medical therapies.

Is the bang worth the buck? A RAID performance study

NASA Technical Reports Server (NTRS)

Hauser, Susan E.; Berman, Lewis E.; Thoma, George R.

1996-01-01

Expecting a high data delivery rate as well as data protection, the Lister Hill National Center for Biomedical Communications procured a RAID system to house image files for image delivery applications. A study was undertaken to determine the configuration of the RAID system that would provide for the fastest retrieval of image files. Average retrieval times with single and with concurrent users were measured for several stripe widths and several numbers of disks for RAID levels 0, 0+1 and 5. These are compared to each other and to average retrieval times for non-RAID configurations of the same hardware. Although the study in ongoing, a few conclusions have emerged regarding the tradeoffs among the different configurations with respect to file retrieval speed and cost.

Bivalent O-glycoside mimetics with S/disulfide/Se substitutions and aromatic core: Synthesis, molecular modeling and inhibitory activity on biomedically relevant lectins in assays of increasing physiological relevance.

PubMed

Kaltner, Herbert; Szabó, Tamás; Fehér, Krisztina; André, Sabine; Balla, Sára; Manning, Joachim C; Szilágyi, László; Gabius, Hans-Joachim

2017-06-15

The emerging significance of recognition of cellular glycans by lectins for diverse aspects of pathophysiology is a strong incentive for considering development of bioactive and non-hydrolyzable glycoside derivatives, for example by introducing S/Se atoms and the disulfide group instead of oxygen into the glycosidic linkage. We report the synthesis of 12 bivalent thio-, disulfido- and selenoglycosides attached to benzene/naphthalene cores. They present galactose, for blocking a plant toxin, or lactose, the canonical ligand of adhesion/growth-regulatory galectins. Modeling reveals unrestrained flexibility and inter-headgroup distances too small to bridge two sites in the same lectin. Inhibitory activity was first detected by solid-phase assays using a surface-presented glycoprotein, with relative activity enhancements per sugar unit relative to free cognate sugar up to nearly 10fold. Inhibitory activity was also seen on lectin binding to surfaces of human carcinoma cells. In order to proceed to characterize this capacity in the tissue context monitoring of lectin binding in the presence of inhibitors was extended to sections of three types of murine organs as models. This procedure proved to be well-suited to determine relative activity levels of the glycocompounds to block binding of the toxin and different human galectins to natural glycoconjugates at different sites in sections. The results on most effective inhibition by two naphthalene-based disulfides and a selenide raise the perspective for broad applicability of the histochemical assay in testing glycoclusters that target biomedically relevant lectins. Copyright © 2017 Elsevier Ltd. All rights reserved.

Measuring Diversity of the National Institutes of Health-Funded Workforce.

PubMed

Heggeness, Misty L; Evans, Lisa; Pohlhaus, Jennifer Reineke; Mills, Sherry L

2016-08-01

To measure diversity within the National Institutes of Health (NIH)-funded workforce. The authors use a relevant labor market perspective to more directly understand what the NIH can influence in terms of enhancing diversity through NIH policies. Using the relevant labor market (defined as persons with advanced degrees working as biomedical scientists in the United States) as the conceptual framework, and informed by accepted economic principles, the authors used the American Community Survey and NIH administrative data to calculate representation ratios of the NIH-funded biomedical workforce from 2008 to 2012 by race, ethnicity, sex, and citizenship status, and compared this against the pool of characteristic individuals in the potential labor market. In general, the U.S. population during this time period was an inaccurate comparison group for measuring diversity of the NIH-funded scientific workforce. Measuring accurately, we found the representation of women and traditionally underrepresented groups in NIH-supported postdoc fellowships and traineeships and mentored career development programs was greater than their representation in the relevant labor market. The same analysis found these demographic groups are less represented in the NIH-funded independent investigator pool. Although these findings provided a picture of the current NIH-funded workforce and a foundation for understanding the federal role in developing, maintaining, and renewing diverse scientific human resources, further study is needed to identify whether junior- and early-stage investigators who are part of more diverse cohorts will naturally transition into independent NIH-funded investigators, or whether they will leave the workforce before achieving independent researcher status.

Measuring Diversity of the National Institutes of Health-Funded Workforce

PubMed Central

Heggeness, Misty L.; Evans, Lisa; Pohlhaus, Jennifer Reineke; Mills, Sherry L.

2017-01-01

Purpose To measure diversity within the National Institutes of Health (NIH) funded workforce. The authors use a relevant labor market perspective to more directly understand what the NIH can influence in terms of enhancing diversity through NIH policies. Method Using the relevant labor market (defined as those persons with advanced degrees working as biomedical scientists in the United States) as the conceptual framework, and informed by accepted economic principles, the authors used the American Community Survey (ACS) and NIH administrative data to calculate representation ratios of the NIH-funded biomedical workforce from 2008–2012 by race, ethnicity, sex, and citizenship status, and compared this to the pool of characteristic individuals in the potential labor market. Results In general, the U.S. population during this same time period was a poor comparison group to the NIH-funded scientific workforce. Furthermore, the representation of women and traditionally underrepresented groups in NIH-supported postdoc fellowships and traineeships and mentored career development programs was greater than their representation in the relevant labor market. The same analysis found that these demographic groups are less represented in the NIH-funded independent investigator pool. Conclusions While these findings provided a picture of current NIH-funded workforce and a foundation for understanding the federal role in developing, maintaining, and renewing diverse scientific human resources, further study is needed to identify whether junior- and early-stage investigators who are part of more diverse cohorts will naturally transition into independent NIH-funded investigators, or whether they will leave the workforce before achieving independent researcher status. PMID:27224301

Translating Alcohol Research

PubMed Central

Batman, Angela M.; Miles, Michael F.

2015-01-01

Alcohol use disorder (AUD) and its sequelae impose a major burden on the public health of the United States, and adequate long-term control of this disorder has not been achieved. Molecular and behavioral basic science research findings are providing the groundwork for understanding the mechanisms underlying AUD and have identified multiple candidate targets for ongoing clinical trials. However, the translation of basic research or clinical findings into improved therapeutic approaches for AUD must become more efficient. Translational research is a multistage process of streamlining the movement of basic biomedical research findings into clinical research and then to the clinical target populations. This process demands efficient bidirectional communication across basic, applied, and clinical science as well as with clinical practitioners. Ongoing work suggests rapid progress is being made with an evolving translational framework within the alcohol research field. This is helped by multiple interdisciplinary collaborative research structures that have been developed to advance translational work on AUD. Moreover, the integration of systems biology approaches with collaborative clinical studies may yield novel insights for future translational success. Finally, appreciation of genetic variation in pharmacological or behavioral treatment responses and optimal communication from bench to bedside and back may strengthen the success of translational research applications to AUD. PMID:26259085

Translating Alcohol Research: Opportunities and Challenges.

PubMed

Batman, Angela M; Miles, Michael F

2015-01-01

Alcohol use disorder (AUD) and its sequelae impose a major burden on the public health of the United States, and adequate long-term control of this disorder has not been achieved. Molecular and behavioral basic science research findings are providing the groundwork for understanding the mechanisms underlying AUD and have identified multiple candidate targets for ongoing clinical trials. However, the translation of basic research or clinical findings into improved therapeutic approaches for AUD must become more efficient. Translational research is a multistage process of stream-lining the movement of basic biomedical research findings into clinical research and then to the clinical target populations. This process demands efficient bidirectional communication across basic, applied, and clinical science as well as with clinical practitioners. Ongoing work suggests rapid progress is being made with an evolving translational framework within the alcohol research field. This is helped by multiple interdisciplinary collaborative research structures that have been developed to advance translational work on AUD. Moreover, the integration of systems biology approaches with collaborative clinical studies may yield novel insights for future translational success. Finally, appreciation of genetic variation in pharmacological or behavioral treatment responses and optimal communication from bench to bedside and back may strengthen the success of translational research applications to AUD.

Summary of ongoing TARDEC Work in Metamaterials Relevant to NATO SET-181

DTIC Science & Technology

2013-08-21

Meitzler, T., Bankowski, E., Tiberkevich, T., and Slavin, A., Book Chapter on Spin-Torque Microwave Detectors, Magnonics - From Fundamentals to...harvesting - spintronic metamaterials; Non-reciprocity without magnetic field – magnonic metamaterials; Stealth and cloaking – optical metamaterials.

Leading to Transgress: Critical Considerations for Transforming Leadership Learning.

PubMed

Osteen, Laura; Guthrie, Kathy L; Jones, Tamara Bertrand

2016-12-01

The culturally relevant leadership learning (CRLL) model is explored through the lens of theory and practice. This creates critical questions to guide leadership educators in the ongoing process of transforming leadership programs. © 2016 Wiley Periodicals, Inc., A Wiley Company.

Readiness of ethics review systems for a changing public health landscape in the WHO African Region.

PubMed

Motari, Marion; Ota, Martin Okechukwu; Kirigia, Joses Muthuri

2015-12-02

The increasing emphasis on research, development and innovation for health in providing solutions to the high burden of diseases in the African Region has warranted a proliferation of studies including clinical trials. This changing public health landscape requires that countries develop adequate ethics review capacities to protect and minimize risks to study participants. Therefore, this study assessed the readiness of national ethics committees to respond to challenges posed by a globalized biomedical research system which is constantly challenged by new public health threats, rapid scientific and technological advancements affecting biomedical research and development, delivery and manufacture of vaccines and therapies, and health technology transfer. This is a descriptive study, which used a questionnaire structured to elicit information on the existence of relevant national legal frameworks, mechanisms for ethical review; as well as capacity requirements for national ethics committees. The questionnaire was available in English and French and was sent to 41 of the then 46 Member States of the WHO African Region, excluding the five Lusophone Member States. Information was gathered from senior officials in ministries of health, who by virtue of their offices were considered to have expert knowledge of research ethics review systems in their respective countries. Thirty three of the 41 countries (80.5 %) responded. Thirty (90.9 %) of respondent countries had a national ethics review committee (NEC); 79 % of which were established by law. Twenty-five (83.3 %) NECs had secretarial and administrative support. Over 50 % of countries with NECs indicated a need for capacity strengthening through periodic training on international guidelines for health research (including clinical trials) ethics; and allocation of funds for administrative and secretariat support. Despite the existing training initiatives, the Region still experiences a shortage of professionals trained in health research ethics/ethicists. Committees continue to face various capacity needs especially for evaluating clinical trials, for monitoring ongoing research, database management and for accrediting institutional ethics committees. Given the growing number of clinical trials involving human participants in the African Region, there is urgent need for supporting countries without NECs to establish them; capacity strengthening where they exist; and creation of a regional network and joint ethical review mechanisms, whose membership would be open to all NECs of the Region.

Automation and apps for clinical dental biomechanics.

PubMed

Adams, Bruce W

2016-09-01

The aim of this research summary is to introduce the current and ongoing work using smartphone video, tracking markers to measure musculoskeletal disorders of cranial and mandibular origin, and the potential significance of the technology to doctors and therapists. The MPA™ biomechanical measuring apps are in beta trials with various doctors and therapists. The technique requires substantial image processing and statistical analysis, best suited to server-side processing. A smartphone environment has enabled a virtual laboratory, which provides automated generation of graphics and in some cases automated interpretation. The system enables highly accurate real-time biomechanics studies using only a smartphone and tracking markers. Despite the technical challenges in setting up and testing of the virtual environment and with interpretation of clinical relevance, the trials have enabled a demonstration of real-time biomechanics studies. The technology has prompted a lot of discussion about the relevance of rapid assessment tools in clinical practice. It seems that a prior bias against motion tracking and its relevance is very strong with occlusion related use cases, yet there has been a general agreement about the use case for cranial movement tracking in managing complex issues related to the head, neck, and TMJ. Measurement of cranial and mandibular functions using a smartphone video as the input have been investigated. Ongoing research will depend upon doctors and therapists to provide feedback as to which uses are considered clinically relevant.

Social Justice in Medical Education: Strengths and Challenges of a Student-Driven Social Justice Curriculum

PubMed Central

Andaya, January M; Yamada, Seiji; Maskarinec, Gregory G

2014-01-01

In the current rapidly evolving healthcare environment of the United States, social justice programs in pre-medical and medical education are needed to cultivate socially conscious and health professionals inclined to interdisciplinary collaborations. To address ongoing healthcare inequalities, medical education must help medical students to become physicians skilled not only in the biomedical management of diseases, but also in identifying and addressing social and structural determinants of the patients' daily lives. Using a longitudinal Problem-Based Learning (PBL) methodology, the medical students and faculty advisers at the University of Hawai‘i John A. Burns School of Medicine (JABSOM) developed the Social Justice Curriculum Program (SJCP) to supplement the biomedical curriculum. The SJCP consists of three components: (1) active self-directed learning and didactics, (2) implementation and action, and (3) self-reflection and personal growth. The purpose of introducing a student-driven SJ curriculum is to expose the students to various components of SJ in health and medicine, and maximize engagement by using their own inputs for content and design. It is our hope that the SJCP will serve as a logistic and research-oriented model for future student-driven SJ programs that respond to global health inequalities by cultivating skills and interest in leadership and community service. PMID:25157325

An Ebola virus-centered knowledge base

PubMed Central

Kamdar, Maulik R.; Dumontier, Michel

2015-01-01

Ebola virus (EBOV), of the family Filoviridae viruses, is a NIAID category A, lethal human pathogen. It is responsible for causing Ebola virus disease (EVD) that is a severe hemorrhagic fever and has a cumulative death rate of 41% in the ongoing epidemic in West Africa. There is an ever-increasing need to consolidate and make available all the knowledge that we possess on EBOV, even if it is conflicting or incomplete. This would enable biomedical researchers to understand the molecular mechanisms underlying this disease and help develop tools for efficient diagnosis and effective treatment. In this article, we present our approach for the development of an Ebola virus-centered Knowledge Base (Ebola-KB) using Linked Data and Semantic Web Technologies. We retrieve and aggregate knowledge from several open data sources, web services and biomedical ontologies. This knowledge is transformed to RDF, linked to the Bio2RDF datasets and made available through a SPARQL 1.1 Endpoint. Ebola-KB can also be explored using an interactive Dashboard visualizing the different perspectives of this integrated knowledge. We showcase how different competency questions, asked by domain users researching the druggability of EBOV, can be formulated as SPARQL Queries or answered using the Ebola-KB Dashboard. Database URL: http://ebola.semanticscience.org. PMID:26055098

An Ebola virus-centered knowledge base.

PubMed

Kamdar, Maulik R; Dumontier, Michel

2015-01-01

Ebola virus (EBOV), of the family Filoviridae viruses, is a NIAID category A, lethal human pathogen. It is responsible for causing Ebola virus disease (EVD) that is a severe hemorrhagic fever and has a cumulative death rate of 41% in the ongoing epidemic in West Africa. There is an ever-increasing need to consolidate and make available all the knowledge that we possess on EBOV, even if it is conflicting or incomplete. This would enable biomedical researchers to understand the molecular mechanisms underlying this disease and help develop tools for efficient diagnosis and effective treatment. In this article, we present our approach for the development of an Ebola virus-centered Knowledge Base (Ebola-KB) using Linked Data and Semantic Web Technologies. We retrieve and aggregate knowledge from several open data sources, web services and biomedical ontologies. This knowledge is transformed to RDF, linked to the Bio2RDF datasets and made available through a SPARQL 1.1 Endpoint. Ebola-KB can also be explored using an interactive Dashboard visualizing the different perspectives of this integrated knowledge. We showcase how different competency questions, asked by domain users researching the druggability of EBOV, can be formulated as SPARQL Queries or answered using the Ebola-KB Dashboard. © The Author(s) 2015. Published by Oxford University Press.

High-throughput literature mining to support read-across ...

EPA Pesticide Factsheets

Building scientific confidence in the development and evaluation of read-across remains an ongoing challenge. Approaches include establishing systematic frameworks to identify sources of uncertainty and ways to address them. One source of uncertainty is related to characterizing biological similarity. Many research efforts are underway such as structuring mechanistic data in adverse outcome pathways and investigating the utility of high throughput (HT)/high content (HC) screening data. A largely untapped resource for read-across to date is the biomedical literature. This information has the potential to support read-across by facilitating the identification of valid source analogues with similar biological and toxicological profiles as well as providing the mechanistic understanding for any prediction made. A key challenge in using biomedical literature is to convert and translate its unstructured form into a computable format that can be linked to chemical structure. We developed a novel text-mining strategy to represent literature information for read across. Keywords were used to organize literature into toxicity signatures at the chemical level. These signatures were integrated with HT in vitro data and curated chemical structures. A rule-based algorithm assessed the strength of the literature relationship, providing a mechanism to rank and visualize the signature as literature ToxPIs (LitToxPIs). LitToxPIs were developed for over 6,000 chemicals for a varie

[Attendance and the change in the praxis of rehabilitation: a study of Centers of Reference in Rehabilitation in the network of the Unified Health System in Belo Horizonte, State of Minas Gerais, Brazil].

PubMed

Mitre, Sandra Minardi; Andrade, Eli Iola Gurgel; Cotta, Rosângela Minardi Mitre

2013-07-01

The rehabilitation centers have emerged and become legitimized in the biomedical model, which from the implementation of attendance, namely the operational guidelines of the national policy of humanization in care and management of the Unified Health System (SUS), have been seeking changes to ensure humanized access and the resolution of health problems. The aim of this study was to analyze the attendance in Rehabilitation Centers of Reference (CCR) of SUS in Belo Horizonte (MG), from the perspectives of professionals and patients. Using a qualitative approach, the research was carried out from August 9 to December 27, 2010, in three CRRs. For data collection, focus groups were conducted with 21 professionals and interviews with 30 patients. This study showed that the current biomedical model in the view of professionals restricts its activities in attendance, limiting the participation and autonomy of patients. The attendance has led to reflections and questions when broadening the vision and governability of the teams. The results reveal the need to equip teams for the construction of innovative practices through ongoing education and the creation of protected spaces for reflection and discussion.

Bias in the reporting of sex and age in biomedical research on mouse models

PubMed Central

Flórez-Vargas, Oscar; Brass, Andy; Karystianis, George; Bramhall, Michael; Stevens, Robert; Cruickshank, Sheena; Nenadic, Goran

2016-01-01

In animal-based biomedical research, both the sex and the age of the animals studied affect disease phenotypes by modifying their susceptibility, presentation and response to treatment. The accurate reporting of experimental methods and materials, including the sex and age of animals, is essential so that other researchers can build on the results of such studies. Here we use text mining to study 15,311 research papers in which mice were the focus of the study. We find that the percentage of papers reporting the sex and age of mice has increased over the past two decades: however, only about 50% of the papers published in 2014 reported these two variables. We also compared the quality of reporting in six preclinical research areas and found evidence for different levels of sex-bias in these areas: the strongest male-bias was observed in cardiovascular disease models and the strongest female-bias was found in infectious disease models. These results demonstrate the ability of text mining to contribute to the ongoing debate about the reproducibility of research, and confirm the need to continue efforts to improve the reporting of experimental methods and materials. DOI: http://dx.doi.org/10.7554/eLife.13615.001 PMID:26939790

Social justice in medical education: strengths and challenges of a student-driven social justice curriculum.

PubMed

Ambrose, Adrian Jacques H; Andaya, January M; Yamada, Seiji; Maskarinec, Gregory G

2014-08-01

In the current rapidly evolving healthcare environment of the United States, social justice programs in pre-medical and medical education are needed to cultivate socially conscious and health professionals inclined to interdisciplinary collaborations. To address ongoing healthcare inequalities, medical education must help medical students to become physicians skilled not only in the biomedical management of diseases, but also in identifying and addressing social and structural determinants of the patients' daily lives. Using a longitudinal Problem-Based Learning (PBL) methodology, the medical students and faculty advisers at the University of Hawai'i John A. Burns School of Medicine (JABSOM) developed the Social Justice Curriculum Program (SJCP) to supplement the biomedical curriculum. The SJCP consists of three components: (1) active self-directed learning and didactics, (2) implementation and action, and (3) self-reflection and personal growth. The purpose of introducing a student-driven SJ curriculum is to expose the students to various components of SJ in health and medicine, and maximize engagement by using their own inputs for content and design. It is our hope that the SJCP will serve as a logistic and research-oriented model for future student-driven SJ programs that respond to global health inequalities by cultivating skills and interest in leadership and community service.

Evaluation Metrics for Biostatistical and Epidemiological Collaborations

PubMed Central

Rubio, Doris McGartland; del Junco, Deborah J.; Bhore, Rafia; Lindsell, Christopher J.; Oster, Robert A.; Wittkowski, Knut M.; Welty, Leah J.; Li, Yi-Ju; DeMets, Dave

2011-01-01

Increasing demands for evidence-based medicine and for the translation of biomedical research into individual and public health benefit have been accompanied by the proliferation of special units that offer expertise in biostatistics, epidemiology, and research design (BERD) within academic health centers. Objective metrics that can be used to evaluate, track, and improve the performance of these BERD units are critical to their successful establishment and sustainable future. To develop a set of reliable but versatile metrics that can be adapted easily to different environments and evolving needs, we consulted with members of BERD units from the consortium of academic health centers funded by the Clinical and Translational Science Award Program of the National Institutes of Health. Through a systematic process of consensus building and document drafting, we formulated metrics that covered the three identified domains of BERD practices: the development and maintenance of collaborations with clinical and translational science investigators, the application of BERD-related methods to clinical and translational research, and the discovery of novel BERD-related methodologies. In this article, we describe the set of metrics and advocate their use for evaluating BERD practices. The routine application, comparison of findings across diverse BERD units, and ongoing refinement of the metrics will identify trends, facilitate meaningful changes, and ultimately enhance the contribution of BERD activities to biomedical research. PMID:21284015

An open annotation ontology for science on web 3.0

PubMed Central

2011-01-01

Background There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Methods Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. Results This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables “stand-off” or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO’s Google Code page: http://code.google.com/p/annotation-ontology/ . Conclusions The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors. PMID:21624159

An open annotation ontology for science on web 3.0.

PubMed

Ciccarese, Paolo; Ocana, Marco; Garcia Castro, Leyla Jael; Das, Sudeshna; Clark, Tim

2011-05-17

There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables "stand-off" or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO's Google Code page: http://code.google.com/p/annotation-ontology/ . The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors.

Super-oxidation of silicon nanoclusters: magnetism and reactive oxygen species at the surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lepeshkin, Sergey; Baturin, Vladimir; Tikhonov, Evgeny

2016-01-01

Oxidation of silicon nanoclusters depending on the temperature and oxygen pressure is explored from first principles using the evolutionary algorithm, and structural and thermodynamic analysis. From our calculations of 90 SinOm clusters we found that under normal conditions oxidation does not stop at the stoichiometric SiO2 composition, as it does in bulk silicon, but goes further placing extra oxygen atoms on the cluster surface. These extra atoms are responsible for light emission, relevant to reactive oxygen species and many of them are magnetic. We argue that the super-oxidation effect is size-independent and discuss its relevance to nanotechnology and miscellaneous applications,more » including biomedical ones.« less

Applications of cobalt ferrite nanoparticles in biomedical nanotechnology.

PubMed

Srinivasan, Sumithra Y; Paknikar, Kishore M; Bodas, Dhananjay; Gajbhiye, Virendra

2018-05-01

Magnetic nanoparticles (MNPs) are very attractive especially for biomedical applications, among which, iron oxide nanoparticles have received substantial attention in the past decade due to the elemental composition that makes them biocompatible and degradable. However recently, other magnetic nanomaterials such as spinel ferrites that can provide improved magnetic properties such as coercivity and anisotropy without compromising on inherent advantages of iron oxide nanoparticles are being researched for better applicability of MNPs. Among various spinel ferrites, cobalt ferrite (CoFe 2 O 4 ) nanoparticles (NPs) are one of the most explored MNPs. Therefore, the intention of this article is to provide a comprehensive review of CoFe 2 O 4 NPs and their inherent properties that make them exceptional candidates, different synthesis methods that influence their properties, and applications of CoFe 2 O 4 NPs and their relevant applications that have been considered in biotechnology and bioengineering.

Representing AIDS in Comics.

PubMed

Czerwiec, M K

2018-02-01

Matthew P. McAllister wrote: "Comic books can and have contributed positively to the discourse about AIDS: images that encourage true education, understanding and compassion can help cope with a biomedical condition which has more than a biomedical relevance" [1]. With this in mind, I combined a 23-narrator oral history and my personal memoir about an inpatient Chicago AIDS hospital unit in my book, Taking Turns: Stories from HIV/AIDS Care Unit 371. In doing so, I built upon the existing rich history of HIV/AIDS in comics, which this article will briefly describe. Although not a comprehensive review of the intersection of AIDS and comics, the book is a tour through influences that proved useful to me. In addition, in making my book, I faced a distinct ethical issue with regard to representing patient experiences with HIV/AIDS, and I describe here how I addressed it. © 2018 American Medical Association. All Rights Reserved.

Essie: A Concept-based Search Engine for Structured Biomedical Text

PubMed Central

Ide, Nicholas C.; Loane, Russell F.; Demner-Fushman, Dina

2007-01-01

This article describes the algorithms implemented in the Essie search engine that is currently serving several Web sites at the National Library of Medicine. Essie is a phrase-based search engine with term and concept query expansion and probabilistic relevancy ranking. Essie’s design is motivated by an observation that query terms are often conceptually related to terms in a document, without actually occurring in the document text. Essie’s performance was evaluated using data and standard evaluation methods from the 2003 and 2006 Text REtrieval Conference (TREC) Genomics track. Essie was the best-performing search engine in the 2003 TREC Genomics track and achieved results comparable to those of the highest-ranking systems on the 2006 TREC Genomics track task. Essie shows that a judicious combination of exploiting document structure, phrase searching, and concept based query expansion is a useful approach for information retrieval in the biomedical domain. PMID:17329729

País de gordos/país de muertos: Obesity, death and nation in biomedical and forensic genetics in Mexico

PubMed Central

García-Deister, Vivette; López-Beltrán, Carlos

2015-01-01

This article provides a comparison between genomic medicine and forensic genetics in Mexico, in light of recent depictions of the nation as a ‘país de gordos’ (country of the fat) and a ‘país de muertos’ (country of the dead). We examine the continuities and ruptures in the public image of genetics in these two areas of attention, health and security, focusing especially on how the relevant publics of genetic science are assembled in each case. Publics of biomedical and forensic genetics are assembled through processes of recruitment and interpellation, in ways that modulate current theorizations of co-production. The comparison also provides a vista onto discussions regarding the involvement of genetics in regimes of governance and citizenship and about the relationship between the state and biopower in a context of perceived health crisis and war-like violence. PMID:27479997

[Computers in biomedical research: I. Analysis of bioelectrical signals].

PubMed

Vivaldi, E A; Maldonado, P

2001-08-01

A personal computer equipped with an analog-to-digital conversion card is able to input, store and display signals of biomedical interest. These signals can additionally be submitted to ad-hoc software for analysis and diagnosis. Data acquisition is based on the sampling of a signal at a given rate and amplitude resolution. The automation of signal processing conveys syntactic aspects (data transduction, conditioning and reduction); and semantic aspects (feature extraction to describe and characterize the signal and diagnostic classification). The analytical approach that is at the basis of computer programming allows for the successful resolution of apparently complex tasks. Two basic principles involved are the definition of simple fundamental functions that are then iterated and the modular subdivision of tasks. These two principles are illustrated, respectively, by presenting the algorithm that detects relevant elements for the analysis of a polysomnogram, and the task flow in systems that automate electrocardiographic reports.

Surface-enhanced Raman scattering biomedical applications of plasmonic colloidal particles.

PubMed

Abalde-Cela, Sara; Aldeanueva-Potel, Paula; Mateo-Mateo, Cintia; Rodríguez-Lorenzo, Laura; Alvarez-Puebla, Ramón A; Liz-Marzán, Luis M

2010-08-06

This review article presents a general view of the recent progress in the fast developing area of surface-enhanced Raman scattering spectroscopy as an analytical tool for the detection and identification of molecular species in very small concentrations, with a particular focus on potential applications in the biomedical area. We start with a brief overview of the relevant concepts related to the choice of plasmonic nanostructures for the design of suitable substrates, their implementation into more complex materials that allow generalization of the method and detection of a wide variety of (bio)molecules and the strategies that can be used for both direct and indirect sensing. In relation to indirect sensing, we devote the final section to a description of SERS-encoded particles, which have found wide application in biomedicine (among other fields), since they are expected to face challenges such as multiplexing and high-throughput screening.

XCEDE: An Extensible Schema For Biomedical Data

PubMed Central

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

2013-01-01

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/ PMID:21479735

Pharmaceutical and biomedical applications of lipid-based nanocarriers.

PubMed

Carbone, Claudia; Leonardi, Antonio; Cupri, Sarha; Puglisi, Giovanni; Pignatello, Rosario

2014-03-01

Increasing attention is being given to lipid nanocarriers (LNs) as drug delivery systems, due to the advantages offered of a higher biocompatibility and lower toxicity compared with polymeric nanoparticles. Many administration routes are being investigated for LNs, including topical, oral and parenteral ones. LNs are also proposed for specific applications such as cancer treatment, gene therapy, diagnosis and medical devices production. However, the high number of published research articles does not match an equal amount of patents. A recent Review of ours, published in Pharmaceutical Patent Analyst, reported the patents proposing novel methods for the production of LNs. This review work discusses recent patents, filed in 2007-2013 and dealing with the industrial applications of lipid-based nanocarriers for the vectorization of therapeutically relevant molecules, as well as biotech products such as proteins, gene material and vaccines, in the pharmaceutical, diagnostic and biomedical areas.

País de gordos/país de muertos: Obesity, death and nation in biomedical and forensic genetics in Mexico.

PubMed

García-Deister, Vivette; López-Beltrán, Carlos

2015-12-01

This article provides a comparison between genomic medicine and forensic genetics in Mexico, in light of recent depictions of the nation as a 'país de gordos' (country of the fat) and a 'país de muertos' (country of the dead). We examine the continuities and ruptures in the public image of genetics in these two areas of attention, health and security, focusing especially on how the relevant publics of genetic science are assembled in each case. Publics of biomedical and forensic genetics are assembled through processes of recruitment and interpellation, in ways that modulate current theorizations of co-production. The comparison also provides a vista onto discussions regarding the involvement of genetics in regimes of governance and citizenship and about the relationship between the state and biopower in a context of perceived health crisis and war-like violence.

Surface-enhanced Raman scattering biomedical applications of plasmonic colloidal particles

PubMed Central

Abalde-Cela, Sara; Aldeanueva-Potel, Paula; Mateo-Mateo, Cintia; Rodríguez-Lorenzo, Laura; Alvarez-Puebla, Ramón A.; Liz-Marzán, Luis M.

2010-01-01

This review article presents a general view of the recent progress in the fast developing area of surface-enhanced Raman scattering spectroscopy as an analytical tool for the detection and identification of molecular species in very small concentrations, with a particular focus on potential applications in the biomedical area. We start with a brief overview of the relevant concepts related to the choice of plasmonic nanostructures for the design of suitable substrates, their implementation into more complex materials that allow generalization of the method and detection of a wide variety of (bio)molecules and the strategies that can be used for both direct and indirect sensing. In relation to indirect sensing, we devote the final section to a description of SERS-encoded particles, which have found wide application in biomedicine (among other fields), since they are expected to face challenges such as multiplexing and high-throughput screening. PMID:20462878

An expanding universe of noncoding RNAs between the poles of basic science and clinical investigations.

PubMed

Weil, Patrick P; Hensel, Kai O; Weber, David; Postberg, Jan

2016-03-01

The Keystone Symposium 'MicroRNAs and Noncoding RNAs in Cancer', Keystone, CO, USA, 7-12 June 2015 Since the discovery of RNAi, great efforts have been undertaken to unleash the potential biomedical applicability of small noncoding RNAs, mainly miRNAs, involving their use as biomarkers for personalized diagnostics or their usability as active agents or therapy targets. The research's focus on the noncoding RNA world is now slowly moving from a phase of basic discoveries into a new phase, where every single molecule out of many hundreds of cataloged noncoding RNAs becomes dissected in order to investigate these molecules' biomedical relevance. In addition, RNA classes neglected before, such as long noncoding RNAs or circular RNAs attract more attention. Numerous timely results and hypotheses were presented at the 2015 Keystone Symposium 'MicroRNAs and Noncoding RNAs in Cancer'.

12 CFR 917.5 - Strategic business plan.

Code of Federal Regulations, 2010 CFR

2010-01-01

... ongoing market research and consultations with members, associates and public and private organizations... quantitative performance goals for Bank products related to multi-family housing, small business, small farm... existing activities; and (5) Be supported by appropriate and timely research and analysis of relevant...

12 CFR 917.5 - Strategic business plan.

Code of Federal Regulations, 2014 CFR

2014-01-01

... ongoing market research and consultations with members, associates and public and private organizations... quantitative performance goals for Bank products related to multi-family housing, small business, small farm... existing activities; and (5) Be supported by appropriate and timely research and analysis of relevant...

12 CFR 917.5 - Strategic business plan.

Code of Federal Regulations, 2013 CFR

2013-01-01

... ongoing market research and consultations with members, associates and public and private organizations... quantitative performance goals for Bank products related to multi-family housing, small business, small farm... existing activities; and (5) Be supported by appropriate and timely research and analysis of relevant...

12 CFR 917.5 - Strategic business plan.

Code of Federal Regulations, 2012 CFR

2012-01-01

... ongoing market research and consultations with members, associates and public and private organizations... quantitative performance goals for Bank products related to multi-family housing, small business, small farm... existing activities; and (5) Be supported by appropriate and timely research and analysis of relevant...

12 CFR 917.5 - Strategic business plan.

Code of Federal Regulations, 2011 CFR

2011-01-01

... ongoing market research and consultations with members, associates and public and private organizations... quantitative performance goals for Bank products related to multi-family housing, small business, small farm... existing activities; and (5) Be supported by appropriate and timely research and analysis of relevant...

Assessment of relevant prior and ongoing research for the concept development and needs identification for integrated dynamic transit operations.

DOT National Transportation Integrated Search

2011-11-01

In support of USDOTs Intelligent Transportation Systems (ITS) Mobility Program, the Dynamic Mobility Applications (DMA) program seeks to create applications that fully leverage frequently collected and rapidly disseminated multi-source data gat...

Research Skills for Gifted Elementary School Pupils.

ERIC Educational Resources Information Center

Lamb, Pose; And Others

1993-01-01

This paper outlines the elementary school gifted pupil's need for instruction in research strategies as an integral part of an ongoing unit. A program is described in which pupils select areas of investigation and participate in gathering, organizing, interpreting, and sharing relevant data. (JDD)

Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance

PubMed Central

2016-01-01

The Cancer Target Discovery and Development (CTD2) Network was established to accelerate the transformation of “Big Data” into novel pharmacological targets, lead compounds, and biomarkers for rapid translation into improved patient outcomes. It rapidly became clear in this collaborative network that a key central issue was to define what constitutes sufficient computational or experimental evidence to support a biologically or clinically relevant finding. This manuscript represents a first attempt to delineate the challenges of supporting and confirming discoveries arising from the systematic analysis of large-scale data resources in a collaborative work environment and to provide a framework that would begin a community discussion to resolve these challenges. The Network implemented a multi-Tier framework designed to substantiate the biological and biomedical relevance as well as the reproducibility of data and insights resulting from its collaborative activities. The same approach can be used by the broad scientific community to drive development of novel therapeutic and biomarker strategies for cancer. PMID:27401613

Critical race theory as a bridge in science training: the California State University, Northridge BUILD PODER program.

PubMed

Saetermoe, Carrie L; Chavira, Gabriela; Khachikian, Crist S; Boyns, David; Cabello, Beverly

2017-01-01

Unconscious bias and explicit forms of discrimination continue to pervade academic institutions. Multicultural and diversity training activities have not been sufficient in making structural and social changes leading to equity, therefore, a new form of critical consciousness is needed to train diverse scientists with new research questions, methods, and perspectives. The purpose of this paper is to describe Building Infrastructure Leading to Diversity (BUILD); Promoting Opportunities for Diversity in Education and Research (PODER), which is an undergraduate biomedical research training program based on transformative framework rooted in Critical Race Theory (CRT). By employing a CRT-informed curriculum and training in BUILD PODER, students are empowered not only to gain access but also to thrive in graduate programs and beyond. Poder means "power" or "to be able to" in Spanish. Essentially, we are "building power" using students' strengths and empowering them as learners. The new curriculum helps students understand institutional policies and practices that may prevent them from persisting in higher education, learn to become their own advocates, and successfully confront social barriers and instances of inequities and discrimination. To challenge these barriers and sustain campus changes in support of students, BUILD PODER works toward changing campus culture and research mentoring relationships. By joining with ongoing university structures such as the state university Graduation Initiative, we include CRT tenets into the campus dialogue and stimulate campus-wide discussions around institutional change. Strong ties with five community college partners also enrich BUILD PODER's student body and strengthen mentor diversity. Preliminary evaluation data suggest that BUILD PODER's program has enhanced the racial/ethnic consciousness of the campus community, is effective in encouraging more egalitarian and respectful faculty-student relationships, and is a rigorous program of biomedical research training that supports students as they achieve their goals. Biomedical research programs may benefit from a reanalysis of the fit between current training programs and student strengths. By incorporating the voices of talented youth, drawing upon their native strengths, we will generate a new science that links biomedical research to community health and social justice, generating progress toward health equity through a promising new generation of scholars.

Understanding the Structure-Function Relationships of Dendrimers in Environmental and Biomedical Applications

NASA Astrophysics Data System (ADS)

Wang, Bo

We are living an era wherein nanoparticles (NPs) have been widely applied in our lives. Dendrimers are special polymeric NPs with unique physiochemical properties, which have been intensely explored for a variety of applications. Current studies on dendrimers are bottlenecked by insufficient understandings of their structure and dynamic behaviors from a molecular level. With primarily computational approaches supplemented by many other experimental technics, this dissertation aims to establish structure-function relationships of dendrimers in environmental and biomedical applications. More specifically, it thoroughly investigates the interactions between dendrimers and different biomolecules including carbon-based NPs, metal-based NPs, and proteins/peptides. Those results not only provide profound knowledge for evaluating the impacts of dendrimers on environmental and biological systems but also facilitate designing next-generation functional polymeric nanomaterials. The dissertation is organized as following. Chapter 1 provides an overview of current progresses on dendrimer studies, where methodology of Discrete Molecular Dynamics (DMD), my major research tool, is also introduced. Two directions of utilizing dendrimers will be discussed in following chapters. Chapter 2 will focus on environmental applications of dendrimers, where two back-to-back studies are presented. I will start from describing some interesting observations from experiments i.e. dendrimers dispersed model oil molecules. Then, I will reveal why surface chemistries of dendrimers lead to different remediation efficiencies by computational modelings. Finally, I will demonstrate different scenarios of dendrimer-small molecules association. Chapter 3 is centered on dendrimers in the biomedical applications including two subtopics. In the first topic, we will discuss dendrimers as surfactants that modulating the interactions between proteins and NPs. Some fundamental concepts regarding to NPs-Protein interactions such as NP-protein corona are also explained. In the following topic, I will look into amyloid protein aggregation mediated by dendrimers, which is of high expectations for combating amyloidogenic-related diseases. Chapter 4 concludes the whole dissertation. It also briefly introduces my ongoing projects and future research directions about dendrimers. This dissertation has presented a systematic study of dendrimers in environmental and biomedical applications which might provide valuable information for future dendrimer design thus benefit the nanobiotechnology.

[Thoughts on the complex relationship between medicine and animals: a death prayer for a loyal cat].

PubMed

Cabello C, Felipe

2013-11-01

From its basis in the writings of the philosopher Peter Singer and the bioethical shortcomings of animal experimentation and animal husbandry, the animal rights movement has evolved into an important societal movement critical of animal experimentation in biomedical research. A lack of dialogue and transparency, an absence of understanding and an unreasonable radicalization of different positions regarding animal experimentation has frequently resulted in an adversarial relationship between some members of the scientific community and societal groups aggressively protecting animal rights. In response to this problem, both the bioethical regulations pertaining to biomedical experimentation with animals and the powers of animal care committees (IACUCs) have been strengthened. Careful analysis of the relevance of animal models to human conditions, replacement of these models with non-animal models when possible, adequate re-examination of existing knowledge before undertaking new experimental projects involving animals, and the improvement of methods to avoid animal stress and pain have further strengthened the bioethical basis of animal experimentation. To improve the ethical integrity of research conducted with animals, it is also necessary to increase the editorial scrutiny of the bioethical standards of potentially publishable research utilizing animals. Of note is also the recent use of animals in alternative animal associated therapies (AAT) to ameliorate several medical conditions. Education of the biomedical community, including students and professionals, and of societal groups concerned about this issue as well as directness and continuous dialogue among all the stakeholders are essential to insure the wellbeing of animals and the ethical integrity of biomedical research.

Nanotubular surface modification of metallic implants via electrochemical anodization technique.

PubMed

Wang, Lu-Ning; Jin, Ming; Zheng, Yudong; Guan, Yueping; Lu, Xin; Luo, Jing-Li

2014-01-01

Due to increased awareness and interest in the biomedical implant field as a result of an aging population, research in the field of implantable devices has grown rapidly in the last few decades. Among the biomedical implants, metallic implant materials have been widely used to replace disordered bony tissues in orthopedic and orthodontic surgeries. The clinical success of implants is closely related to their early osseointegration (ie, the direct structural and functional connection between living bone and the surface of a load-bearing artificial implant), which relies heavily on the surface condition of the implant. Electrochemical techniques for modifying biomedical implants are relatively simple, cost-effective, and appropriate for implants with complex shapes. Recently, metal oxide nanotubular arrays via electrochemical anodization have become an attractive technique to build up on metallic implants to enhance the biocompatibility and bioactivity. This article will thoroughly review the relevance of electrochemical anodization techniques for the modification of metallic implant surfaces in nanoscale, and cover the electrochemical anodization techniques used in the development of the types of nanotubular/nanoporous modification achievable via electrochemical approaches, which hold tremendous potential for bio-implant applications. In vitro and in vivo studies using metallic oxide nanotubes are also presented, revealing the potential of nanotubes in biomedical applications. Finally, an outlook of future growth of research in metallic oxide nanotubular arrays is provided. This article will therefore provide researchers with an in-depth understanding of electrochemical anodization modification and provide guidance regarding the design and tuning of new materials to achieve a desired performance and reliable biocompatibility.

Nanotubular surface modification of metallic implants via electrochemical anodization technique

PubMed Central

Wang, Lu-Ning; Jin, Ming; Zheng, Yudong; Guan, Yueping; Lu, Xin; Luo, Jing-Li

2014-01-01

Due to increased awareness and interest in the biomedical implant field as a result of an aging population, research in the field of implantable devices has grown rapidly in the last few decades. Among the biomedical implants, metallic implant materials have been widely used to replace disordered bony tissues in orthopedic and orthodontic surgeries. The clinical success of implants is closely related to their early osseointegration (ie, the direct structural and functional connection between living bone and the surface of a load-bearing artificial implant), which relies heavily on the surface condition of the implant. Electrochemical techniques for modifying biomedical implants are relatively simple, cost-effective, and appropriate for implants with complex shapes. Recently, metal oxide nanotubular arrays via electrochemical anodization have become an attractive technique to build up on metallic implants to enhance the biocompatibility and bioactivity. This article will thoroughly review the relevance of electrochemical anodization techniques for the modification of metallic implant surfaces in nanoscale, and cover the electrochemical anodization techniques used in the development of the types of nanotubular/nanoporous modification achievable via electrochemical approaches, which hold tremendous potential for bio-implant applications. In vitro and in vivo studies using metallic oxide nanotubes are also presented, revealing the potential of nanotubes in biomedical applications. Finally, an outlook of future growth of research in metallic oxide nanotubular arrays is provided. This article will therefore provide researchers with an in-depth understanding of electrochemical anodization modification and provide guidance regarding the design and tuning of new materials to achieve a desired performance and reliable biocompatibility. PMID:25258532

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

PubMed

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.

Study design and rationale for biomedical shirt-based electrocardiography monitoring in relevant clinical situations: ECG-shirt study.

PubMed

Balsam, Paweł; Lodziński, Piotr; Tymińska, Agata; Ozierański, Krzysztof; Januszkiewicz, Łukasz; Główczyńska, Renata; Wesołowska, Katarzyna; Peller, Michał; Pietrzak, Radosław; Książczyk, Tomasz; Borodzicz, Sonia; Kołtowski, Łukasz; Borkowski, Mariusz; Werner, Bożena; Opolski, Grzegorz; Grabowski, Marcin

2018-01-01

Today, the main challenge for researchers is to develop new technologies which may help to improve the diagnoses of cardiovascular disease (CVD), thereby reducing healthcare costs and improving the quality of life for patients. This study aims to show the utility of biomedical shirt-based electrocardiography (ECG) monitoring of patients with CVD in different clinical situations using the Nuubo® ECG (nECG) system. An investigator-initiated, multicenter, prospective observational study was carried out in a cardiology (adult and pediatric) and cardiac rehabilitation wards. ECG monitoring was used with the biomedical shirt in the following four independent groups of patients: 1) 30 patients after pulmonary vein isolation (PVI), 2) 30 cardiac resynchronization therapy (CRT) recipients, 3) 120 patients during cardiac rehabilitation after myocardial infarction, and 4) 40 pediatric patients with supraventricular tachycardia (SVT) before electrophysiology study. Approval for all study groups was obtained from the institutional review board. The biomedical shirt captures the electrocardiographic signal via textile electrodes integrated into a garment. The software allows the visualization and analysis of data such as ECG, heart rate, arrhythmia detecting algorithm and relative position of the body is captured by an electronic device. The major advantages of the nECG system are continuous ECG monitoring during daily activities, high quality of ECG recordings, as well as assurance of a proper adherence due to adequate comfort while wearing the shirt. There are only a few studies that have examined wearable systems, especially in pediatric populations. This study is registered in ClinicalTrials.gov: Identifier NCT03068169. (Cardiol J 2018; 25, 1: 52-59).

Scientists Still Behaving Badly? A Survey Within Industry and Universities.

PubMed

Godecharle, Simon; Fieuws, Steffen; Nemery, Ben; Dierickx, Kris

2017-10-02

Little is known about research misconduct within industry and how it compares to universities, even though a lot of biomedical research is performed by-or in collaboration with-commercial entities. Therefore, we sent an e-mail invitation to participate in an anonymous computer-based survey to all university researchers having received a biomedical research grant or scholarship from one of the two national academic research funders of Belgium between 2010 and 2014, and to researchers working in large biomedical companies or spin-offs in Belgium. The validated survey included questions about various types of research misconduct committed by respondents themselves and observed among their colleagues in the last three years. Prevalences of misconduct were compared between university and industry respondents using binary logistic regression models, with adjustments for relevant personal characteristics, and with significance being accepted for p < 0.01. The survey was sent to 1766 people within universities and an estimated 255 people from industry. Response rates were 43 (767/1766) and 48% (123/255), and usable information was available for 617 and 100 respondents, respectively. In general, research misconduct was less likely to be reported by industry respondents compared to university respondents. Significant differences were apparent for one admitted action (gift authorship) and three observed actions (plagiarism, gift authorship, and circumventing animal-subjects research requirements), always with lower prevalences for industry compared to universities, except for plagiarism. This survey, based on anonymous self-report, shows that research misconduct occurs to a substantial degree among biomedical researchers from both industry and universities.

Observer properties for understanding dynamical displays: Capacities, limitations, and defaults

NASA Technical Reports Server (NTRS)

Proffitt, Dennis R.; Kaiser, Mary K.

1991-01-01

People's ability to extract relevant information while viewing ongoing events is discussed in terms of human capabilities, limitations, and defaults. A taxonomy of event complexity is developed which predicts which dynamical events people can and cannot construe. This taxonomy is related to the distinction drawn in classical mechanics between particle and extended body motions. People's commonsense understandings of simple mechanical systems are impacted little by formal training, but rather reflect heuristical simplifications that focus on a single dimension of perceived dynamical relevance.

Connecting Advanced and Secondary Mathematics

ERIC Educational Resources Information Center

Murray, Eileen; Baldinger, Erin; Wasserman, Nicholas; Broderick, Shawn; White, Diana

2017-01-01

There is an ongoing debate among scholars in understanding what mathematical knowledge secondary teachers should have in order to provide effective instruction. We explore connections between advanced and secondary mathematics as an entry point into this debate. In many cases, advanced mathematics is considered relevant for secondary teachers…

Concept development and needs identification for Intelligent Network Flow Optimization (INFLO) : assessment of relevant prior and ongoing research.

DOT National Transportation Integrated Search

2012-03-01

Through the USDOT Dynamic Mobility Applications (DMA) program, a number of high-priority mobility applications have been assessed and identified that can connect vehicles, travelers, and infrastructure in order to provide better information to travel...

The Art of Influencing Decision Makers.

ERIC Educational Resources Information Center

Diegmueller, Karen

1992-01-01

Influencing educational decision makers requires creating ongoing relationships, keeping everyone informed, and developing persuasive skills. Persuasion requires preparation, refinement, hard work, and a sound understanding of the people being lobbied. Lobbying must be factual and relevant to the audience. The article looks at influence from the…

Eye movements provide insights into the conscious use of context in prospective memory.

PubMed

Bowden, Vanessa K; Smith, Rebekah E; Loft, Shayne

2017-07-01

Prior research examining the impact of context on prospective memory (PM) has produced mixed results. Our study aimed to determine whether providing progressive context information could increase PM accuracy and reduce costs to ongoing tasks. Seventy-two participants made ongoing true/false judgements for simple sentences while maintaining a PM intention to respond differently to four memorised words. The context condition were informed of the trial numbers where PM targets could appear, and eye-tracking recorded trial number fixation frequency. The context condition showed reduced costs during irrelevant contexts, increased costs during relevant contexts, and had better PM accuracy compared to a standard condition that was not provided with context. The context condition also made an increasing number of trial number fixations leading up to relevant contexts, indicating the conscious use of context. Furthermore, this trial number checking was beneficial to PM, with participants who checked more frequently having better PM accuracy. Copyright © 2017 Elsevier Inc. All rights reserved.

Cataloging the biomedical world of pain through semi-automated curation of molecular interactions

PubMed Central

Jamieson, Daniel G.; Roberts, Phoebe M.; Robertson, David L.; Sidders, Ben; Nenadic, Goran

2013-01-01

The vast collection of biomedical literature and its continued expansion has presented a number of challenges to researchers who require structured findings to stay abreast of and analyze molecular mechanisms relevant to their domain of interest. By structuring literature content into topic-specific machine-readable databases, the aggregate data from multiple articles can be used to infer trends that can be compared and contrasted with similar findings from topic-independent resources. Our study presents a generalized procedure for semi-automatically creating a custom topic-specific molecular interaction database through the use of text mining to assist manual curation. We apply the procedure to capture molecular events that underlie ‘pain’, a complex phenomenon with a large societal burden and unmet medical need. We describe how existing text mining solutions are used to build a pain-specific corpus, extract molecular events from it, add context to the extracted events and assess their relevance. The pain-specific corpus contains 765 692 documents from Medline and PubMed Central, from which we extracted 356 499 unique normalized molecular events, with 261 438 single protein events and 93 271 molecular interactions supplied by BioContext. Event chains are annotated with negation, speculation, anatomy, Gene Ontology terms, mutations, pain and disease relevance, which collectively provide detailed insight into how that event chain is associated with pain. The extracted relations are visualized in a wiki platform (wiki-pain.org) that enables efficient manual curation and exploration of the molecular mechanisms that underlie pain. Curation of 1500 grouped event chains ranked by pain relevance revealed 613 accurately extracted unique molecular interactions that in the future can be used to study the underlying mechanisms involved in pain. Our approach demonstrates that combining existing text mining tools with domain-specific terms and wiki-based visualization can facilitate rapid curation of molecular interactions to create a custom database. Database URL: ••• PMID:23707966

Cataloging the biomedical world of pain through semi-automated curation of molecular interactions.

PubMed

Jamieson, Daniel G; Roberts, Phoebe M; Robertson, David L; Sidders, Ben; Nenadic, Goran

2013-01-01

The vast collection of biomedical literature and its continued expansion has presented a number of challenges to researchers who require structured findings to stay abreast of and analyze molecular mechanisms relevant to their domain of interest. By structuring literature content into topic-specific machine-readable databases, the aggregate data from multiple articles can be used to infer trends that can be compared and contrasted with similar findings from topic-independent resources. Our study presents a generalized procedure for semi-automatically creating a custom topic-specific molecular interaction database through the use of text mining to assist manual curation. We apply the procedure to capture molecular events that underlie 'pain', a complex phenomenon with a large societal burden and unmet medical need. We describe how existing text mining solutions are used to build a pain-specific corpus, extract molecular events from it, add context to the extracted events and assess their relevance. The pain-specific corpus contains 765 692 documents from Medline and PubMed Central, from which we extracted 356 499 unique normalized molecular events, with 261 438 single protein events and 93 271 molecular interactions supplied by BioContext. Event chains are annotated with negation, speculation, anatomy, Gene Ontology terms, mutations, pain and disease relevance, which collectively provide detailed insight into how that event chain is associated with pain. The extracted relations are visualized in a wiki platform (wiki-pain.org) that enables efficient manual curation and exploration of the molecular mechanisms that underlie pain. Curation of 1500 grouped event chains ranked by pain relevance revealed 613 accurately extracted unique molecular interactions that in the future can be used to study the underlying mechanisms involved in pain. Our approach demonstrates that combining existing text mining tools with domain-specific terms and wiki-based visualization can facilitate rapid curation of molecular interactions to create a custom database. Database URL: •••

Reproducibility of results in preclinical studies: a perspective from the bone field.

PubMed

Manolagas, Stavros C; Kronenberg, Henry M

2014-10-01

The biomedical research enterprise-and the public support for it-is predicated on the belief that discoveries and the conclusions drawn from them can be trusted to build a body of knowledge which will be used to improve human health. As in all other areas of scientific inquiry, knowledge and understanding grow by layering new discoveries upon earlier ones. The process self-corrects and distills knowledge by discarding false ideas and unsubstantiated claims. Although self-correction is inexorable in the long-term, in recent years biomedical scientists and the public alike have become alarmed and deeply troubled by the fact that many published results cannot be reproduced. The chorus of concern reached a high pitch with a recent commentary from the NIH Director, Francis S. Collins, and Principal Deputy Director, Lawrence A. Tabak, and their announcement of specific plans to enhance reproducibility of preclinical research that relies on animal models. In this invited perspective, we highlight the magnitude of the problem across biomedical fields and address the relevance of these concerns to the field of bone and mineral metabolism. We also suggest how our specialty journals, our scientific organizations, and our community of bone and mineral researchers can help to overcome this troubling trend. © 2014 American Society for Bone and Mineral Research.

The limitations of 'Black MSM' as a category: Why gender, sexuality, and desire still matter for social and biomedical HIV prevention methods.

PubMed

Garcia, Jonathan; Parker, Richard G; Parker, Caroline; Wilson, Patrick A; Philbin, Morgan; Hirsch, Jennifer S

2016-01-01

The USA faces disproportionate and increasing HIV incidence rates among Black men who have sex with men (BMSM). New biomedical technologies such as pre-exposure prophylaxis (PrEP) have been developed to address their HIV risk. Very little consideration, however, has been given to the diversity obscured by 'BMSM' as a category, to how this diversity relates to men's sexual partnering strategies, or to the relevance of these issues for new HIV prevention methods. We conducted a community-based ethnography from June 2013 to May 2014 documenting factors that affect the acceptance of and adherence to PrEP among BMSM. We conducted in-depth interviews with 31 BMSM and 17 community stakeholders, and participant observation. To demonstrate the diversity of social identities, we present a taxonomy of indigenous categories organised along the axes of sexual identity, sexual positioning, and gender performance. We analyse how HIV prevention strategies, such as PrEP, may be more effective if programmes consider how gender, sexuality, and sexual desire shape sexual partnering strategies. This article underlines the importance of attending to the diversity of sexual and social subjectivities among BMSM, of bringing the study of sexuality back into HIV prevention, and of integrating biomedical prevention approaches into community-based programmes.

Introducing Kuhn et al.'s paper "Informatics and medicine: from molecules to populations" and invited papers on this special topic.

PubMed

Kulikowski, C A

2008-01-01

To introduce the paper by Kuhn et al. "Informatics and Medicine: From Molecules to Populations" and the papers that follow on this special topic in this issue of Methods of Information in Medicine, which opens a debate on the Kuhn et al. paper's assertions by an international panel of invited researchers in biomedical informatics. An introductory summary and comparative review of the Kuhn et al. paper and the debate papers, with some personal observations. The Kuhn et al. paper makes a strong case for interdisciplinary education in biomedical informatics across institutions at the graduate level, which could be strengthened by analysis of previous relevant interdisciplinary experiences elsewhere, and the challenges they have faced, which point to more pervasive and earlier-stage needs for both education and practice bridging the research and healthcare communities. The experts debating the Kuhn et al. paper strongly and broadly support the key recommendation of developing graduate education in biomedical informatics in a more comprehensive way, yet at the same time make some incisive comments about the limitations of the "positivistic" and excessively technological orientation of the paper, which could benefit from greater attention to the narrative and care-giving aspects of health practice, with more emphasis on its human and social aspects.

Biologically Relevant Heterogeneity: Metrics and Practical Insights

PubMed Central

Gough, A; Stern, AM; Maier, J; Lezon, T; Shun, T-Y; Chennubhotla, C; Schurdak, ME; Haney, SA; Taylor, DL

2017-01-01

Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications including basic biomedical research, drug discovery, diagnostics and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell level data, as well as the need for standard metrics of the spatial, temporal and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics and the design of optimal therapeutic strategies for individual patients. PMID:28231035

Supramolecular Biofunctional Materials

PubMed Central

Zhou, Jie; Li, Jie; Du, Xuewen; Xu, Bing

2017-01-01

This review discusses supramolecular biofunctional materials, a novel class of biomaterials formed by small molecules that are held together via noncovalent interactions. The complexity of biology and relevant biomedical problems not only inspire, but also demand effective molecular design for functional materials. Supramolecular biofunctional materials offer (almost) unlimited possibilities and opportunities to address challenging biomedical problems. Rational molecular design of supramolecular biofunctional materials exploit powerful and versatile noncovalent interactions, which offer many advantages, such as responsiveness, reversibility, tunability, biomimicry, modularity, predictability, and, most importantly, adaptiveness. In this review, besides elaborating on the merits of supramolecular biofunctional materials (mainly in the form of hydrogels and/or nanoscale assemblies) resulting from noncovalent interactions, we also discuss the advantages of small peptides as a prevalent molecular platform to generate a wide range of supramolecular biofunctional materials for the applications in drug delivery, tissue engineering, immunology, cancer therapy, fluorescent imaging, and stem cell regulation. This review aims to provide a brief synopsis of recent achievements at the intersection of supramolecular chemistry and biomedical science in hope of contributing to the multidisciplinary research on supramolecular biofunctional materials for a wide range of applications. We envision that supramolecular biofunctional materials will contribute to the development of new therapies that will ultimately lead to a paradigm shift for developing next generation biomaterials for medicine. PMID:28319779

Supramolecular biofunctional materials.

PubMed

Zhou, Jie; Li, Jie; Du, Xuewen; Xu, Bing

2017-06-01

This review discusses supramolecular biofunctional materials, a novel class of biomaterials formed by small molecules that are held together via noncovalent interactions. The complexity of biology and relevant biomedical problems not only inspire, but also demand effective molecular design for functional materials. Supramolecular biofunctional materials offer (almost) unlimited possibilities and opportunities to address challenging biomedical problems. Rational molecular design of supramolecular biofunctional materials exploit powerful and versatile noncovalent interactions, which offer many advantages, such as responsiveness, reversibility, tunability, biomimicry, modularity, predictability, and, most importantly, adaptiveness. In this review, besides elaborating on the merits of supramolecular biofunctional materials (mainly in the form of hydrogels and/or nanoscale assemblies) resulting from noncovalent interactions, we also discuss the advantages of small peptides as a prevalent molecular platform to generate a wide range of supramolecular biofunctional materials for the applications in drug delivery, tissue engineering, immunology, cancer therapy, fluorescent imaging, and stem cell regulation. This review aims to provide a brief synopsis of recent achievements at the intersection of supramolecular chemistry and biomedical science in hope of contributing to the multidisciplinary research on supramolecular biofunctional materials for a wide range of applications. We envision that supramolecular biofunctional materials will contribute to the development of new therapies that will ultimately lead to a paradigm shift for developing next generation biomaterials for medicine. Copyright © 2017 Elsevier Ltd. All rights reserved.

Encouraging minority undergraduates to choose science careers: career paths survey results.

PubMed

Villarejo, Merna; Barlow, Amy E L; Kogan, Deborah; Veazey, Brian D; Sweeney, Jennifer K

2008-01-01

To explore the reasons for the dearth of minorities in Ph.D.-level biomedical research and identify opportunities to increase minority participation, we surveyed high-achieving alumni of an undergraduate biology enrichment program for underrepresented minorities. Respondents were asked to describe their career paths and to reflect on the influences that guided their career choices. We particularly probed for attitudes and experiences that influenced students to pursue a research career, as well as factors relevant to their choice between medicine (the dominant career choice) and basic science. In agreement with earlier studies, alumni strongly endorsed supplemental instruction as a mechanism for achieving excellence in basic science courses. Undergraduate research was seen as broadening by many and was transformative for half of the alumni who ultimately decided to pursue Ph.D.s in biomedical research. That group had expressed no interest in research careers at college entry and credits their undergraduate research experience with putting them on track toward a research career. A policy implication of these results is that making undergraduate research opportunities widely available to biology students (including "premed" students) in the context of a structured educational enrichment program should increase the number of minority students who choose to pursue biomedical Ph.D.s.

[Bioethical considerations in the approach to patients with amyotrophic lateral sclerosis].

PubMed

Calzada Sierra, D J

The traditional doctor-patient relation has become a great bioethical challenge due to the advances in science in recent years. This is particularly true when patients suffer diseases such as amyotrophic lateral sclerosis (ALS), a neurodegenerative disease with a relentless course and in spite of modern treatment 50% of the patients die within three years of first having symptoms of the disease. It therefore causes great psychological and social impact. To analyze the great bioethical challenge which arises when diagnosing and treating a patient with ALS. In this paper we analyze the doctor-patient relationship, the principles of doing no harm and of being beneficial, and more modern concepts such as informed consent, biomedical investigations and euthanasia, as well as the importance of palliative medicine and rehabilitation to alleviate suffering and improve quality of life. Biomedical investigations should conform to the relevant national and international rules. We discuss the right of patients to be given truthful information. We recommend better training of doctors in all aspects of attention to these patients, with emphasis on the diagnosis and importance of rehabilitation, palliative medicine and the management of psychological aspects. Biomedical investigations should fulfil current regulations. We recommend discretion, complete or partial, with regard to information given to the patients and their relatives so as not to cause despair.

Feasibility study for a biomedical experimental facility based on LEIR at CERN.

PubMed

Abler, Daniel; Garonna, Adriano; Carli, Christian; Dosanjh, Manjit; Peach, Ken

2013-07-01

In light of the recent European developments in ion beam therapy, there is a strong interest from the biomedical research community to have more access to clinically relevant beams. Beamtime for pre-clinical studies is currently very limited and a new dedicated facility would allow extensive research into the radiobiological mechanisms of ion beam radiation and the development of more refined techniques of dosimetry and imaging. This basic research would support the current clinical efforts of the new treatment centres in Europe (for example HIT, CNAO and MedAustron). This paper presents first investigations on the feasibility of an experimental biomedical facility based on the CERN Low Energy Ion Ring LEIR accelerator. Such a new facility could provide beams of light ions (from protons to neon ions) in a collaborative and cost-effective way, since it would rely partly on CERN's competences and infrastructure. The main technical challenges linked to the implementation of a slow extraction scheme for LEIR and to the design of the experimental beamlines are described and first solutions presented. These include introducing new extraction septa into one of the straight sections of the synchrotron, changing the power supply configuration of the magnets, and designing a new horizontal beamline suitable for clinical beam energies, and a low-energy vertical beamline for particular radiobiological experiments.

Feasibility study for a biomedical experimental facility based on LEIR at CERN

PubMed Central

Abler, Daniel; Garonna, Adriano; Carli, Christian; Dosanjh, Manjit; Peach, Ken

2013-01-01

In light of the recent European developments in ion beam therapy, there is a strong interest from the biomedical research community to have more access to clinically relevant beams. Beamtime for pre-clinical studies is currently very limited and a new dedicated facility would allow extensive research into the radiobiological mechanisms of ion beam radiation and the development of more refined techniques of dosimetry and imaging. This basic research would support the current clinical efforts of the new treatment centres in Europe (for example HIT, CNAO and MedAustron). This paper presents first investigations on the feasibility of an experimental biomedical facility based on the CERN Low Energy Ion Ring LEIR accelerator. Such a new facility could provide beams of light ions (from protons to neon ions) in a collaborative and cost-effective way, since it would rely partly on CERN's competences and infrastructure. The main technical challenges linked to the implementation of a slow extraction scheme for LEIR and to the design of the experimental beamlines are described and first solutions presented. These include introducing new extraction septa into one of the straight sections of the synchrotron, changing the power supply configuration of the magnets, and designing a new horizontal beamline suitable for clinical beam energies, and a low-energy vertical beamline for particular radiobiological experiments. PMID:23824122

Insights into the virulence of oral biofilms: discoveries from proteomics.

PubMed

Kuboniwa, Masae; Tribble, Gena D; Hendrickson, Erik L; Amano, Atsuo; Lamont, Richard J; Hackett, Murray

2012-06-01

This review covers developments in the study of polymicrobial communities, biofilms and selected areas of host response relevant to dental plaque and related areas of oral biology. The emphasis is on recent studies in which proteomic methods, particularly those using mass spectrometry as a readout, have played a major role in the investigation. The last 5-10 years have seen a transition of such methods from the periphery of oral biology to the mainstream, as in other areas of biomedical science. For reasons of focus and space, the authors do not discuss biomarker studies relevant to improved diagnostics for oral health, as this literature is rather substantial in its own right and deserves a separate treatment. Here, global gene regulation studies of plaque-component organisms, biofilm formation, multispecies interactions and host-microbe interactions are discussed. Several aspects of proteomics methodology that are relevant to the studies of multispecies systems are commented upon.

TU-F-BRD-01: Biomedical Informatics for Medical Physicists

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phillips, M; Kalet, I; McNutt, T

Biomedical informatics encompasses a very large domain of knowledge and applications. This broad and loosely defined field can make it difficult to navigate. Physicists often are called upon to provide informatics services and/or to take part in projects involving principles of the field. The purpose of the presentations in this symposium is to help medical physicists gain some knowledge about the breadth of the field and how, in the current clinical and research environment, they can participate and contribute. Three talks have been designed to give an overview from the perspective of physicists and to provide a more in-depth discussionmore » in two areas. One of the primary purposes, and the main subject of the first talk, is to help physicists achieve a perspective about the range of the topics and concepts that fall under the heading of 'informatics'. The approach is to de-mystify topics and jargon and to help physicists find resources in the field should they need them. The other talks explore two areas of biomedical informatics in more depth. The goal is to highlight two domains of intense current interest--databases and models--in enough depth into current approaches so that an adequate background for independent inquiry is achieved. These two areas will serve as good examples of how physicists, using informatics principles, can contribute to oncology practice and research. Learning Objectives: To understand how the principles of biomedical informatics are used by medical physicists. To put the relevant informatics concepts in perspective with regard to biomedicine in general. To use clinical database design as an example of biomedical informatics. To provide a solid background into the problems and issues of the design and use of data and databases in radiation oncology. To use modeling in the service of decision support systems as an example of modeling methods and data use. To provide a background into how uncertainty in our data and knowledge can be incorporated into modeling methods.« less

Organizing human functioning and rehabilitation research into distinct scientific fields. Part I: Developing a comprehensive structure from the cell to society.

PubMed

Stucki, Gerold; Grimby, Gunnar

2007-05-01

There is a need to organize rehabilitation and related research into distinct scientific fields in order to overcome the current limitations of rehabilitation research. Based on the general distinction in basic, applied and professional sciences applicable to research in general, and the rehabilitation relevant distinction between the comprehensive perspective based on WHO's integrative model of human functioning (ICF) and the partial perspective focusing on the biomedical aspects of functioning, it is possible to identify 5 distinct scientific fields of human functioning and rehabilitation research. These are the emerging human functioning sciences and integrative rehabilitation sciences from the comprehensive perspective, the established biosciences and biomedical rehabilitation sciences and engineering from the partial perspective, and the professional rehabilitation sciences at the cutting edge of research and practice. The human functioning sciences aim to understand human functioning and to identify targets for comprehensive interventions, with the goal of contributing to the minimization of the experience of disability in the population. The biosciences in rehabilitation aim to explain body injury and repair and to identify targets for biomedical interventions. The integrative rehabilitation sciences design and study comprehensive assessments and interventions that integrate biomedical, personal factor and environmental approaches suited to optimize people's performance. The biomedical rehabilitation sciences and engineering study diagnostic measures and interventions suitable to minimize impairment, including symptom control, and to optimize people's capacity. The professional rehabilitation sciences study how to provide best care with the goal of enabling people with health conditions experiencing or likely to experience disability to achieve and maintain optimal functioning in interaction with the environment. The organization of human functioning and rehabilitation research into the 5 distinct scientific fields facilitates the development of academic training programs and career building as well as the development of research structures dedicated to human functioning and rehabilitation research.

Comparison of health conditions treated with traditional and biomedical health care in a Quechua community in rural Bolivia.

PubMed

Vandebroek, Ina; Thomas, Evert; Sanca, Sabino; Van Damme, Patrick; Puyvelde, Luc Van; De Kimpe, Norbert

2008-01-14

The objective of the present study was to reveal patterns in the treatment of health conditions in a Quechua-speaking community in the Bolivian Andes based on plant use data from traditional healers and patient data from a primary health care (PHC) service, and to demonstrate similarities and differences between the type of illnesses treated with traditional and biomedical health care, respectively. A secondary analysis of plant use data from semi-structured interviews with eight healers was conducted and diagnostic data was collected from 324 patients in the community PHC service. Health conditions were ranked according to: (A) the percentage of patients in the PHC service diagnosed with these conditions; and (B) the citation frequency of plant use reports to treat these conditions by healers. Healers were also queried about the payment modalities they offer to their patients. Plant use reports from healers yielded 1166 responses about 181 medicinal plant species, which are used to treat 67 different health conditions, ranging from general symptoms (e.g. fever and body pain), to more specific ailments, such as arthritis, biliary colic and pneumonia. The results show that treatment offered by traditional medicine overlaps with biomedical health care in the case of respiratory infections, wounds and bruises, fever and biliary colic/cholecystitis. Furthermore, traditional health care appears to be complementary to biomedical health care for chronic illnesses, especially arthritis, and for folk illnesses that are particularly relevant within the local cultural context. Payment from patients to healers included flexible, outcome contingent and non-monetary options. Traditional medicine in the study area is adaptive because it corresponds well with local patterns of morbidity, health care needs in relation to chronic illnesses, cultural perceptions of health conditions and socio-economic aspects of health care. The quantitative analysis of plant use reports and patient data represents a novel approach to compare the contribution of traditional and biomedical health care to treatment of particular health conditions.

Comparison of health conditions treated with traditional and biomedical health care in a Quechua community in rural Bolivia

PubMed Central

Vandebroek, Ina; Thomas, Evert; Sanca, Sabino; Van Damme, Patrick; Puyvelde, Luc Van; De Kimpe, Norbert

2008-01-01

Background The objective of the present study was to reveal patterns in the treatment of health conditions in a Quechua-speaking community in the Bolivian Andes based on plant use data from traditional healers and patient data from a primary health care (PHC) service, and to demonstrate similarities and differences between the type of illnesses treated with traditional and biomedical health care, respectively. Methods A secondary analysis of plant use data from semi-structured interviews with eight healers was conducted and diagnostic data was collected from 324 patients in the community PHC service. Health conditions were ranked according to: (A) the percentage of patients in the PHC service diagnosed with these conditions; and (B) the citation frequency of plant use reports to treat these conditions by healers. Healers were also queried about the payment modalities they offer to their patients. Results Plant use reports from healers yielded 1166 responses about 181 medicinal plant species, which are used to treat 67 different health conditions, ranging from general symptoms (e.g. fever and body pain), to more specific ailments, such as arthritis, biliary colic and pneumonia. The results show that treatment offered by traditional medicine overlaps with biomedical health care in the case of respiratory infections, wounds and bruises, fever and biliary colic/cholecystitis. Furthermore, traditional health care appears to be complementary to biomedical health care for chronic illnesses, especially arthritis, and for folk illnesses that are particularly relevant within the local cultural context. Payment from patients to healers included flexible, outcome contingent and non-monetary options. Conclusion Traditional medicine in the study area is adaptive because it corresponds well with local patterns of morbidity, health care needs in relation to chronic illnesses, cultural perceptions of health conditions and socio-economic aspects of health care. The quantitative analysis of plant use reports and patient data represents a novel approach to compare the contribution of traditional and biomedical health care to treatment of particular health conditions. PMID:18194568

Development and pilot testing of an online module for ethics education based on the Nigerian National Code for Health Research Ethics.

PubMed

Ogunrin, Olubunmi A; Ogundiran, Temidayo O; Adebamowo, Clement

2013-01-02

The formulation and implementation of national ethical regulations to protect research participants is fundamental to ethical conduct of research. Ethics education and capacity are inadequate in developing African countries. This study was designed to develop a module for online training in research ethics based on the Nigerian National Code of Health Research Ethics and assess its ease of use and reliability among biomedical researchers in Nigeria. This was a three-phased evaluation study. Phase one involved development of an online training module based on the Nigerian Code of Health Research Ethics (NCHRE) and uploading it to the Collaborative Institutional Training Initiative (CITI) website while the second phase entailed the evaluation of the module for comprehensibility, readability and ease of use by 45 Nigerian biomedical researchers. The third phase involved modification and re-evaluation of the module by 30 Nigerian biomedical researchers and determination of test-retest reliability of the module using Cronbach's alpha. The online module was easily accessible and comprehensible to 95% of study participants. There were significant differences in the pretest and posttest scores of study participants during the evaluation of the online module (p = 0.001) with correlation coefficients of 0.9 and 0.8 for the pretest and posttest scores respectively. The module also demonstrated excellent test-retest reliability and internal consistency as shown by Cronbach's alpha coefficients of 0.92 and 0.84 for the pretest and posttest respectively. The module based on the Nigerian Code was developed, tested and made available online as a valuable tool for training in cultural and societal relevant ethical principles to orient national and international biomedical researchers working in Nigeria. It would complement other general research ethics and Good Clinical Practice modules. Participants suggested that awareness of the online module should be increased through seminars, advertisement on government websites and portals used by Nigerian biomedical researchers, and incorporation of the Code into the undergraduate medical training curriculum.

TopFed: TCGA tailored federated query processing and linking to LOD.

PubMed

Saleem, Muhammad; Padmanabhuni, Shanmukha S; Ngomo, Axel-Cyrille Ngonga; Iqbal, Aftab; Almeida, Jonas S; Decker, Stefan; Deus, Helena F

2014-01-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to catalogue genetic mutations responsible for cancer using genome analysis techniques. One of the aims of this project is to create a comprehensive and open repository of cancer related molecular analysis, to be exploited by bioinformaticians towards advancing cancer knowledge. However, devising bioinformatics applications to analyse such large dataset is still challenging, as it often requires downloading large archives and parsing the relevant text files. Therefore, it is making it difficult to enable virtual data integration in order to collect the critical co-variates necessary for analysis. We address these issues by transforming the TCGA data into the Semantic Web standard Resource Description Format (RDF), link it to relevant datasets in the Linked Open Data (LOD) cloud and further propose an efficient data distribution strategy to host the resulting 20.4 billion triples data via several SPARQL endpoints. Having the TCGA data distributed across multiple SPARQL endpoints, we enable biomedical scientists to query and retrieve information from these SPARQL endpoints by proposing a TCGA tailored federated SPARQL query processing engine named TopFed. We compare TopFed with a well established federation engine FedX in terms of source selection and query execution time by using 10 different federated SPARQL queries with varying requirements. Our evaluation results show that TopFed selects on average less than half of the sources (with 100% recall) with query execution time equal to one third to that of FedX. With TopFed, we aim to offer biomedical scientists a single-point-of-access through which distributed TCGA data can be accessed in unison. We believe the proposed system can greatly help researchers in the biomedical domain to carry out their research effectively with TCGA as the amount and diversity of data exceeds the ability of local resources to handle its retrieval and parsing.

Is it relevant? Influence of trial manipulations of prospective memory context on task interference.

PubMed

Lourenço, Joana S; Maylor, Elizabeth A

2014-01-01

Prospective memory (PM) research has often investigated if having an intention interferes with ongoing activities, but rarely by linking the intention to a particular context. We examined effects of trial-by-trial changes in whether the context (defined by colour) was relevant for the nonfocal PM task. The ongoing task involved speeded decisions about the position (left/right) of the upper-case letter in a pair, and the PM task consisted of pressing an additional key if the upper-case and lower-case letters were in a specified colour and the same letter. Trials switched between two colours either randomly or predictably in eight-trial blocks. We also manipulated the presence/absence of occasional same-letter pairs in the irrelevant context. Results showed higher cost of having a nonfocal PM task when ongoing stimuli matched than when they mismatched the target's colour. Moreover, cost for intention-irrelevant stimuli was minimized, though never eliminated, by blocking match/mismatch trials. These findings highlight the role that local changes in intention-related context play in task interference and support a view of monitoring as a flexible mechanism. Additionally, the study introduced a novel way of embedding intention-related events in the irrelevant context shortly before the occurrence of PM targets, with results tentatively suggesting that such events might impair target detection.

Automated identification of molecular effects of drugs (AIMED)

PubMed Central

Fathiamini, Safa; Johnson, Amber M; Zeng, Jia; Araya, Alejandro; Holla, Vijaykumar; Bailey, Ann M; Litzenburger, Beate C; Sanchez, Nora S; Khotskaya, Yekaterina; Xu, Hua; Meric-Bernstam, Funda; Bernstam, Elmer V

2016-01-01

Introduction Genomic profiling information is frequently available to oncologists, enabling targeted cancer therapy. Because clinically relevant information is rapidly emerging in the literature and elsewhere, there is a need for informatics technologies to support targeted therapies. To this end, we have developed a system for Automated Identification of Molecular Effects of Drugs, to help biomedical scientists curate this literature to facilitate decision support. Objectives To create an automated system to identify assertions in the literature concerning drugs targeting genes with therapeutic implications and characterize the challenges inherent in automating this process in rapidly evolving domains. Methods We used subject-predicate-object triples (semantic predications) and co-occurrence relations generated by applying the SemRep Natural Language Processing system to MEDLINE abstracts and ClinicalTrials.gov descriptions. We applied customized semantic queries to find drugs targeting genes of interest. The results were manually reviewed by a team of experts. Results Compared to a manually curated set of relationships, recall, precision, and F2 were 0.39, 0.21, and 0.33, respectively, which represents a 3- to 4-fold improvement over a publically available set of predications (SemMedDB) alone. Upon review of ostensibly false positive results, 26% were considered relevant additions to the reference set, and an additional 61% were considered to be relevant for review. Adding co-occurrence data improved results for drugs in early development, but not their better-established counterparts. Conclusions Precision medicine poses unique challenges for biomedical informatics systems that help domain experts find answers to their research questions. Further research is required to improve the performance of such systems, particularly for drugs in development. PMID:27107438

Increasing health policy and systems research capacity in low- and middle-income countries: results from a bibliometric analysis.

PubMed

English, Krista M; Pourbohloul, Babak

2017-07-28

For 20 years, substantial effort has been devoted to catalyse health policy and systems research (HPSR) to support vulnerable populations and resource-constrained regions through increased funding, institutional capacity-building and knowledge production; yet, participation from low- and middle-income countries (LMICs) is underrepresented in HPSR knowledge production. A bibliometric analysis of HPSR literature was conducted using a high-level keyword search. Health policy and/or health systems literature with a topic relevant to LMICs and whose lead author's affiliation is in an LMIC were included for analysis. The trends in knowledge production from 1990 to 2015 were examined to understand how investment in HPSR benefits those it means to serve. The total number of papers published in PubMed increases each year. HPSR publications represent approximately 10% of these publications, but this percentage is increasing at a greater rate than PubMed publications overall and the discipline is holding this momentum. HPSR publications with topics relevant to LMICs and an LMIC-affiliated lead authors (specifically from low-income countries) are increasing at a greater rate than any other category within the scope of this analysis. While the absolute number of publications remains low, lead authors from an LMIC have participated exponentially in the life and biomedical sciences (PubMed) since the early 2000s. HPSR publications with a topic relevant to LMICs and an LMIC lead author continue to increase at a greater rate than the life and biomedical science topics in general. This correlation is likely due to increased capacity for research within LMICs and the support for publications surrounding large HPSR initiatives. These findings provide strong evidence that continued support is key to the longevity and enhancement of HPSR toward its mandate.

The role of autologous hematopoietic progenitor and cell reinfusion for intensive chemotherapy in women with poor-prognosis breast cancer. Clinical studies with ex-vivo expanded cells produced with the Aastrom Replicell technology.

PubMed

Chabannon, C; Novakovitch, G; Blache, J L; Olivero, S; Camerlo, J; Genre, D; Maraninchi, D; Viens, P

1999-04-01

In recent years, we have initiated two clinical studies, to evaluate the usefulness of ex-vivo expanded cells in patients with breast cancer who receive sequential high-dose chemotherapy. Ex-vivo expanded cells were produced from autologous cryopreserved bone marrow nucleated cells, using a biomedical device. The Aastrom Replicell system cultures cells in animal serum-replete medium, with a combination of flt3-L, PIXY321 and Epo, for 12 days. The initial pilot trial was set up to establish the feasibility and safety of the technique: 6 patients completed the study. An ongoing randomized study searches to establish whether ex-vivo expanded cells provide a clinical benefit.

Hazardous Effects of Titanium Dioxide Nanoparticles in Ecosystem

PubMed Central

Hussain, Muzammal; Khan, Muzaffar

2017-01-01

Although nanoparticles (NPs) have made incredible progress in the field of nanotechnology and biomedical research and their applications are demanded throughout industrial world particularly over the past decades, little is known about the fate of nanoparticles in ecosystem. Concerning the biosafety of nanotechnology, nanotoxicity is going to be the second most priority of nanotechnology that needs to be properly addressed. This review covers the chemical as well as the biological concerns about nanoparticles particularly titanium dioxide (TiO2) NPs and emphasizes the toxicological profile of TiO2 at the molecular level in both in vitro and in vivo systems. In addition, the challenges and future prospects of nanotoxicology are discussed that may provide better understanding and new insights into ongoing and future research in this field. PMID:28373829

Polysaccharide‐Based Controlled Release Systems for Therapeutics Delivery and Tissue Engineering: From Bench to Bedside

PubMed Central

Miao, Tianxin; Wang, Junqing; Zeng, Yun; Chen, Xiaoyuan

2018-01-01

Abstract Polysaccharides or polymeric carbohydrate molecules are long chains of monosaccharides that are linked by glycosidic bonds. The naturally based structural materials are widely applied in biomedical applications. This article covers four different types of polysaccharides (i.e., alginate, chitosan, hyaluronic acid, and dextran) and emphasizes their chemical modification, preparation approaches, preclinical studies, and clinical translations. Different cargo fabrication techniques are also presented in the third section. Recent progresses in preclinical applications are then discussed, including tissue engineering and treatment of diseases in both therapeutic and monitoring aspects. Finally, clinical translational studies with ongoing clinical trials are summarized and reviewed. The promise of new development in nanotechnology and polysaccharide chemistry helps clinical translation of polysaccharide‐based drug delivery systems. PMID:29721408

PuReD-MCL: a graph-based PubMed document clustering methodology.

PubMed

Theodosiou, T; Darzentas, N; Angelis, L; Ouzounis, C A

2008-09-01

Biomedical literature is the principal repository of biomedical knowledge, with PubMed being the most complete database collecting, organizing and analyzing such textual knowledge. There are numerous efforts that attempt to exploit this information by using text mining and machine learning techniques. We developed a novel approach, called PuReD-MCL (Pubmed Related Documents-MCL), which is based on the graph clustering algorithm MCL and relevant resources from PubMed. PuReD-MCL avoids using natural language processing (NLP) techniques directly; instead, it takes advantage of existing resources, available from PubMed. PuReD-MCL then clusters documents efficiently using the MCL graph clustering algorithm, which is based on graph flow simulation. This process allows users to analyse the results by highlighting important clues, and finally to visualize the clusters and all relevant information using an interactive graph layout algorithm, for instance BioLayout Express 3D. The methodology was applied to two different datasets, previously used for the validation of the document clustering tool TextQuest. The first dataset involves the organisms Escherichia coli and yeast, whereas the second is related to Drosophila development. PuReD-MCL successfully reproduces the annotated results obtained from TextQuest, while at the same time provides additional insights into the clusters and the corresponding documents. Source code in perl and R are available from http://tartara.csd.auth.gr/~theodos/

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.

PubMed

Liu, Yifeng; Liang, Yongjie; Wishart, David

2015-07-01

PolySearch2 (http://polysearch.ca) is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies. PolySearch2 supports a generalized 'Given X, find all associated Ys' query, where X and Y can be selected from the aforementioned biomedical entities. An example query might be: 'Find all diseases associated with Bisphenol A'. To find its answers, PolySearch2 searches for associations against comprehensive collections of free-text collections, including local versions of MEDLINE abstracts, PubMed Central full-text articles, Wikipedia full-text articles and US Patent application abstracts. PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage. PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more

PubMed Central

Liu, Yifeng; Liang, Yongjie; Wishart, David

2015-01-01

PolySearch2 (http://polysearch.ca) is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies. PolySearch2 supports a generalized ‘Given X, find all associated Ys’ query, where X and Y can be selected from the aforementioned biomedical entities. An example query might be: ‘Find all diseases associated with Bisphenol A’. To find its answers, PolySearch2 searches for associations against comprehensive collections of free-text collections, including local versions of MEDLINE abstracts, PubMed Central full-text articles, Wikipedia full-text articles and US Patent application abstracts. PolySearch2 also searches 14 widely used, text-rich biological databases such as UniProt, DrugBank and Human Metabolome Database to improve its accuracy and coverage. PolySearch2 maintains an extensive thesaurus of biological terms and exploits the latest search engine technology to rapidly retrieve relevant articles and databases records. PolySearch2 also generates, ranks and annotates associative candidates and present results with relevancy statistics and highlighted key sentences to facilitate user interpretation. PMID:25925572

The human mouth: oral functions in a social complexity perspective.

PubMed

Eriksen, Harald M; Dimitrov, Vladimir

2003-06-01

In the dental and medical literature, the mouth and oral functions are usually presented in a biomedical context. However, there may be a need for a broader perspective if we are to appreciate the importance of the human mouth as an organ with diverse functions. The paradigm of complexity appears to be of relevance in our understanding the social and psychological characteristics of the human mouth in addition to its biological functions. Examples such as the pleasures of taste, social aspects of eating, the importance of linguistics and communication are illustrations of some of the social and psychological aspects of oral functions. Professional knowledge related to such issues is important in our understanding the patient's priorities and in performing the relevant diagnosis and treatment planning.

The Relevance of Arieti's Work in the Age of Medication.

PubMed

Balbuena Rivera, Francisco

2016-09-01

This paper looks at the relevance of psychoanalysis as a treatment option for psychotic individuals at a time when psychosis is invariably considered to be a biologically-based brain disease, for which the preferred course of treatment is psychotropic medication. In recent years, the use of psychoanalysis has declined noticeably in favor of evidenced-based biomedical approaches, which rely heavily upon statistical probabilities for ameliorating specific psychotic symptoms. Well-publicized biological approaches have proliferated, often to the detriment of the psychotic individual's general health, emotional recovery, and long-term rehabilitation. Sadly, these approaches may also be a significant factor affecting mortality rates in those suffering with psychosis, known to be about 25 years shorter, on average, than the general population.

Development of practice principles for the management of ongoing suicidal ideation in young people diagnosed with major depressive disorder.

PubMed

Rice, Simon M; Simmons, Magenta B; Bailey, Alan P; Parker, Alexandra G; Hetrick, Sarah E; Davey, Christopher G; Phelan, Mark; Blaikie, Simon; Edwards, Jane

2014-01-01

There is a lack of clear guidance regarding the management of ongoing suicidality in young people experiencing major depressive disorder. This study utilised an expert consensus approach in identifying practice principles to complement relevant clinical guidelines for the treatment of major depressive disorder in young people. The study also sought to outline a broad treatment framework for clinical intervention with young people experiencing ongoing suicidal ideation. In-depth focus groups were undertaken with a specialist multidisciplinary clinical team (the Youth Mood Clinic at Orygen Youth Health Clinical Program, Melbourne) working with young people aged 15-25 years experiencing ongoing suicidal ideation. Each focus group was audio recorded and transcribed verbatim using orthographic conventions. Principles of grounded theory and thematic analysis were used to analyse and code the resultant data. The identified codes were subsequently synthesised into eight practice principles reflecting engagement and consistency of care, ongoing risk assessment and documentation, individualised crisis planning, engaging systems of support, engendering hopefulness, development of adaptive coping, management of acute risk, and consultation and supervision. The identified practice principles provide a broad management framework, and may assist to improve treatment consistency and clinical management of young people experiencing ongoing suicidal ideation. The practice principles may be of use to health professionals working within a team-based setting involved in the provision of care, even if peripherally, to young people with ongoing suicidal ideation. Findings address the lack of treatment consistency and shared terminology and may provide containment and guidance to multidisciplinary clinicians working with this at-risk group.

Mental Retardation and the Law: A Report on Status of Current Court Cases.

ERIC Educational Resources Information Center

Levine, Jan Martin, Ed.

Brief reports on the status of approximately 75 ongoing or recently decided court cases in states of relevance to the mentally retarded are provided. Cases cover the following issues: commitment, community living and services, criminal law, discrimination, guardianship, institutions and deinstitutionalization, medical/legal issues, parental rights…

Learning Objects for Educational Applications via PDA Technology

ERIC Educational Resources Information Center

Churchill, Daniel

2008-01-01

This article discusses an ongoing study into issues relevant to the design of learning objects for educational applications via portable digital assistant (PDA) technology. The specific areas of inquiry in this study are: the kinds of learning objects that are effective for PDA delivery; contexts for their effective educational applications; and…

Integrating Community into the Classroom: Community Gardening, Community Involvement, and Project-Based Learning.

ERIC Educational Resources Information Center

Langhout, Regina Day; Rappaport, Julian; Simmons, Doretha

2002-01-01

Culturally relevant, ongoing project-based learning was facilitated in a predominantly African American urban elementary school via a community garden project. The project involved teachers, students, university members, and community members. This article evaluates the project through two classroom-community collaboration models, noting common…

MOOCs, High Technology, and Higher Learning

ERIC Educational Resources Information Center

Rhoads, Robert A.

2015-01-01

In "MOOCs, High Technology, and Higher Learning," Robert A. Rhoads places the OpenCourseWare (OCW) movement into the larger context of a revolution in educational technology. In doing so, he seeks to bring greater balance to increasingly polarized discussions of massively open online courses (MOOCs) and show their ongoing relevance to…

Improving Fluency Skills of Secondary-Level Students from Diverse Backgrounds

ERIC Educational Resources Information Center

O'Shea, Doris J.; McQuiston, Kathleen; McCollin, Michelle

2009-01-01

Many secondary-level students from culturally and linguistically diverse (CLD) backgrounds need to nurture their ongoing literacy growth to become independent, tenacious readers. Middle and high school teachers' use of direct and explicit strategies that are focused on culturally and linguistically responsive practices (e.g., use of relevant texts…

Searching for Grey Literature for Systematic Reviews: Challenges and Benefits

ERIC Educational Resources Information Center

Mahood, Quenby; Van Eerd, Dwayne; Irvin, Emma

2014-01-01

There is ongoing interest in including grey literature in systematic reviews. Including grey literature can broaden the scope to more relevant studies, thereby providing a more complete view of available evidence. Searching for grey literature can be challenging despite greater access through the Internet, search engines and online bibliographic…

Applied Linguistics: The Challenge of Theory

ERIC Educational Resources Information Center

McNamara, Tim

2015-01-01

Language has featured prominently in contemporary social theory, but the relevance of this fact to the concerns of Applied Linguistics, with its necessary orientation to practical issues of language in context, represents an ongoing challenge. This article supports the need for a greater engagement with theory in Applied Linguistics. It considers…

British Register of Reading Research. No. 2.

ERIC Educational Resources Information Center

Goodacre, Elizabeth J., Comp.; Bentley, Diana, Comp.

Separate listings of both ongoing and completed reading research in Great Britain between 1974 and 1977--including relevant language studies and research on spelling--are arranged alphabetically by researcher, reporting the research title, the institution at which the research was conducted, the years started and completed, and the type of…

A Method to Assess Climate-Relevant Decisions: Application in the Chesapeake Bay (2010 External Review Draft)

EPA Science Inventory

The goal of this study is to formalize an approach to inventory and analyze management decisions in order to produce useful information targeted toward effective adaptation to climate change. The approach uses as its starting point ongoing planning processes and decisions geared ...

Business Technology Education in the Early 21st Century: The Ongoing Quest for Relevance

ERIC Educational Resources Information Center

Andriole, Stephen J.

2006-01-01

The field of information technology is changing and those responsible for educating the next generation of technology professionals have responded with a new computing curriculum, which identifies five distinct technology majors: computer engineering, computer science, software engineering, information systems and information technology.…

Market Demand for Sustainability in Management Education

ERIC Educational Resources Information Center

Gitsham, Matthew; Clark, Timothy S.

2014-01-01

Purpose: This paper aims to contribute to the ongoing debate about the relevance of sustainability in management education through exploration of the needs and expectations of a key group of business schools' stakeholders--senior executives of leading corporations. Design/methodology/approach: The paper presents findings from a survey regarding…

A Collaborative Professional Development Initiative Supporting Early Literacy Coaches

ERIC Educational Resources Information Center

Mraz, Maryann; Kissel, Brian; Algozzine, Bob; Babb, Julie; Foxworth, Kimberly

2011-01-01

Many believe that the key to translating research into successful practice lies in providing teachers with continuous professional development and ongoing coaching support. In this article, we provide an overview of the relevant coaching literature and describe 4 critical features of an evidence-based preschool literacy coaching model: the coach…

Educational Leadership and Social Justice: Theory into Practice.

ERIC Educational Resources Information Center

Bogotch, Ira E.

Connecting theory and practice to the moral use of power reveals why social justice, as an educational intervention, is relevant in every era. Social justice requires ongoing struggle and cannot be separated from the educational theories and practices of professionals, schools, academic disciplines, and governmental agents. Insights from John…

SARS: caring for patients in Hong Kong.

PubMed

Chung, Betty Pui Man; Wong, Thomas Kwok Shing; Suen, Esther Suk Bing; Chung, Joanne Wai Yee

2005-04-01

To explore in depth the experiences of nurses' caring for SARS patients in Hong Kong. Severe Acute Respiratory Syndrome (SARS) dramatically demonstrates the global havoc that can be wreaked by a newly emerging infectious disease. The current literature either has a predominantly biomedical focus or deals with the psychological impact on healthcare workers. Published studies on the lived experience of nurses caring for SARS patients are currently lacking. A phenomenological design. Using methods consistent with Husserl's philosophy, eight Registered Nurses working in three regional hospitals in Hong Kong were invited to participate in sharing their lived experience of caring for SARS patients and data were analysed using Colaizzi's approach. The three major themes explicated were: the various emotions experienced in caring for SARS patients, the concept of uncertainty and revisiting the 'taken for granted' features of nursing. These themes, when taken together, describe the essence of the voyage undertaken by nurses who cared for SARS patients during the outbreak. The findings of this study indicate that extensive and ongoing support is needed to prepare and enable nurses to care for SARS patients during a crisis and make it easier for nurses to deal with the various uncertainties. The essence of caring for SARS patients is highlighted in this study. The experience of caring for SARS patients prompts nurses to find meaning in their experience(s), and to develop knowledge and attitudes on how best to care for patients and prepare for a new crisis in the future. This paper considers a more in-depth understanding of the lived experience of nurses during the crisis and the relevance of this perspective for education and support of nurses.

Multimodal optical setup based on spectrometer and cameras combination for biological tissue characterization with spatially modulated illumination

NASA Astrophysics Data System (ADS)

Baruch, Daniel; Abookasis, David

2017-04-01

The application of optical techniques as tools for biomedical research has generated substantial interest for the ability of such methodologies to simultaneously measure biochemical and morphological parameters of tissue. Ongoing optimization of optical techniques may introduce such tools as alternative or complementary to conventional methodologies. The common approach shared by current optical techniques lies in the independent acquisition of tissue's optical properties (i.e., absorption and reduced scattering coefficients) from reflected or transmitted light. Such optical parameters, in turn, provide detailed information regarding both the concentrations of clinically relevant chromophores and macroscopic structural variations in tissue. We couple a noncontact optical setup with a simple analysis algorithm to obtain absorption and scattering coefficients of biological samples under test. Technically, a portable picoprojector projects serial sinusoidal patterns at low and high spatial frequencies, while a spectrometer and two independent CCD cameras simultaneously acquire the reflected diffuse light through a single spectrometer and two separate CCD cameras having different bandpass filters at nonisosbestic and isosbestic wavelengths in front of each. This configuration fills the gaps in each other's capabilities for acquiring optical properties of tissue at high spectral and spatial resolution. Experiments were performed on both tissue-mimicking phantoms as well as hands of healthy human volunteers to quantify their optical properties as proof of concept for the present technique. In a separate experiment, we derived the optical properties of the hand skin from the measured diffuse reflectance, based on a recently developed camera model. Additionally, oxygen saturation levels of tissue measured by the system were found to agree well with reference values. Taken together, the present results demonstrate the potential of this integrated setup for diagnostic and research applications.

Social and emotional wellbeing assessment instruments for use with Indigenous Australians: A critical review.

PubMed

Le Grande, M; Ski, C F; Thompson, D R; Scuffham, P; Kularatna, S; Jackson, A C; Brown, A

2017-08-01

There is growing recognition that in addition to universally recognised domains and indicators of wellbeing (such as population health and life expectancy), additional frameworks are required to fully explain and measure Indigenous wellbeing. In particular, Indigenous Australian wellbeing is largely determined by colonisation, historical trauma, grief, loss, and ongoing social marginalisation. Dominant mainstream indicators of wellbeing based on the biomedical model may therefore be inadequate and not entirely relevant in the Indigenous context. It is possible that "standard" wellbeing instruments fail to adequately assess indicators of health and wellbeing within societies that have a more holistic view of health. The aim of this critical review was to identify, document, and evaluate the use of social and emotional wellbeing measures within the Australian Indigenous community. The instruments were systematically described regarding their intrinsic properties (e.g., generic v. disease-specific, domains assessed, extent of cross-cultural adaptation and psychometric characteristics) and their purpose of utilisation in studies (e.g., study setting, intervention, clinical purpose or survey). We included 33 studies, in which 22 distinct instruments were used. Three major categories of social and emotional wellbeing instruments were identified: unmodified standard instruments (10), cross-culturally adapted standard instruments (6), and Indigenous developed measures (6). Recommendations are made for researchers and practitioners who assess social and emotional wellbeing in Indigenous Australians, which may also be applicable to other minority groups where a more holistic framework of wellbeing is applied. It is advised that standard instruments only be used if they have been subject to a formal cross-cultural adaptation process, and Indigenous developed measures continue to be developed, refined, and validated within a diverse range of research and clinical settings. Copyright © 2017 Elsevier Ltd. All rights reserved.

Insights from clinical research completed during the west Africa Ebola virus disease epidemic

PubMed Central

Rojek, Amanda; Horby, Peter; Dunning, Jake

2018-01-01

The west Africa Ebola virus disease (EVD) epidemic was extraordinary in scale. Now that the epidemic has ended, it is a relevant time to examine published studies with direct relevance to clinical care and, more broadly, to examine the implications of the clinical research response mounted. Clinically relevant research includes literature detailing risk factors for and clinical manifestations of EVD, laboratory and other investigation findings in patients, experimental vaccine and therapeutic clinical trials, and analyses of survivor syndrome. In this Review, we discuss new insights from patient-oriented research completed during the west Africa epidemic, identify ongoing knowledge gaps, and suggest priorities for future research. PMID:28461209

Chapter 1: Biomedical knowledge integration.

PubMed

Payne, Philip R O

2012-01-01

The modern biomedical research and healthcare delivery domains have seen an unparalleled increase in the rate of innovation and novel technologies over the past several decades. Catalyzed by paradigm-shifting public and private programs focusing upon the formation and delivery of genomic and personalized medicine, the need for high-throughput and integrative approaches to the collection, management, and analysis of heterogeneous data sets has become imperative. This need is particularly pressing in the translational bioinformatics domain, where many fundamental research questions require the integration of large scale, multi-dimensional clinical phenotype and bio-molecular data sets. Modern biomedical informatics theory and practice has demonstrated the distinct benefits associated with the use of knowledge-based systems in such contexts. A knowledge-based system can be defined as an intelligent agent that employs a computationally tractable knowledge base or repository in order to reason upon data in a targeted domain and reproduce expert performance relative to such reasoning operations. The ultimate goal of the design and use of such agents is to increase the reproducibility, scalability, and accessibility of complex reasoning tasks. Examples of the application of knowledge-based systems in biomedicine span a broad spectrum, from the execution of clinical decision support, to epidemiologic surveillance of public data sets for the purposes of detecting emerging infectious diseases, to the discovery of novel hypotheses in large-scale research data sets. In this chapter, we will review the basic theoretical frameworks that define core knowledge types and reasoning operations with particular emphasis on the applicability of such conceptual models within the biomedical domain, and then go on to introduce a number of prototypical data integration requirements and patterns relevant to the conduct of translational bioinformatics that can be addressed via the design and use of knowledge-based systems.

Chapter 1: Biomedical Knowledge Integration

PubMed Central

Payne, Philip R. O.

2012-01-01

The modern biomedical research and healthcare delivery domains have seen an unparalleled increase in the rate of innovation and novel technologies over the past several decades. Catalyzed by paradigm-shifting public and private programs focusing upon the formation and delivery of genomic and personalized medicine, the need for high-throughput and integrative approaches to the collection, management, and analysis of heterogeneous data sets has become imperative. This need is particularly pressing in the translational bioinformatics domain, where many fundamental research questions require the integration of large scale, multi-dimensional clinical phenotype and bio-molecular data sets. Modern biomedical informatics theory and practice has demonstrated the distinct benefits associated with the use of knowledge-based systems in such contexts. A knowledge-based system can be defined as an intelligent agent that employs a computationally tractable knowledge base or repository in order to reason upon data in a targeted domain and reproduce expert performance relative to such reasoning operations. The ultimate goal of the design and use of such agents is to increase the reproducibility, scalability, and accessibility of complex reasoning tasks. Examples of the application of knowledge-based systems in biomedicine span a broad spectrum, from the execution of clinical decision support, to epidemiologic surveillance of public data sets for the purposes of detecting emerging infectious diseases, to the discovery of novel hypotheses in large-scale research data sets. In this chapter, we will review the basic theoretical frameworks that define core knowledge types and reasoning operations with particular emphasis on the applicability of such conceptual models within the biomedical domain, and then go on to introduce a number of prototypical data integration requirements and patterns relevant to the conduct of translational bioinformatics that can be addressed via the design and use of knowledge-based systems. PMID:23300416

Predictors of Student Productivity in Biomedical Graduate School Applications.

PubMed

Hall, Joshua D; O'Connell, Anna B; Cook, Jeanette G

2017-01-01

Many US biomedical PhD programs receive more applications for admissions than they can accept each year, necessitating a selective admissions process. Typical selection criteria include standardized test scores, undergraduate grade point average, letters of recommendation, a resume and/or personal statement highlighting relevant research or professional experience, and feedback from interviews with training faculty. Admissions decisions are often founded on assumptions that these application components correlate with research success in graduate school, but these assumptions have not been rigorously tested. We sought to determine if any application components were predictive of student productivity measured by first-author student publications and time to degree completion. We collected productivity metrics for graduate students who entered the umbrella first-year biomedical PhD program at the University of North Carolina at Chapel Hill from 2008-2010 and analyzed components of their admissions applications. We found no correlations of test scores, grades, amount of previous research experience, or faculty interview ratings with high or low productivity among those applicants who were admitted and chose to matriculate at UNC. In contrast, ratings from recommendation letter writers were significantly stronger for students who published multiple first-author papers in graduate school than for those who published no first-author papers during the same timeframe. We conclude that the most commonly used standardized test (the general GRE) is a particularly ineffective predictive tool, but that qualitative assessments by previous mentors are more likely to identify students who will succeed in biomedical graduate research. Based on these results, we conclude that admissions committees should avoid over-reliance on any single component of the application and de-emphasize metrics that are minimally predictive of student productivity. We recommend continual tracking of desired training outcomes combined with retrospective analysis of admissions practices to guide both application requirements and holistic application review.

Financial, nonfinancial and editors' conflicts of interest in high-impact biomedical journals.

PubMed

Bosch, Xavier; Pericas, Juan M; Hernández, Cristina; Doti, Pamela

2013-07-01

To assess financial, nonfinancial and editors' conflicts of interest (COI) disclosure policies among the most influential biomedical journals publishing original research. We conducted a cross-sectional study of 399 high-impact biomedical journals in 27 biomedical categories of the Journal Citation Reports (JCR) in December 2011. Information relevant to COI and requirements for disclosures that was publicly available on journal websites was collected. While financial COI disclosures were required by 358 (89.7%) and nonfinancial by 280 (70.2%) journals, 155 (38.8%) required editors' disclosures. Journals in the first decile of the JCR classification scored significantly higher than those in the second decile for all disclosure policies. Ninety (22.6%) journals were published by Elsevier and 59 (14.8%) by Wiley-Blackwell, with Elsevier scoring significantly better in financial disclosure policies (P = 0.022). Clinical journals scored significantly higher than basic journals for all disclosure policies. No differences were observed between open-access (n = 25) and nonopen-access (n = 374) journals for any type of disclosure. Somewhat incoherently, authors' disclosure statements were included in some published manuscript in 57.1% of journals without any COI disclosure policies. Authors' financial COI disclosures were required by about 90% of high-impact clinical and basic journals publishing original research. Unlike recent studies showing a significantly lower prevalence of nonfinancial compared with financial disclosures, the former were required by about 70% of journals, suggesting that editors are increasingly concerned about nonfinancial competing interests. Only 40% of journals required disclosure of editors' COI, in conflict with the recommendations of the most influential editors' associations. © 2013 Stichting European Society for Clinical Investigation Journal Foundation. Published by John Wiley & Sons Ltd.

Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains

PubMed Central

Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A.; Noy, Natalya F.

2014-01-01

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50, 000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology-engineering projects and tools in the biomedical domain. PMID:24953242

Project-based learning with international collaboration for training biomedical engineers.

PubMed

Krishnan, Shankar

2011-01-01

Training biomedical engineers while effectively keeping up with the fast paced scientific breakthroughs and the growth in technical innovations poses arduous challenges for educators. Traditional pedagogical methods are employed for coping with the increasing demands in biomedical engineering (BME) training and continuous improvements have been attempted with some success. Project-based learning (PBL) is an academic effort that challenges students by making them carry out interdisciplinary projects aimed at accomplishing a wide range of student learning outcomes. PBL has been shown to be effective in the medical field and has been adopted by other fields including engineering. The impact of globalization in healthcare appears to be steadily increasing which necessitates the inclusion of awareness of relevant international activities in the curriculum. Numerous difficulties are encountered when the formation of a collaborative team is tried, and additional difficulties occur as the collaboration team is extended to international partners. Understanding and agreement of responsibilities becomes somewhat complex and hence the collaborative project has to be planned and executed with clear understanding by all partners and participants. A model for training BME students by adopting PBL with international collaboration is proposed. The results of previous BME project work with international collaboration fit partially into the model. There were many logistic issues and constraints; however, the collaborative projects themselves greatly enhanced the student learning outcomes. This PBL type of learning experience tends to promote long term retention of multidisciplinary material and foster high-order cognitive activities such as analysis, synthesis and evaluation. In addition to introducing the students to experiences encountered in the real-life workforce, the proposed approach enhances developing professional contracts and global networking. In conclusion, despite initial challenges, adopting project-based learning with international collaboration has strong potentials to be valuable in the training of biomedical engineering students.

A semantic graph-based approach to biomedical summarisation.

PubMed

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.

Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

PubMed

Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A; Noy, Natalya F

2014-10-01

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology-engineering projects and tools in the biomedical domain. Copyright © 2014 Elsevier Inc. All rights reserved.

Relevance of Linear Stability Results to Enhanced Oil Recovery

NASA Astrophysics Data System (ADS)

Ding, Xueru; Daripa, Prabir

2012-11-01

How relevant can the results based on linear stability theory for any problem for that matter be to full scale simulation results? Put it differently, is the optimal design of a system based on linear stability results is optimal or even near optimal for the complex nonlinear system with certain objectives of interest in mind? We will address these issues in the context of enhanced oil recovery by chemical flooding. This will be based on an ongoing work. Supported by Qatar National Research Fund (a member of the Qatar Foundation).

Point-of-Care Diagnostics for Niche Applications

PubMed Central

Cummins, Brian M.; Ligler, Frances S.; Walker, Glenn M.

2016-01-01

Point-of-care or point-of-use diagnostics are analytical devices that provide clinically relevant information without the need for a core clinical laboratory. In this review we define point-of-care diagnostics as portable versions of assays performed in a traditional clinical chemistry laboratory. This review discusses five areas relevant to human and animal health where increased attention could produce significant impact: veterinary medicine, space travel, sports medicine, emergency medicine, and operating room efficiency. For each of these areas, clinical need, available commercial products, and ongoing research into new devices are highlighted. PMID:26837054

Evaluation metrics for biostatistical and epidemiological collaborations.

PubMed

Rubio, Doris McGartland; Del Junco, Deborah J; Bhore, Rafia; Lindsell, Christopher J; Oster, Robert A; Wittkowski, Knut M; Welty, Leah J; Li, Yi-Ju; Demets, Dave

2011-10-15

Increasing demands for evidence-based medicine and for the translation of biomedical research into individual and public health benefit have been accompanied by the proliferation of special units that offer expertise in biostatistics, epidemiology, and research design (BERD) within academic health centers. Objective metrics that can be used to evaluate, track, and improve the performance of these BERD units are critical to their successful establishment and sustainable future. To develop a set of reliable but versatile metrics that can be adapted easily to different environments and evolving needs, we consulted with members of BERD units from the consortium of academic health centers funded by the Clinical and Translational Science Award Program of the National Institutes of Health. Through a systematic process of consensus building and document drafting, we formulated metrics that covered the three identified domains of BERD practices: the development and maintenance of collaborations with clinical and translational science investigators, the application of BERD-related methods to clinical and translational research, and the discovery of novel BERD-related methodologies. In this article, we describe the set of metrics and advocate their use for evaluating BERD practices. The routine application, comparison of findings across diverse BERD units, and ongoing refinement of the metrics will identify trends, facilitate meaningful changes, and ultimately enhance the contribution of BERD activities to biomedical research. Copyright © 2011 John Wiley & Sons, Ltd.

Dynamic Consent: a potential solution to some of the challenges of modern biomedical research.

PubMed

Budin-Ljøsne, Isabelle; Teare, Harriet J A; Kaye, Jane; Beck, Stephan; Bentzen, Heidi Beate; Caenazzo, Luciana; Collett, Clive; D'Abramo, Flavio; Felzmann, Heike; Finlay, Teresa; Javaid, Muhammad Kassim; Jones, Erica; Katić, Višnja; Simpson, Amy; Mascalzoni, Deborah

2017-01-25

Innovations in technology have contributed to rapid changes in the way that modern biomedical research is carried out. Researchers are increasingly required to endorse adaptive and flexible approaches to accommodate these innovations and comply with ethical, legal and regulatory requirements. This paper explores how Dynamic Consent may provide solutions to address challenges encountered when researchers invite individuals to participate in research and follow them up over time in a continuously changing environment. An interdisciplinary workshop jointly organised by the University of Oxford and the COST Action CHIP ME gathered clinicians, researchers, ethicists, lawyers, research participants and patient representatives to discuss experiences of using Dynamic Consent, and how such use may facilitate the conduct of specific research tasks. The data collected during the workshop were analysed using a content analysis approach. Dynamic Consent can provide practical, sustainable and future-proof solutions to challenges related to participant recruitment, the attainment of informed consent, participant retention and consent management, and may bring economic efficiencies. Dynamic Consent offers opportunities for ongoing communication between researchers and research participants that can positively impact research. Dynamic Consent supports inter-sector, cross-border approaches and large scale data-sharing. Whilst it is relatively easy to set up and maintain, its implementation will require that researchers re-consider their relationship with research participants and adopt new procedures.

Attractive mechanical properties of a lightweight highly sensitive bi layer thermistor: polycarbonate/organic molecular conductor

NASA Astrophysics Data System (ADS)

Laukhina, E.; Lebedev, V.; Rovira, C.; Laukhin, V.; Veciana, J.

2016-03-01

The paper covers some of the basic mechanical characteristics of a recently developed bi layer thermistor: polycarbonate/(001) oriented layer of organic molecular conductor α’-(BEDT-TTF)2IxBr3-x, were BEDT-TTF=bis(ethylenedithio)tetrathiafulvalen. The nano and macro mechanical properties have been studied in order to use this flexible, low cost thermistor in sensing applications by proper way. The nano-mechanical properties of the temperature sensitive semiconducting layer of α’-(BEDT-TTF)2IxBr3-x were tested using nanoindentation method. The value of Young's modulus in direction being perpendicular to the layer plan was found as 9.0 ±1.4 GPa. The macro mechanical properties of the thermistor were studied using a 5848 MicroTester. The tensile tests showed that basic mechanical characteristics of the thermistor are close to those of polycarbonate films. This indicates a good mechanical strength of the developed sensor. Therefore, the thermistor can be used in technologies that need to be instrumented with highly robustness lightweight low cost temperature sensors. The paper also reports synthetic details on fabricating temperature sensing e-textile. As the temperature control is becoming more and more important in biomedical technologies like healthcare monitoring, this work strongly contributes on the ongoing research on engineering sensitive conducting materials for biomedical applications.

Blogging in support of health information outreach.

PubMed

Sapp, Lara; Cogdill, Keith

2010-07-01

Social media technologies are transforming the way librarians are collaborating, creating, and disseminating information. This article discusses how librarians at the University of Texas Health Science Center at San Antonio created a blog to support their health information outreach activities. Launched in 2007, the Staying Well Connected blog was established with the goal of promoting access to biomedical and health information for consumers and health professionals in the South Texas region. Postings highlight relevant health news, conferences, funding opportunities, and outreach events.

Minds That Matter: 2007 Gairdner International Awards Lectures

PubMed Central

Krasnoshtein, F.; Nikolov, N.

2007-01-01

On October 25 and 26, 2007, at the University of Toronto, the Gairdner Foundation in partnership with Canadian Institutes of Health Research presented a two-day international symposium titled Minds That Matter. The symposium featured academic lectures by Gairdner Award winners past and present and by other leading biomedical scientists. These distinguished researchers share many characteristics in common: creativity, vision, tenacity, and driving curiosity to illuminate discovery with high degree of relevance. The present article summarizes the 2007 Gairdner Award lectures.

Synthesis of ceramic-based porous gradient structures for applications in energy conversion and related fields

NASA Astrophysics Data System (ADS)

Graule, Thomas; Ozog, Paulina; Durif, Caroline; Wilkens-Heinecke, Judit; Kata, Dariusz

2016-06-01

Porous, graded ceramic structures are of high relevance in the field of energy conversion as well as in catalysis, and additionally in filtration technology and in biomedical applications. Among different technologies for the tailored design for such structures we demonstrate here a new environmental friendly UV curing-based concept to prepare laminated structures with pore sizes ranging from a few microns up to 50 microns in diameter and with porosities ranging from 10% up to 75 vol.% porosity.

Twelfth International Symposium on Methodologies for Intelligent Systems (ISMIS󈧄) Held in Charlotte, North Carolina on October 11-14, 2000

DTIC Science & Technology

2000-10-14

without any knowledge of the problem area. Therefore, Darwinian-type evolutionary computation has found a very wide range of applications, including many ...the author examined many biomedical studies that included literature searches. The Science Citation Index (SCL) Abstracts of these studies...yield many records that are non-relevant to the main technical themes of the study. In summary, these types of simple limited queries can result in two

Exploration of Global Trend on Biomedical Application of Polyhydroxyalkanoate (PHA): A Patent Survey.

PubMed

Ponnaiah, Paulraj; Vnoothenei, Nagiah; Chandramohan, Muruganandham; Thevarkattil, Mohamed Javad Pazhayakath

2018-01-30

Polyhydroxyalkanoates are bio-based, biodegradable naturally occurring polymers produced by a wide range of organisms, from bacteria to higher mammals. The properties and biocompatibility of PHA make it possible for a wide spectrum of applications. In this context, we analyze the potential applications of PHA in biomedical science by exploring the global trend through the patent survey. The survey suggests that PHA is an attractive candidate in such a way that their applications are widely distributed in the medical industry, drug delivery system, dental material, tissue engineering, packaging material as well as other useful products. In our present study, we explored patents associated with various biomedical applications of polyhydroxyalkanoates. Patent databases of European Patent Office, United States Patent and Trademark Office and World Intellectual Property Organization were mined. We developed an intensive exploration approach to eliminate overlapping patents and sort out significant patents. We demarcated the keywords and search criterions and established search patterns for the database request. We retrieved documents within the recent 6 years, 2010 to 2016 and sort out the collected data stepwise to gather the most appropriate documents in patent families for further scrutiny. By this approach, we retrieved 23,368 patent documents from all the three databases and the patent titles were further analyzed for the relevance of polyhydroxyalkanoates in biomedical applications. This ensued in the documentation of approximately 226 significant patents associated with biomedical applications of polyhydroxyalkanoates and the information was classified into six major groups. Polyhydroxyalkanoates has been patented in such a way that their applications are widely distributed in the medical industry, drug delivery system, dental material, tissue engineering, packaging material as well as other useful products. There are many avenues through which PHA & PHB could be used. Our analysis shows patent information can be used to identify various applications of PHA and its representatives in the biomedical field. Upcoming studies can focus on the application of PHA in the different field to discover the related topics and associate to this study. We believe that this approach of analysis and findings can initiate new researchers to undertake similar kind of studies in their represented field to fill the gap between the patent articles and researchpublications. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Technical editing of research reports in biomedical journals.

PubMed

Wager, Elizabeth; Middleton, Philippa

2008-10-08

Most journals try to improve their articles by technical editing processes such as proof-reading, editing to conform to 'house styles', grammatical conventions and checking accuracy of cited references. Despite the considerable resources devoted to technical editing, we do not know whether it improves the accessibility of biomedical research findings or the utility of articles. This is an update of a Cochrane methodology review first published in 2003. To assess the effects of technical editing on research reports in peer-reviewed biomedical journals, and to assess the level of accuracy of references to these reports. We searched The Cochrane Library Issue 2, 2007; MEDLINE (last searched July 2006); EMBASE (last searched June 2007) and checked relevant articles for further references. We also searched the Internet and contacted researchers and experts in the field. Prospective or retrospective comparative studies of technical editing processes applied to original research articles in biomedical journals, as well as studies of reference accuracy. Two review authors independently assessed each study against the selection criteria and assessed the methodological quality of each study. One review author extracted the data, and the second review author repeated this. We located 32 studies addressing technical editing and 66 surveys of reference accuracy. Only three of the studies were randomised controlled trials. A 'package' of largely unspecified editorial processes applied between acceptance and publication was associated with improved readability in two studies and improved reporting quality in another two studies, while another study showed mixed results after stricter editorial policies were introduced. More intensive editorial processes were associated with fewer errors in abstracts and references. Providing instructions to authors was associated with improved reporting of ethics requirements in one study and fewer errors in references in two studies, but no difference was seen in the quality of abstracts in one randomised controlled trial. Structuring generally improved the quality of abstracts, but increased their length. The reference accuracy studies showed a median citation error rate of 38% and a median quotation error rate of 20%. Surprisingly few studies have evaluated the effects of technical editing rigorously. However there is some evidence that the 'package' of technical editing used by biomedical journals does improve papers. A substantial number of references in biomedical articles are cited or quoted inaccurately.

Sharing all types of clinical data and harmonizing journal standards.

PubMed

Barbui, Corrado

2016-04-03

Despite recent efforts to enforce policies requiring the sharing of data underlying clinical findings, current policies of biomedical journals remain largely heterogeneous. As this heterogeneity does not optimally serve the cause of data sharing, a first step towards better harmonization would be the requirement of a data sharing statement for all clinical studies and not simply for randomized studies. Although the publication of a data sharing statement does not imply that all data is made readily available, such a policy would swiftly implement a cultural change in the definition of scientific outputs. Currently, a scientific output only corresponds to a study report published in a medical journal, while in the near future it might consist of all materials described in the manuscript, including all relevant raw data. When such a cultural shift has been achieved, the logical conclusion would be for biomedical journals to require authors to make all data fully available without restriction as a condition for publication.

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

PubMed Central

Koscielny, Gautier; Yaikhom, Gagarine; Iyer, Vivek; Meehan, Terrence F.; Morgan, Hugh; Atienza-Herrero, Julian; Blake, Andrew; Chen, Chao-Kung; Easty, Richard; Di Fenza, Armida; Fiegel, Tanja; Grifiths, Mark; Horne, Alan; Karp, Natasha A.; Kurbatova, Natalja; Mason, Jeremy C.; Matthews, Peter; Oakley, Darren J.; Qazi, Asfand; Regnart, Jack; Retha, Ahmad; Santos, Luis A.; Sneddon, Duncan J.; Warren, Jonathan; Westerberg, Henrik; Wilson, Robert J.; Melvin, David G.; Smedley, Damian; Brown, Steve D. M.; Flicek, Paul; Skarnes, William C.; Mallon, Ann-Marie; Parkinson, Helen

2014-01-01

The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and standardized protocols for the experimentation, collection and dissemination of data. Dedicated ‘data wranglers’ work with each phenotyping center to collate data and perform quality control of data. An automated statistical analysis pipeline has been developed to identify knockout strains with a significant change in the phenotype parameters. Annotation with biomedical ontologies allows biologists and clinicians to easily find mouse strains with phenotypic traits relevant to their research. Data integration with other resources will provide insights into mammalian gene function and human disease. As phenotype data become available for every gene in the mouse, the IMPC web portal will become an invaluable tool for researchers studying the genetic contributions of genes to human diseases. PMID:24194600

Integration of medicine and basic science in dentistry: the role of oral and maxillofacial surgery in the pre-doctoral dental curriculum.

PubMed

Dennis, Matthew J

2010-05-01

It is the premise of this paper that the need for medical and basic science instruction in dentistry will increase over time. However, student and faculty appreciation of the relevance and significance of medicine and basic science to clinical dentistry has been elusive, largely due to difficulties linking biomedical science instruction and clinical dental instruction. The scope of traditional procedure based oral surgery instruction can be expanded in an attempt to bridge the medical science-clinical gap. Topics such as health status evaluation, medical risk assessment, and a variety of other biomedical issues can be presented to students in a way which imparts specific dental meaning to basic medical science in real-life clinical situations. Using didactic and chair side instruction in an oral surgery clinical environment, students are confronted with the need to understand these issues and how they relate to the patients they encounter who present for dental care.

Biomedical potentials of crown ethers: prospective antitumor agents.

PubMed

Kralj, Marijeta; Tusek-Bozić, Ljerka; Frkanec, Leo

2008-10-01

Crown ethers are of enormous interest and importance in chemistry, biochemistry, materials science, catalysis, separation, transport and encapsulated processes, as well as in the design and synthesis of various synthetic systems with specific properties, diverse capabilities, and programmable functions. Classical crown ethers are macrocyclic polyethers that contain 3-20 oxygen atoms separated from each other by two or more carbon atoms. They are exceptionally versatile in selectively binding a range of metal ions and a variety of organic neutral and ionic species. Crown ethers are currently being studied and used in a variety of applications beyond their traditional place in chemistry. This review presents additional applications and the ever-increasing biomedical potentials of these intriguing compounds, with particular emphasis on the prospects of their relevance as anticancer agents. We believe that further research in this direction should be encouraged, as crown compounds could either induce toxicities that are different from those of conventional antitumor drugs, or complement drugs in current use, thereby providing a valuable adjunct to therapy.

New Perspectives on Biomedical Applications of Iron Oxide Nanoparticles.

PubMed

Magro, Massimiliano; Baratella, Davide; Bonaiuto, Emanuela; de A Roger, Jessica; Vianello, Fabio

2018-02-12

Iron oxide nanomaterials are considered promising tools for improved therapeutic efficacy and diagnostic applications in biomedicine. Accordingly, engineered iron oxide nanomaterials are increasingly proposed in biomedicine, and the interdisciplinary researches involving physics, chemistry, biology (nanotechnology) and medicine have led to exciting developments in the last decades. The progresses of the development of magnetic nanoparticles with tailored physico-chemical and surface properties produced a variety of clinically relevant applications, spanning from magnetic resonance imaging (MRI), drug delivery, magnetic hyperthermia, to in vitro diagnostics. Notwithstanding the wellknown conventional synthetic procedures and their wide use, along with recent advances in the synthetic methods open the door to new generations of naked iron oxide nanoparticles possessing peculiar surface chemistries, suitable for other competitive biomedical applications. New abilities to rationally manipulate iron oxides and their physical, chemical, and biological properties, allow the emersion of additional possibilities for designing novel nanomaterials for theranostic applications. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Using Galaxy to Perform Large-Scale Interactive Data Analyses

PubMed Central

Hillman-Jackson, Jennifer; Clements, Dave; Blankenberg, Daniel; Taylor, James; Nekrutenko, Anton

2014-01-01

Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high-throughput data resources to be analyzed. As creating and obtaining data has become easier, the key decision faced by many researchers is a practical one: where and how should an analysis be performed? Datasets are large and analysis tool set-up and use is riddled with complexities outside of the scope of core research activities. The authors believe that Galaxy provides a powerful solution that simplifies data acquisition and analysis in an intuitive Web application, granting all researchers access to key informatics tools previously only available to computational specialists working in Unix-based environments. We will demonstrate through a series of biomedically relevant protocols how Galaxy specifically brings together (1) data retrieval from public and private sources, for example, UCSC's Eukaryote and Microbial Genome Browsers, (2) custom tools (wrapped Unix functions, format standardization/conversions, interval operations), and 3rd-party analysis tools. PMID:22700312

Theory, simulations and the design of functionalized nanoparticles for biomedical applications: A Soft Matter Perspective

NASA Astrophysics Data System (ADS)

Angioletti-Uberti, Stefano

2017-11-01

Functionalised nanoparticles for biomedical applications represents an incredibly exciting and rapidly growing field of research. Considering the complexity of the nano-bio interface, an important question is to what extent can theory and simulations be used to study these systems in a realistic, meaningful way. In this review, we will argue for a positive answer to this question. Approaching the issue from a "Soft Matter" perspective, we will consider those properties of functionalised nanoparticles that can be captured within a classical description. We will thus not concentrate on optical and electronic properties, but rather on the way nanoparticles' interactions with the biological environment can be tuned by functionalising their surface and exploited in different contexts relevant to applications. In particular, we wish to provide a critical overview of theoretical and computational coarse-grained models, developed to describe these interactions and present to the readers some of the latest results in this fascinating area of research.

Unified Tri-service Cognitive Performance Assessment Battery (UTC-PAB). Part 1: Design and specification of the battery

NASA Astrophysics Data System (ADS)

Englund, C. E.; Reeves, D. L.; Shingledecker, C. A.; Thorne, D. R.; Wilson, K. P.

1987-02-01

The Unified Tri-Service Cognitive Performance Assessment Battery (UTC-PAB) represents the primary metric for a Level 2 evaluation of cognitive performance in the JWGD3 MILPERF chemical defense biomedical drug screening program. Emphasis for UTC-PAB development has been on the standardization of test batteries across participating laboratories with respect to content, computer-based administration, test scoring, and data formatting. This effort has produced a 25-test UTC-PAB that represents the consolidation and unification of independent developments by the Tri-service membership. Test selection was based on established test validity and relevance of military performance. Sensitivity to effects of hostile environments and sustained operations were also considerations involved in test selection. Information processing, decision making, perception, and mental workload capacity are among the processes and abilities addressed in the battery. The UTC-PAB represents a dynamic approach to battery development. The nature of the biomedical drugs screened and information from performance centered task analyses will direct the form of future versions of the battery.

Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions.

PubMed

Agarwal, Shashank; Liu, Feifan; Yu, Hong

2011-10-03

Protein-protein interaction (PPI) is an important biomedical phenomenon. Automatically detecting PPI-relevant articles and identifying methods that are used to study PPI are important text mining tasks. In this study, we have explored domain independent features to develop two open source machine learning frameworks. One performs binary classification to determine whether the given article is PPI relevant or not, named "Simple Classifier", and the other one maps the PPI relevant articles with corresponding interaction method nodes in a standardized PSI-MI (Proteomics Standards Initiative-Molecular Interactions) ontology, named "OntoNorm". We evaluated our system in the context of BioCreative challenge competition using the standardized data set. Our systems are amongst the top systems reported by the organizers, attaining 60.8% F1-score for identifying relevant documents, and 52.3% F1-score for mapping articles to interaction method ontology. Our results show that domain-independent machine learning frameworks can perform competitively well at the tasks of detecting PPI relevant articles and identifying the methods that were used to study the interaction in such articles. Simple Classifier is available at http://sourceforge.net/p/simpleclassify/home/ and OntoNorm at http://sourceforge.net/p/ontonorm/home/.

Monte Carlo based investigation of berry phase for depth resolved characterization of biomedical scattering samples

NASA Astrophysics Data System (ADS)

Baba, J. S.; Koju, V.; John, D.

2015-03-01

The propagation of light in turbid media is an active area of research with relevance to numerous investigational fields, e.g., biomedical diagnostics and therapeutics. The statistical random-walk nature of photon propagation through turbid media is ideal for computational based modeling and simulation. Ready access to super computing resources provide a means for attaining brute force solutions to stochastic light-matter interactions entailing scattering by facilitating timely propagation of sufficient (>107) photons while tracking characteristic parameters based on the incorporated physics of the problem. One such model that works well for isotropic but fails for anisotropic scatter, which is the case for many biomedical sample scattering problems, is the diffusion approximation. In this report, we address this by utilizing Berry phase (BP) evolution as a means for capturing anisotropic scattering characteristics of samples in the preceding depth where the diffusion approximation fails. We extend the polarization sensitive Monte Carlo method of Ramella-Roman, et al., to include the computationally intensive tracking of photon trajectory in addition to polarization state at every scattering event. To speed-up the computations, which entail the appropriate rotations of reference frames, the code was parallelized using OpenMP. The results presented reveal that BP is strongly correlated to the photon penetration depth, thus potentiating the possibility of polarimetric depth resolved characterization of highly scattering samples, e.g., biological tissues.

The limitations of ‘Black MSM’ as a category: Why gender, sexuality, and desire still matter for social and biomedical HIV prevention methods

PubMed Central

Garcia, Jonathan; Parker, Richard G.; Parker, Caroline; Wilson, Patrick A.; Philbin, Morgan; Hirsch, Jennifer S.

2016-01-01

The USA faces disproportionate and increasing HIV incidence rates among Black men who have sex with men (BMSM). New biomedical technologies such as pre-exposure prophylaxis (PrEP) have been developed to address their HIV risk. Very little consideration, however, has been given to the diversity obscured by ‘BMSM’ as a category, to how this diversity relates to men’s sexual partnering strategies, or to the relevance of these issues for new HIV prevention methods. We conducted a community-based ethnography from June 2013 to May 2014 documenting factors that affect the acceptance of and adherence to PrEP among BMSM. We conducted in-depth interviews with 31 BMSM and 17 community stakeholders, and participant observation. To demonstrate the diversity of social identities, we present a taxonomy of indigenous categories organised along the axes of sexual identity, sexual positioning, and gender performance. We analyse how HIV prevention strategies, such as PrEP, may be more effective if programs consider how gender, sexuality, and sexual desire shape sexual partnering strategies. This article underlines the importance of attending to the diversity of sexual and social subjectivities among BMSM, of bringing the study of sexuality back into HIV prevention, and of integrating biomedical prevention approaches into community-based programs. PMID:26831639

Extraction and labeling high-resolution images from PDF documents

NASA Astrophysics Data System (ADS)

Chachra, Suchet K.; Xue, Zhiyun; Antani, Sameer; Demner-Fushman, Dina; Thoma, George R.

2013-12-01

Accuracy of content-based image retrieval is affected by image resolution among other factors. Higher resolution images enable extraction of image features that more accurately represent the image content. In order to improve the relevance of search results for our biomedical image search engine, Open-I, we have developed techniques to extract and label high-resolution versions of figures from biomedical articles supplied in the PDF format. Open-I uses the open-access subset of biomedical articles from the PubMed Central repository hosted by the National Library of Medicine. Articles are available in XML and in publisher supplied PDF formats. As these PDF documents contain little or no meta-data to identify the embedded images, the task includes labeling images according to their figure number in the article after they have been successfully extracted. For this purpose we use the labeled small size images provided with the XML web version of the article. This paper describes the image extraction process and two alternative approaches to perform image labeling that measure the similarity between two images based upon the image intensity projection on the coordinate axes and similarity based upon the normalized cross-correlation between the intensities of two images. Using image identification based on image intensity projection, we were able to achieve a precision of 92.84% and a recall of 82.18% in labeling of the extracted images.

Monte Carlo based investigation of Berry phase for depth resolved characterization of biomedical scattering samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baba, Justin S; John, Dwayne O; Koju, Vijay

The propagation of light in turbid media is an active area of research with relevance to numerous investigational fields, e.g., biomedical diagnostics and therapeutics. The statistical random-walk nature of photon propagation through turbid media is ideal for computational based modeling and simulation. Ready access to super computing resources provide a means for attaining brute force solutions to stochastic light-matter interactions entailing scattering by facilitating timely propagation of sufficient (>10million) photons while tracking characteristic parameters based on the incorporated physics of the problem. One such model that works well for isotropic but fails for anisotropic scatter, which is the case formore » many biomedical sample scattering problems, is the diffusion approximation. In this report, we address this by utilizing Berry phase (BP) evolution as a means for capturing anisotropic scattering characteristics of samples in the preceding depth where the diffusion approximation fails. We extend the polarization sensitive Monte Carlo method of Ramella-Roman, et al.,1 to include the computationally intensive tracking of photon trajectory in addition to polarization state at every scattering event. To speed-up the computations, which entail the appropriate rotations of reference frames, the code was parallelized using OpenMP. The results presented reveal that BP is strongly correlated to the photon penetration depth, thus potentiating the possibility of polarimetric depth resolved characterization of highly scattering samples, e.g., biological tissues.« less

McTwo: a two-step feature selection algorithm based on maximal information coefficient.

PubMed

Ge, Ruiquan; Zhou, Manli; Luo, Youxi; Meng, Qinghan; Mai, Guoqin; Ma, Dongli; Wang, Guoqing; Zhou, Fengfeng

2016-03-23

High-throughput bio-OMIC technologies are producing high-dimension data from bio-samples at an ever increasing rate, whereas the training sample number in a traditional experiment remains small due to various difficulties. This "large p, small n" paradigm in the area of biomedical "big data" may be at least partly solved by feature selection algorithms, which select only features significantly associated with phenotypes. Feature selection is an NP-hard problem. Due to the exponentially increased time requirement for finding the globally optimal solution, all the existing feature selection algorithms employ heuristic rules to find locally optimal solutions, and their solutions achieve different performances on different datasets. This work describes a feature selection algorithm based on a recently published correlation measurement, Maximal Information Coefficient (MIC). The proposed algorithm, McTwo, aims to select features associated with phenotypes, independently of each other, and achieving high classification performance of the nearest neighbor algorithm. Based on the comparative study of 17 datasets, McTwo performs about as well as or better than existing algorithms, with significantly reduced numbers of selected features. The features selected by McTwo also appear to have particular biomedical relevance to the phenotypes from the literature. McTwo selects a feature subset with very good classification performance, as well as a small feature number. So McTwo may represent a complementary feature selection algorithm for the high-dimensional biomedical datasets.

Professional Learning in Higher Education: Making Good Practice Relevant

ERIC Educational Resources Information Center

Daniels, Jeannie

2017-01-01

Professionals working in a range of contexts are increasingly expected to engage in ongoing professional learning to maintain their skills and develop their practices. In this paper, I focus on professional learning in Higher Education and challenge the standardisation of professional learning that is becoming prevalent in a number of countries. I…

"I'm Sorry + Naming the Offense": A Format for Apologizing

ERIC Educational Resources Information Center

Cirillo, Letizia; Colón de Carvajal, Isabel; Ticca, Anna Claudia

2016-01-01

The present article focuses on "I'm sorry + naming the offense"-formatted apologies occurring in phone calls in English. Apologies of this kind "emerge" and are oriented to as relevant actions when addressing an apologizable that is not the main business in ongoing talk. The sequential analysis of apologies and responses to…

Memory for Recently Accessed Visual Attributes

ERIC Educational Resources Information Center

Jiang, Yuhong V.; Shupe, Joshua M.; Swallow, Khena M.; Tan, Deborah H.

2016-01-01

Recent reports have suggested that the attended features of an item may be rapidly forgotten once they are no longer relevant for an ongoing task (attribute amnesia). This finding relies on a surprise memory procedure that places high demands on declarative memory. We used intertrial priming to examine whether the representation of an item's…

Research on a Community-Initiated Preschool Program. Final Report.

ERIC Educational Resources Information Center

Davies, Norma

This report describes and anlayzes the second year operations of an ongoing successful parent initiated and directed nursery school. Included are: (1) a brief review of relevant issues in early childhood education, such as parent participation and community control in education; (2) a short history of the program's inception and early development;…

What Makes Your Wheels Turn?

ERIC Educational Resources Information Center

DiJulio, Betsy

2010-01-01

In the author's ongoing attempt to design creative challenges that are relevant, based on observational drawing, and that place students squarely in the creative problem-solving driver's seat, she chose cars and engines as subjects. After all, they have a parking lot full of them and their administrative staff members, who park side-by-side, were…

Post-Racial Pedagogy--Challenges and Possibilities

ERIC Educational Resources Information Center

Singh, Gurnam

2018-01-01

Against the backdrop of ongoing discussions about how best to conceptualise, confront and ultimately eradicate racism, this paper seeks to critically examine the relevance of 'post-racial' thinking, both in a general sense, but also in relation to education. The argument is framed around a concern that multi-cultural, and to a lesser extent,…

Overview of Play: Its Uses and Importance in Early Intervention/Early Childhood Special Education

ERIC Educational Resources Information Center

Lifter, Karin; Foster-Sanda, Suzanne; Arzamarski, Caley; Briesch, Jacquelyn; McClure, Ellen

2011-01-01

Play is a natural activity of early childhood, which has great relevance to the fields of early intervention, early childhood special education, and early childhood education. Within these fields, ongoing tensions persist in how play is described and used. These tensions compromise activities of assessment, intervention, and curriculum development…

Traditional Birth Attendant Training and Local Birthing Practices in India

ERIC Educational Resources Information Center

Saravanan, Sheela; Turrell, Gavin; Johnson, Helen; Fraser, Jenny; Patterson, Carla

2011-01-01

Training birth attendants (TBAs) to provide essential maternal and infant health care services during delivery and ongoing community care in developing countries. Despite inadequate evidence of relevance and effectiveness of TBA training programmes, there has been a policy shift since the 1990s in that many donor agencies funding TBA training…

Notes from a Kidwatcher: Selected Writings of Yetta M. Goodman.

ERIC Educational Resources Information Center

Goodman, Yetta M.; Wilde, Sandra, Ed.

The 23 articles chosen for this anthology of Yetta M. Goodman's writings were chosen based on historical importance, centrality to her body of work, availability, and/or ongoing relevance to teachers. The articles in the anthology are grouped to reflect major themes (culture and community; miscue analysis, reading strategies, and comprehension;…

The Relevance of "Personal Mastery" to Leadership: The Case of School Principals in Singapore

ERIC Educational Resources Information Center

Retna, Kala S.

2011-01-01

School leadership literature suggests that school effectiveness and ongoing improvement rely on school leaders and principals. Despite significant contributions made by principals towards teaching and learning in schools, there have been few studies that explore principals' perceptions of the factors underpinning their successes and achievements.…

Five Recession-Driven Strategies for Planning and Managing Campus Facilities

ERIC Educational Resources Information Center

Rudden, Michael S.

2010-01-01

Colleges and universities continue to face significant fiscal challenges in the current recession. A review of ongoing campus facilities planning projects, coupled with a review of more than 30 recent campus master planning requests for proposals and the relevant literature, indicates that colleges and universities are finding innovative ways to…

Management needs assessment for the Copper River Delta, Alaska.

Treesearch

L.E. Kruger; C.B. Tyler

1995-01-01

This report assesses needs, problems, and perceptions relevant to management for the Copper River Delta (Alaska)—the largest coastal wetland on the Pacific coast of North America. The assessment provides a basis for planning and decisionmaking and a framework for ongoing research, development, and application. It also underscores concerns about human impacts...

Finding One's Voice: The Pacesetter Model for More Equitable Assessment.

ERIC Educational Resources Information Center

Badger, Elizabeth

1996-01-01

Describes the College Board's Pacesetter Program, high school courses developed using principles of ongoing performance testing and portfolios, standards, and curriculum. The model is illustrated in a description of the Voices of Modern Culture language arts course. Argues that this assessment process has systemic validity and is more relevant to…

MSW Students' Perceptions of Relevance and Application of Statistics: Implications for Field Education

ERIC Educational Resources Information Center

Davis, Ashley; Mirick, Rebecca G.

2015-01-01

Many social work students feel anxious when taking a statistics course. Their attitudes, beliefs, and behaviors after learning statistics are less known. However, such information could help instructors support students' ongoing development of statistical knowledge. With a sample of MSW students (N = 101) in one program, this study examined…

Dynamic reorganization of human resting-state networks during visuospatial attention.

PubMed

Spadone, Sara; Della Penna, Stefania; Sestieri, Carlo; Betti, Viviana; Tosoni, Annalisa; Perrucci, Mauro Gianni; Romani, Gian Luca; Corbetta, Maurizio

2015-06-30

Fundamental problems in neuroscience today are understanding how patterns of ongoing spontaneous activity are modified by task performance and whether/how these intrinsic patterns influence task-evoked activation and behavior. We examined these questions by comparing instantaneous functional connectivity (IFC) and directed functional connectivity (DFC) changes in two networks that are strongly correlated and segregated at rest: the visual (VIS) network and the dorsal attention network (DAN). We measured how IFC and DFC during a visuospatial attention task, which requires dynamic selective rerouting of visual information across hemispheres, changed with respect to rest. During the attention task, the two networks remained relatively segregated, and their general pattern of within-network correlation was maintained. However, attention induced a decrease of correlation in the VIS network and an increase of the DAN→VIS IFC and DFC, especially in a top-down direction. In contrast, within the DAN, IFC was not modified by attention, whereas DFC was enhanced. Importantly, IFC modulations were behaviorally relevant. We conclude that a stable backbone of within-network functional connectivity topography remains in place when transitioning between resting wakefulness and attention selection. However, relative decrease of correlation of ongoing "idling" activity in visual cortex and synchronization between frontoparietal and visual cortex were behaviorally relevant, indicating that modulations of resting activity patterns are important for task performance. Higher order resting connectivity in the DAN was relatively unaffected during attention, potentially indicating a role for simultaneous ongoing activity as a "prior" for attention selection.

Rhythms of Consciousness: Binocular Rivalry Reveals Large-Scale Oscillatory Network Dynamics Mediating Visual Perception

PubMed Central

Doesburg, Sam M.; Green, Jessica J.; McDonald, John J.; Ward, Lawrence M.

2009-01-01

Consciousness has been proposed to emerge from functionally integrated large-scale ensembles of gamma-synchronous neural populations that form and dissolve at a frequency in the theta band. We propose that discrete moments of perceptual experience are implemented by transient gamma-band synchronization of relevant cortical regions, and that disintegration and reintegration of these assemblies is time-locked to ongoing theta oscillations. In support of this hypothesis we provide evidence that (1) perceptual switching during binocular rivalry is time-locked to gamma-band synchronizations which recur at a theta rate, indicating that the onset of new conscious percepts coincides with the emergence of a new gamma-synchronous assembly that is locked to an ongoing theta rhythm; (2) localization of the generators of these gamma rhythms reveals recurrent prefrontal and parietal sources; (3) theta modulation of gamma-band synchronization is observed between and within the activated brain regions. These results suggest that ongoing theta-modulated-gamma mechanisms periodically reintegrate a large-scale prefrontal-parietal network critical for perceptual experience. Moreover, activation and network inclusion of inferior temporal cortex and motor cortex uniquely occurs on the cycle immediately preceding responses signaling perceptual switching. This suggests that the essential prefrontal-parietal oscillatory network is expanded to include additional cortical regions relevant to tasks and perceptions furnishing consciousness at that moment, in this case image processing and response initiation, and that these activations occur within a time frame consistent with the notion that conscious processes directly affect behaviour. PMID:19582165

Longitudinal trends in thyroid function in relation to iodine intake: ongoing changes of thyroid function despite adequate current iodine status.

PubMed

van de Ven, Annenienke C; Netea-Maier, Romana T; Ross, H Alec; van Herwaarden, Teun A E; Holewijn, Suzanne; de Graaf, Jacqueline; Kiemeney, Bart L A; van Tienoven, Doorlène; Wetzels, Jack F M; Smit, Johannes W; Sweep, Fred C G J; Hermus, Ad R M M; den Heijer, Martin

2014-01-01

Several cross-sectional studies on populations with iodine deficiency showed that TSH-levels are negatively associated with age, while in populations with high iodine intake TSH is positively associated with age. The question is whether such an age-thyroid function relation is an ongoing process apparent also in longitudinal studies and whether it reflects an actual iodine deficiency or an iodine insufficiency in the past. In an area with a borderline iodine status in the past, we studied 980 participants of the Nijmegen Biomedical Study. We measured serum TSH, free thyroxine (FT₄), total triiodothyronine (T₃), peroxidase antibodies, and the urine iodine and creatinine concentration 4 years after our initial survey of thyroid function, in which we reported a negative association between TSH and age. within 4 years, TSH decreased by 5.4% (95% ci 2.58.3%) and FT₄ increased by 3.7% (95% ci 2.94.6%). median urinary iodine concentration was 130 μg/l. estimated 24-h iodine excretion was not associated with TSH, T₃, change of TSH, or FT₄ over time or with the presence of antibodies against thyroid peroxidase. Only FT₄ appeared to be somewhat higher at lower urine iodine levels: a 1.01% (95% CI 0.17-1.84%) higher FT₄ for each lower iodine quintile. In this longitudinal study, we found an ongoing decrease in TSH and increase in FT₄ in a previously iodine insufficient population, despite the adequate iodine status at present. This suggests that low iodine intake at young age leads to thyroid autonomy (and a tendency to hyperthyroidism) that persists despite normal iodine intake later in life.

Revealing mesoscopic structural universality with diffusion.

PubMed

Novikov, Dmitry S; Jensen, Jens H; Helpern, Joseph A; Fieremans, Els

2014-04-08

Measuring molecular diffusion is widely used for characterizing materials and living organisms noninvasively. This characterization relies on relations between macroscopic diffusion metrics and structure at the mesoscopic scale commensurate with the diffusion length. Establishing such relations remains a fundamental challenge, hindering progress in materials science, porous media, and biomedical imaging. Here we show that the dynamical exponent in the time dependence of the diffusion coefficient distinguishes between the universality classes of the mesoscopic structural complexity. Our approach enables the interpretation of diffusion measurements by objectively selecting and modeling the most relevant structural features. As an example, the specific values of the dynamical exponent allow us to identify the relevant mesoscopic structure affecting MRI-measured water diffusion in muscles and in brain, and to elucidate the structural changes behind the decrease of diffusion coefficient in ischemic stroke.

Private wealth and public health: a critique of Richard Epstein's defense of the "old" public health.

PubMed

Novak, William J

2003-01-01

This article is a response to Richard Epstein's recent legal and economic critiques of contemporary public health law. The power of Epstein's critical position stems from the convergence of three problems, each with distinctive intellectual histories: (1) an age-old debate within political liberalism about the proper relationship of individual right and state power; (2) a somewhat more recent biomedical policy contest over the necessary scale and scope of public health interventions in modern societies; and (3) an ongoing legal-jurisprudential argument about the overall trajectory and implications of American constitutional history. My critique of Epstein's position follows this same tripartite format, moving from an initial discussion of the history of liberalism to the history of public health and, finally, to a critique of Epstein's general legal history of state regulation in America.

NIH Precision Medicine Initiative: Implications for Diabetes Research

PubMed Central

Fradkin, Judith E.; Hanlon, Mary C.; Rodgers, Griffin P.

2016-01-01

In his January 2015 State of the Union address, President Barack Obama announced a new Precision Medicine Initiative (PMI) to personalize approaches toward improving health and treating disease (www.whitehouse.gov/precision-medicine). He stated that the goal of such an initiative was “to bring us closer to curing diseases like cancer and diabetes, and to give all of us access to the personalized information we need to keep ourselves and our families healthier.” Since that time, the National Institutes of Health (NIH) has taken a leadership role in implementing the President’s vision related to biomedical research (www.nih.gov/precisionmedicine). Here, we discuss the NIH component of the PMI, related ongoing diabetes research, and near-term research that could position the diabetes field to take full advantage of the opportunities that stem from the PMI. PMID:27289128

Common law morality.

PubMed

Arras, John D

1990-01-01

Arras reviews A.R. Jonsen and S. Toulmin's The Abuse of Casuistry: A History of Moral Reasoning (University of California Press; 1988). Jonsen and Toulmin, both of whom worked with the federal National Commission for the Protection of Human Subjects, critique the role of ethical theory in practical deliberation and attack the belief that moral theories are "universal, mutually exclusive sources of...ethical truth." They argue that "all genuine ethics is already concrete and particular," and champion casuistical reasoning with its emphasis on particularity and practical judgment. Arras find The Abuse of Casuistry to be "a fascinating and thought-provoking study of moral methodology that will enrich our understanding of moral reasoning and quicken the ongoing debate over the appropriate role of ethical theory in bioethical analysis." He questions, however, the authors' faith in casuistry as the means to achieve social consensus on biomedical controversies.

Biomedical technology transfer. Applications of NASA science and technology

NASA Technical Reports Server (NTRS)

Harrison, D. C.

1980-01-01

Ongoing projects described address: (1) intracranial pressure monitoring; (2) versatile portable speech prosthesis; (3) cardiovascular magnetic measurements; (4) improved EMG biotelemetry for pediatrics; (5) ultrasonic kidney stone disintegration; (6) pediatric roentgen densitometry; (7) X-ray spatial frequency multiplexing; (8) mechanical impedance determination of bone strength; (9) visual-to-tactile mobility aid for the blind; (10) Purkinje image eyetracker and stabilized photocoalqulator; (11) neurological applications of NASA-SRI eyetracker; (12) ICU synthesized speech alarm; (13) NANOPHOR: microelectrophoresis instrument; (14) WRISTCOM: tactile communication system for the deaf-blind; (15) medical applications of NASA liquid-circulating garments; and (16) hip prosthesis with biotelemetry. Potential transfer projects include a person-portable versatile speech prosthesis, a critical care transport sytem, a clinical information system for cardiology, a programmable biofeedback orthosis for scoliosis a pediatric long-bone reconstruction, and spinal immobilization apparatus.

Man/Machine Interaction Dynamics And Performance (MMIDAP) capability

NASA Technical Reports Server (NTRS)

Frisch, Harold P.

1991-01-01

The creation of an ability to study interaction dynamics between a machine and its human operator can be approached from a myriad of directions. The Man/Machine Interaction Dynamics and Performance (MMIDAP) project seeks to create an ability to study the consequences of machine design alternatives relative to the performance of both machine and operator. The class of machines to which this study is directed includes those that require the intelligent physical exertions of a human operator. While Goddard's Flight Telerobotic's program was expected to be a major user, basic engineering design and biomedical applications reach far beyond telerobotics. Ongoing efforts are outlined of the GSFC and its University and small business collaborators to integrate both human performance and musculoskeletal data bases with analysis capabilities necessary to enable the study of dynamic actions, reactions, and performance of coupled machine/operator systems.

The Academy for Future Science Faculty: randomized controlled trial of theory-driven coaching to shape development and diversity of early-career scientists.

PubMed

Thakore, Bhoomi K; Naffziger-Hirsch, Michelle E; Richardson, Jennifer L; Williams, Simon N; McGee, Richard

2014-08-02

Approaches to training biomedical scientists have created a talented research community. However, they have failed to create a professional workforce that includes many racial and ethnic minorities and women in proportion to their representation in the population or in PhD training. This is particularly true at the faculty level. Explanations for the absence of diversity in faculty ranks can be found in social science theories that reveal processes by which individuals develop identities, experiences, and skills required to be seen as legitimate within the profession. Using the social science theories of Communities of Practice, Social Cognitive Career Theory, identity formation, and cultural capital, we have developed and are testing a novel coaching-based model to address some of the limitations of previous diversity approaches. This coaching intervention (The Academy for Future Science Faculty) includes annual in-person meetings of students and trained faculty Career Coaches, along with ongoing virtual coaching, group meetings and communication. The model is being tested as a randomized controlled trial with two cohorts of biomedical PhD students from across the U.S., one recruited at the start of their PhDs and one nearing completion. Stratification into the experimental and control groups, and to coaching groups within the experimental arms, achieved equal numbers of students by race, ethnicity and gender to the extent possible. A fundamental design element of the Academy is to teach and make visible the social science principles which highly influence scientific advancement, as well as acknowledging the extra challenges faced by underrepresented groups working to be seen as legitimate within the scientific communities. The strategy being tested is based upon a novel application of the well-established principles of deploying highly skilled coaches, selected and trained for their ability to develop talents of others. This coaching model is intended to be a complement, rather than a substitute, for traditional mentoring in biomedical research training, and is being tested as such.

Coping styles as moderating the relationships between terrorist attacks and well-being outcomes.

PubMed

Braun-Lewensohn, Orna; Celestin-Westreich, Smadar; Celestin, Leon-Patrice; Verleye, Gino; Verté, Dominique; Ponjaert-Kristoffersen, Ingrid

2009-06-01

This study aims to explore use of coping strategies among adolescents and their relationships with well being in the context of ongoing terrorism. Furthermore, we aim to explore to what extent coping styles in addition to exposure variables explain well being of adolescents facing ongoing terror. During September 2003, after three years of ongoing terror attacks, 913 Israeli adolescents aged 12-18 years, completed the following questionnaires during regular class sessions: Demographics, Achenbach's Youth Self Report; Exposure to Terror and Post Traumatic Stress (PTS) questionnaire; Adolescent Coping Scale (ACS) and Brief Symptoms Inventory. Adolescents employed mainly problem solving strategies which mean they have the capacity to cope well in spite of stressful events. Emotional focused coping was associated with PTS and mental health problems. Regression analysis of different exposure and coping variables revealed that exposure, appraisal (subjective exposure) and coping styles explained 26-37% of the variance of different psychological problems. The findings highlight the importance of appraisal (subjective exposure) and coping strategies, for understanding adolescents' mental health outcomes. Moreover, these findings are relevant to the development of prevention/intervention programs that facilitate youth's cognitive and emotional adjustments to ongoing trauma risks and terror threats.

Probiotics for induction of remission in ulcerative colitis.

PubMed

Mallon, P; McKay, D; Kirk, S; Gardiner, K

2007-10-17

Ulcerative Colitis (UC) is an inflammatory condition affecting the colon with an incidence of approximately 10-20 per 100,000 per year. No existing intervention is effective in all patients with a proportion requiring colectomy. There are significant proportion of patients who experience adverse effects with current therapies. Consequently, new alternatives for the treatment of UC are constantly being sought. Probiotics are live microbial feed supplements that may beneficially affect the host by improving intestinal microbial balance, enhancing gut barrier function and improving local immune response. To assess the efficacy of probiotics compared with placebo or standard medical treatment (5-aminosalicylates, sulfasalazine or corticosteroids) for the induction of remission in active ulcerative colitis. A comprehensive search for relevant randomised controlled trials (RCT's) was carried out using MEDLINE (1966-January 2006), EMBASE (January 1985- 2006) and CENTRAL. The Cochrane IBD/FBD Review Group Specialised Trials Registrar was also searched. The Australasian Medical Index, Chinese Biomedical Literature Database, Latin American Caribbean Health Sciences Literature (LILACS), and the Japan Information Centre of Science and Technology File on Science, Technology and Medicine (JICST-E) were also used to identify abstracts. Conference proceedings from the Falk Symposium, Digestive Disease Week (DDW) and the United European Digestive Disease week were hand-searched. Authors of relevant studies and drug companies were contacted regarding ongoing or unpublished trials that may be relevant to the review. Randomised controlled trials investigating the effectiveness of probiotics compared to standard treatments in the induction of remission of active ulcerative colitis Two authors independently assessed trial quality and extracted data for analysis. Data were analysed using RevMan 4.2.7. A formal meta-analysis was not preformed due to differences in probiotics, outcomes and trial methodology. None of the included studies reported any statistically significant differences in remission or clinical improvement rates between probiotic and placebo or active comparator groups. Conventional therapy combined with a probiotic does not improve overall remission rates in patients with mild to moderate ulcerative colitis. However, there is limited evidence that probiotics added to standard therapy may provide modest benefits in terms of reduction of disease activity in patients with mild to moderately severe ulcerative colitis. Whether probiotics are as effective in patients with severe and more extensive disease and whether they can be used as an alternative to existing therapies is unknown. Further well designed, larger randomised controlled trials are needed to determine whether probiotics can be used as an alternative to current treatment modalities.

Creating a classification of image types in the medical literature for visual categorization

NASA Astrophysics Data System (ADS)

Müller, Henning; Kalpathy-Cramer, Jayashree; Demner-Fushman, Dina; Antani, Sameer

2012-02-01

Content-based image retrieval (CBIR) from specialized collections has often been proposed for use in such areas as diagnostic aid, clinical decision support, and teaching. The visual retrieval from broad image collections such as teaching files, the medical literature or web images, by contrast, has not yet reached a high maturity level compared to textual information retrieval. Visual image classification into a relatively small number of classes (20-100) on the other hand, has shown to deliver good results in several benchmarks. It is, however, currently underused as a basic technology for retrieval tasks, for example, to limit the search space. Most classification schemes for medical images are focused on specific areas and consider mainly the medical image types (modalities), imaged anatomy, and view, and merge them into a single descriptor or classification hierarchy. Furthermore, they often ignore other important image types such as biological images, statistical figures, flowcharts, and diagrams that frequently occur in the biomedical literature. Most of the current classifications have also been created for radiology images, which are not the only types to be taken into account. With Open Access becoming increasingly widespread particularly in medicine, images from the biomedical literature are more easily available for use. Visual information from these images and knowledge that an image is of a specific type or medical modality could enrich retrieval. This enrichment is hampered by the lack of a commonly agreed image classification scheme. This paper presents a hierarchy for classification of biomedical illustrations with the goal of using it for visual classification and thus as a basis for retrieval. The proposed hierarchy is based on relevant parts of existing terminologies, such as the IRMA-code (Image Retrieval in Medical Applications), ad hoc classifications and hierarchies used in imageCLEF (Image retrieval task at the Cross-Language Evaluation Forum) and NLM's (National Library of Medicine) OpenI. Furtheron, mappings to NLM's MeSH (Medical Subject Headings), RSNA's RadLex (Radiological Society of North America, Radiology Lexicon), and the IRMA code are also attempted for relevant image types. Advantages derived from such hierarchical classification for medical image retrieval are being evaluated through benchmarks such as imageCLEF, and R&D systems such as NLM's OpenI. The goal is to extend this hierarchy progressively and (through adding image types occurring in the biomedical literature) to have a terminology for visual image classification based on image types distinguishable by visual means and occurring in the medical open access literature.

Consumer-operated service program members' explanatory models of mental illness and recovery.

PubMed

Hoy, Janet M

2014-10-01

Incorporating individuals' understandings and explanations of mental illness into service delivery offers benefits relating to increased service relevance and meaning. Existing research delineates explanatory models of mental illness held by individuals in home, outpatient, and hospital-based contexts; research on models held by those in peer-support contexts is notably absent. In this article, I describe themes identified within and across explanatory models of mental illness and recovery held by mental health consumers (N = 24) at one peer center, referred to as a consumer-operated service center (COSP). Participants held explanatory models inclusive of both developmental stressors and biomedical causes, consistent with a stress-diathesis model (although no participant explicitly referenced such). Explicit incorporation of stress-diathesis constructs into programming at this COSP offers the potential of increasing service meaning and relevance. Identifying and incorporating shared meanings across individuals' understandings of mental illness likewise can increase relevance and meaning for particular subgroups of service users. © The Author(s) 2014.

Simulating Expert Clinical Comprehension: Adapting Latent Semantic Analysis to Accurately Extract Clinical Concepts from Psychiatric Narrative

PubMed Central

Cohen, Trevor; Blatter, Brett; Patel, Vimla

2008-01-01

Cognitive studies reveal that less-than-expert clinicians are less able to recognize meaningful patterns of data in clinical narratives. Accordingly, psychiatric residents early in training fail to attend to information that is relevant to diagnosis and the assessment of dangerousness. This manuscript presents cognitively motivated methodology for the simulation of expert ability to organize relevant findings supporting intermediate diagnostic hypotheses. Latent Semantic Analysis is used to generate a semantic space from which meaningful associations between psychiatric terms are derived. Diagnostically meaningful clusters are modeled as geometric structures within this space and compared to elements of psychiatric narrative text using semantic distance measures. A learning algorithm is defined that alters components of these geometric structures in response to labeled training data. Extraction and classification of relevant text segments is evaluated against expert annotation, with system-rater agreement approximating rater-rater agreement. A range of biomedical informatics applications for these methods are suggested. PMID:18455483

Research Ethics in the Context of Transition: Gaps in Policies and Programs on the Protection of Research Participants in the Selected Countries of Central and Eastern Europe.

PubMed

Famenka, Andrei

2016-12-01

This paper examines the ability of countries in Central and Eastern Europe (CEE) to ensure appropriate protection of research participants in the field of increasingly globalizing biomedical research. By applying an analytical framework for identifying gaps in policies and programs for human subjects protection to four countries of CEE-Belarus, Latvia, Lithuania, and Poland, substantial gaps in the scope and content of relevant policies and major impediments to program performance have been revealed. In these countries, public policies on the protection of research participants lack consistency and reliable mechanisms for their implementation. Impediments to program performance most often relate to inadequacies in the national research ethics systems with regard to organizational structure, budgetary support, supervision, and training. The level of research ethics capacity varies from country to country and depends on socio-economic and political factors of post-communist transition. The breadth and depth of the problems identified suggest that the current level of protection for research participants in CEE might be inadequate to the challenges posed by the globalization of biomedical research. In CEE countries, there is a need for strengthening research ethics capacity through modification of relevant policies and improvement of program management. The differences among the countries call for further research on identifying the best approaches for filling the gaps in the policies and programs aimed at ensuring effective protection of research participants.

The Value of Traditional Ecological Knowledge for the Environmental Health Sciences and Biomedical Research

PubMed Central

Herne, Mose; Castille, Dorothy

2017-01-01

Background: Traditional Ecological Knowledge (TEK) is a term, relatively new to Western science, that encompasses a subset of traditional knowledge maintained by Indigenous nations about the relationships between people and the natural environment. The term was first shared by tribal elders in the 1980s to help raise awareness of the importance of TEK. TEK has become a construct that Western scientists have increasingly considered for conducting culturally relevant research with Tribal nations. Objectives: The authors aim to position TEK in relation to other emerging schools of thought, that is, concepts such as the exposome, social determinants of health (SDoH), and citizen science, and to explore TEK’s relevance to environmental health research. This article provides examples of successful application of TEK principles in federally funded research when implemented with respect for the underlying cultural context and in partnership with Indigenous communities. Discussion: Rather than treating TEK as an adjunct or element to be quantified or incorporated into Western scientific studies, TEK can instead ground our understanding of the environmental, social, and biomedical determinants of health and improve our understanding of health and disease. This article provides historical and recent examples of how TEK has informed Western scientific research. Conclusions: This article provides recommendations for researchers and federal funders to ensure respect for the contributions of TEK to research and to ensure equity and self-determination for Tribal nations who participate in research. https://doi.org/10.1289/EHP858 PMID:28858824

Developing Educational Resources to Advance Umbilical Cord Blood Banking and Research: A Canadian Perspective.

PubMed

Beak, Carla Pereira; Chargé, Sophie B; Isasi, Rosario; Knoppers, Bartha M

2015-05-01

In 2013 Canadian Blood Services (CBS) launched the National Public Cord Blood Bank (NPCBB), a program to collect, process, test, and store cord blood units donated for use in transplantation. A key component of the creation of the NPCBB is the establishment of a program that enables cord blood not suitable for banking or transplantation to be used for biomedical research purposes. Along with the development of processes and policies to manage the NPCBB and the cord blood research program, CBS-in collaboration with researchers from the Stem Cell Network-have also developed educational tools to provide relevant information for target audiences to aid implementation and operation. We describe here one of these tools, the REB Primer on Research and Cord Blood Donation (the Primer), which highlights key ethical and legal considerations and identifies Canadian documents that are relevant to the use of cord blood in biomedical research. The Primer also introduces the NPCBB and describes the systems CBS is implementing to address ethical issues. The Primer is intended to assist research ethics boards in evaluating the ethical acceptability of research protocols, to facilitate harmonized decision-making by providing a common reference, and to highlight the role of research ethics boards in governance frameworks. With the Primer we hope to illustrate how the development of such educational tools can facilitate the ethical implementation and governance of programs related to stem cell research in Canada and abroad.

Research ethics in the context of transition: gaps in policies and programs on the protection of research participants in the selected countries of Central and Eastern Europe

PubMed Central

Famenka, Andrei

2015-01-01

This paper examines the ability of countries in Central and Eastern Europe (CEE) to ensure appropriate protection of research participants in the field of increasingly globalizing biomedical research. By applying an analytical framework for identifying gaps in policies and programs for human subjects protection to four countries of CEE – Belarus, Latvia, Lithuania, and Poland, substantial gaps in the scope and content of relevant policies and major impediments to program performance have been revealed. In these countries, public policies on the protection of research participants lack consistency and reliable mechanisms for their implementation. Impediments to program performance most often relate to inadequacies in the national research ethics systems with regard to organizational structure, budgetary support, supervision, and training. The level of research ethics capacity varies from country to country and depends on socio-economic and political factors of post-communist transition. The breadth and depth of the problems identified suggest that the current level of protection for research participants in CEE might be inadequate to the challenges posed by the globalization of biomedical research. In CEE countries, there is a need for strengthening research ethics capacity through modification of relevant policies and improvement of program management. The differences among the countries call for further research on identifying the best approaches for filling the gaps in the policies and programs aimed at ensuring effective protection of research participants. PMID:26548313

Jorge A. Swieca's contributions to quantum field theory in the 60s and 70s and their relevance in present research

NASA Astrophysics Data System (ADS)

Schroer, B.

2010-07-01

After revisiting some high points of particle physics and QFT of the two decades from 1960 to 1980, I comment on the work by Jorge André Swieca. I explain how it fits into the quantum field theory during these two decades and draw attention to its relevance to the ongoing particle physics research. A particular aim of this article is to direct the readers mindfulness to the relevance of what at the time of Swieca was called “the Schwinger Higgs screening mechanism” which, together with recent ideas which generalize the concept of gauge theories, has all the ingredients to revolutionize the issue of gauge theories and the standard model.

People with low back pain perceive needs for non-biomedical services in workplace, financial, social and household domains: a systematic review.

PubMed

Chou, Louisa; Cicuttini, Flavia M; Urquhart, Donna M; Anthony, Shane N; Sullivan, Kaye; Seneviwickrama, Maheeka; Briggs, Andrew M; Wluka, Anita E

2018-04-01

What needs of non-biomedical services are perceived by people with low back pain? Systematic review of qualitative and quantitative studies examining perceived needs of non-biomedical services for low back pain, identified through searching of MEDLINE, EMBASE, CINAHL and PsycINFO (1990 to 2016). Adults with low back pain of any duration. Descriptive data regarding study design and methodology were extracted. The preferences, expectations and satisfaction with non-biomedical services reported by people with low back pain were identified and categorised within areas of perceived need. Twenty studies (19 qualitative and one quantitative) involving 522 unique participants (total pool of 590) were included in this systematic review. Four areas emerged. Workplace: people with low back pain experience pressure to return to work despite difficulties with the demands of their occupation. They want their employers to be informed about low back pain and they desire workplace accommodations. Financial: people with low back pain want financial support, but have concerns about the inefficiencies of compensation systems and the stigma associated with financial remuneration. Social: people with low back pain report feeling disconnected from social networks and want back-specific social support. Household: people with low back pain report difficulties with household duties; however, there are few data regarding their need for auxiliary devices and domestic help. People with low back pain identified work place, financial and social pressures, and difficulties with household duties as areas of need beyond their healthcare requirements that affect their ability to comply with management of their condition. Consideration of such needs may inform physiotherapists, the wider health system, social networks and the workplace to provide more relevant and effective services. [Chou L, Cicuttini FM, Urquhart DM, Anthony SN, Sullivan K, Seneviwickrama M, Briggs AM, Wluka AE (2018) People with low back pain perceive needs for non-biomedical services in workplace, financial, social and household domains: a systematic review. Journal of Physiotherapy 64: 74-83]. Copyright © 2018 Australian Physiotherapy Association. Published by Elsevier B.V. All rights reserved.

Biomedical Risk Factors of Achilles Tendinopathy in Physically Active People: a Systematic Review.

PubMed

Kozlovskaia, Maria; Vlahovich, Nicole; Ashton, Kevin J; Hughes, David C

2017-12-01

Achilles tendinopathy is the most prevalent tendon disorder in people engaged in running and jumping sports. Aetiology of Achilles tendinopathy is complex and requires comprehensive research of contributing risk factors. There is relatively little research focussing on potential biomedical risk factors for Achilles tendinopathy. The purpose of this systematic review is to identify studies and summarise current knowledge of biomedical risk factors of Achilles tendinopathy in physically active people. Research databases were searched for relevant articles followed by assessment in accordance with PRISMA statement and standards of Cochrane collaboration. Levels of evidence and quality assessment designation were implemented in accordance with OCEBM levels of evidence and Newcastle-Ottawa Quality Assessment Scale, respectively. A systematic review of the literature identified 22 suitable articles. All included studies had moderate level of evidence (2b) with the Newcastle-Ottawa score varying between 6 and 9. The majority (17) investigated genetic polymorphisms involved in tendon structure and homeostasis and apoptosis and inflammation pathways. Overweight as a risk factor of Achilles tendinopathy was described in five included studies that investigated non-genetic factors. COL5A1 genetic variants were the most extensively studied, particularly in association with genetic variants in the genes involved in regulation of cell-matrix interaction in tendon and matrix homeostasis. It is important to investigate connections and pathways whose interactions might be disrupted and therefore alter collagen structure and lead to the development of pathology. Polymorphisms in genes involved in apoptosis and inflammation, and Achilles tendinopathy did not show strong association and, however, should be considered for further investigation. This systematic review suggests that biomedical risk factors are an important consideration in the future study of propensity to the development of Achilles tendinopathy. The presence of certain medical comorbidities and genetic markers should be considered when contemplating the aetiology of Achilles tendinopathy. Further elucidation of biomedical risk factors will aid in the understanding of tendon pathology and patient risk, thereby informing prevention and management strategies for Achilles tendinopathy. PROSPERO CRD42016036558.

Development and pilot testing of an online module for ethics education based on the Nigerian National Code for Health Research Ethics

PubMed Central

2013-01-01

Background The formulation and implementation of national ethical regulations to protect research participants is fundamental to ethical conduct of research. Ethics education and capacity are inadequate in developing African countries. This study was designed to develop a module for online training in research ethics based on the Nigerian National Code of Health Research Ethics and assess its ease of use and reliability among biomedical researchers in Nigeria. Methodology This was a three-phased evaluation study. Phase one involved development of an online training module based on the Nigerian Code of Health Research Ethics (NCHRE) and uploading it to the Collaborative Institutional Training Initiative (CITI) website while the second phase entailed the evaluation of the module for comprehensibility, readability and ease of use by 45 Nigerian biomedical researchers. The third phase involved modification and re-evaluation of the module by 30 Nigerian biomedical researchers and determination of test-retest reliability of the module using Cronbach’s alpha. Results The online module was easily accessible and comprehensible to 95% of study participants. There were significant differences in the pretest and posttest scores of study participants during the evaluation of the online module (p = 0.001) with correlation coefficients of 0.9 and 0.8 for the pretest and posttest scores respectively. The module also demonstrated excellent test-retest reliability and internal consistency as shown by Cronbach’s alpha coefficients of 0.92 and 0.84 for the pretest and posttest respectively. Conclusion The module based on the Nigerian Code was developed, tested and made available online as a valuable tool for training in cultural and societal relevant ethical principles to orient national and international biomedical researchers working in Nigeria. It would complement other general research ethics and Good Clinical Practice modules. Participants suggested that awareness of the online module should be increased through seminars, advertisement on government websites and portals used by Nigerian biomedical researchers, and incorporation of the Code into the undergraduate medical training curriculum. PMID:23281968

Point-of-care diagnostics for niche applications.

PubMed

Cummins, Brian M; Ligler, Frances S; Walker, Glenn M

2016-01-01

Point-of-care or point-of-use diagnostics are analytical devices that provide clinically relevant information without the need for a core clinical laboratory. In this review we define point-of-care diagnostics as portable versions of assays performed in a traditional clinical chemistry laboratory. This review discusses five areas relevant to human and animal health where increased attention could produce significant impact: veterinary medicine, space travel, sports medicine, emergency medicine, and operating room efficiency. For each of these areas, clinical need, available commercial products, and ongoing research into new devices are highlighted. Copyright © 2016 Elsevier Inc. All rights reserved.

Dynamic synchronization of ongoing neuronal activity across spinal segments regulates sensory information flow

PubMed Central

Contreras-Hernández, E; Chávez, D; Rudomin, P

2015-01-01

Previous studies on the correlation between spontaneous cord dorsum potentials recorded in the lumbar spinal segments of anaesthetized cats suggested the operation of a population of dorsal horn neurones that modulates, in a differential manner, transmission along pathways mediating Ib non-reciprocal postsynaptic inhibition and pathways mediating primary afferent depolarization and presynaptic inhibition. In order to gain further insight into the possible neuronal mechanisms that underlie this process, we have measured changes in the correlation between the spontaneous activity of individual dorsal horn neurones and the cord dorsum potentials associated with intermittent activation of these inhibitory pathways. We found that high levels of neuronal synchronization within the dorsal horn are associated with states of incremented activity along the pathways mediating presynaptic inhibition relative to pathways mediating Ib postsynaptic inhibition. It is suggested that ongoing changes in the patterns of functional connectivity within a distributed ensemble of dorsal horn neurones play a relevant role in the state-dependent modulation of impulse transmission along inhibitory pathways, among them those involved in the central control of sensory information. This feature would allow the same neuronal network to be involved in different functional tasks. Key points We have examined, in the spinal cord of the anaesthetized cat, the relationship between ongoing correlated fluctuations of dorsal horn neuronal activity and state-dependent activation of inhibitory reflex pathways. We found that high levels of synchronization between the spontaneous activity of dorsal horn neurones occur in association with the preferential activation of spinal pathways leading to primary afferent depolarization and presynaptic inhibition relative to activation of pathways mediating Ib postsynaptic inhibition. It is suggested that changes in synchronization of ongoing activity within a distributed network of dorsal horn neurones play a relevant role in the configuration of structured (non-random) patterns of functional connectivity that shape the interaction of sensory inputs with spinal reflex pathways subserving different functional tasks. PMID:25653206

Allowing Brief Delays in Responding Improves Event-Based Prospective Memory for Young Adults Living with HIV Disease

PubMed Central

Loft, Shayne; Doyle, Katie L.; Naar-King, Sylvie; Outlaw, Angulique Y.; Nichols, Sharon L.; Weber, Erica; Blackstone, Kaitlin; Woods, Steven Paul

2014-01-01

Event-based prospective memory (PM) tasks require individuals to remember to perform an action when they encounter a specific cue in the environment, and have clear relevance for daily functioning for individuals with HIV. In many everyday tasks, the individual must not only maintain the intent to perform the PM task, but the PM task response also competes with the alternative and more habitual task response. The current study examined whether event-based PM can be improved by slowing down the pace of the task environment. Fifty-seven young adults living with HIV performed an ongoing lexical decision task while simultaneously performing a PM task of monitoring for a specific word (which was focal to the ongoing task of making lexical decisions) or syllable contained in a word (which was nonfocal). Participants were instructed to refrain from making task responses until after a tone was presented, which occurred at varying onsets (0–1600ms) after each stimulus appeared. Improvements in focal and non-focal PM accuracy were observed with response delays of 600ms. Furthermore, the difference in PM accuracy between the low demand focal PM task and the resource demanding non-focal PM task was reduced by half across increasingly longer delays, falling from 31% at 0ms delay to only 14% at 1600ms delay. The degree of ongoing task response slowing for the PM conditions, relative to a control condition that did not have a PM task and made lexical decisions only, also decreased with increased delay. Overall, the evidence indicates that delaying the task responses of younger HIV-infected adults increased the probability that the PM relevant features of task stimuli were adequately assessed prior to the ongoing task response, and by implication that younger HIV infected adults can more adequately achieve PM goals when the pace of the task environment is slowed down. PMID:25116075