WorldWideScience

Sample records for biomedical knowledge extraction

  1. Text mining patents for biomedical knowledge.

    Science.gov (United States)

    Rodriguez-Esteban, Raul; Bundschus, Markus

    2016-06-01

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

  2. An integrated biomedical knowledge extraction and analysis platform: using federated search and document clustering technology.

    Science.gov (United States)

    Taylor, Donald P

    2007-01-01

    High content screening (HCS) requires time-consuming and often complex iterative information retrieval and assessment approaches to optimally conduct drug discovery programs and biomedical research. Pre- and post-HCS experimentation both require the retrieval of information from public as well as proprietary literature in addition to structured information assets such as compound libraries and projects databases. Unfortunately, this information is typically scattered across a plethora of proprietary bioinformatics tools and databases and public domain sources. Consequently, single search requests must be presented to each information repository, forcing the results to be manually integrated for a meaningful result set. Furthermore, these bioinformatics tools and data repositories are becoming increasingly complex to use; typically they fail to allow for more natural query interfaces. Vivisimo has developed an enterprise software platform to bridge disparate silos of information. The platform automatically categorizes search results into descriptive folders without the use of taxonomies to drive the categorization. A new approach to information retrieval for HCS experimentation is proposed.

  3. Figure text extraction in biomedical literature.

    Directory of Open Access Journals (Sweden)

    Daehyun Kim

    2011-01-01

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

  4. A hybrid model based on neural networks for biomedical relation extraction.

    Science.gov (United States)

    Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Zhang, Shaowu; Sun, Yuanyuan; Yang, Liang

    2018-05-01

    Biomedical relation extraction can automatically extract high-quality biomedical relations from biomedical texts, which is a vital step for the mining of biomedical knowledge hidden in the literature. Recurrent neural networks (RNNs) and convolutional neural networks (CNNs) are two major neural network models for biomedical relation extraction. Neural network-based methods for biomedical relation extraction typically focus on the sentence sequence and employ RNNs or CNNs to learn the latent features from sentence sequences separately. However, RNNs and CNNs have their own advantages for biomedical relation extraction. Combining RNNs and CNNs may improve biomedical relation extraction. In this paper, we present a hybrid model for the extraction of biomedical relations that combines RNNs and CNNs. First, the shortest dependency path (SDP) is generated based on the dependency graph of the candidate sentence. To make full use of the SDP, we divide the SDP into a dependency word sequence and a relation sequence. Then, RNNs and CNNs are employed to automatically learn the features from the sentence sequence and the dependency sequences, respectively. Finally, the output features of the RNNs and CNNs are combined to detect and extract biomedical relations. We evaluate our hybrid model using five public (protein-protein interaction) PPI corpora and a (drug-drug interaction) DDI corpus. The experimental results suggest that the advantages of RNNs and CNNs in biomedical relation extraction are complementary. Combining RNNs and CNNs can effectively boost biomedical relation extraction performance. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Enhancing biomedical text summarization using semantic relation extraction.

    Directory of Open Access Journals (Sweden)

    Yue Shang

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

  6. Enhancing biomedical text summarization using semantic relation extraction.

    Science.gov (United States)

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

    2011-01-01

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

  7. Biomedical informatics discovering knowledge in big data

    CERN Document Server

    Holzinger, Andreas

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Sunwon Lee

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

  9. A collaborative filtering-based approach to biomedical knowledge discovery.

    Science.gov (United States)

    Lever, Jake; Gakkhar, Sitanshu; Gottlieb, Michael; Rashnavadi, Tahereh; Lin, Santina; Siu, Celia; Smith, Maia; Jones, Martin R; Krzywinski, Martin; Jones, Steven J M; Wren, Jonathan

    2018-02-15

    The increase in publication rates makes it challenging for an individual researcher to stay abreast of all relevant research in order to find novel research hypotheses. Literature-based discovery methods make use of knowledge graphs built using text mining and can infer future associations between biomedical concepts that will likely occur in new publications. These predictions are a valuable resource for researchers to explore a research topic. Current methods for prediction are based on the local structure of the knowledge graph. A method that uses global knowledge from across the knowledge graph needs to be developed in order to make knowledge discovery a frequently used tool by researchers. We propose an approach based on the singular value decomposition (SVD) that is able to combine data from across the knowledge graph through a reduced representation. Using cooccurrence data extracted from published literature, we show that SVD performs better than the leading methods for scoring discoveries. We also show the diminishing predictive power of knowledge discovery as we compare our predictions with real associations that appear further into the future. Finally, we examine the strengths and weaknesses of the SVD approach against another well-performing system using several predicted associations. All code and results files for this analysis can be accessed at https://github.com/jakelever/knowledgediscovery. sjones@bcgsc.ca. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  10. The biomedical disciplines and the structure of biomedical and clinical knowledge.

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    Nederbragt, H

    2000-11-01

    The relation between biomedical knowledge and clinical knowledge is discussed by comparing their respective structures. The knowledge of a disease as a biological phenomenon is constructed by the interaction of facts and theories from the main biomedical disciplines: epidemiology, diagnostics, clinical trial, therapy development and pathogenesis. Although these facts and theories are based on probabilities and extrapolations, the interaction provides a reliable and coherent structure, comparable to a Kuhnian paradigma. In the structure of clinical knowledge, i.e. knowledge of the patient with the disease, not only biomedical knowledge contributes to the structure but also economic and social relations, ethics and personal experience. However, the interaction between each of the participating "knowledges" in clinical knowledge is not based on mutual dependency and accumulation of different arguments from each, as in biomedical knowledge, but on competition and partial exclusion. Therefore, the structure of biomedical knowledge is different from that of clinical knowledge. This difference is used as the basis for a discussion in which the place of technology, evidence-based medicine and the gap between scientific and clinical knowledge are evaluated.

  11. Exploiting graph kernels for high performance biomedical relation extraction.

    Science.gov (United States)

    Panyam, Nagesh C; Verspoor, Karin; Cohn, Trevor; Ramamohanarao, Kotagiri

    2018-01-30

    Relation extraction from biomedical publications is an important task in the area of semantic mining of text. Kernel methods for supervised relation extraction are often preferred over manual feature engineering methods, when classifying highly ordered structures such as trees and graphs obtained from syntactic parsing of a sentence. Tree kernels such as the Subset Tree Kernel and Partial Tree Kernel have been shown to be effective for classifying constituency parse trees and basic dependency parse graphs of a sentence. Graph kernels such as the All Path Graph kernel (APG) and Approximate Subgraph Matching (ASM) kernel have been shown to be suitable for classifying general graphs with cycles, such as the enhanced dependency parse graph of a sentence. In this work, we present a high performance Chemical-Induced Disease (CID) relation extraction system. We present a comparative study of kernel methods for the CID task and also extend our study to the Protein-Protein Interaction (PPI) extraction task, an important biomedical relation extraction task. We discuss novel modifications to the ASM kernel to boost its performance and a method to apply graph kernels for extracting relations expressed in multiple sentences. Our system for CID relation extraction attains an F-score of 60%, without using external knowledge sources or task specific heuristic or rules. In comparison, the state of the art Chemical-Disease Relation Extraction system achieves an F-score of 56% using an ensemble of multiple machine learning methods, which is then boosted to 61% with a rule based system employing task specific post processing rules. For the CID task, graph kernels outperform tree kernels substantially, and the best performance is obtained with APG kernel that attains an F-score of 60%, followed by the ASM kernel at 57%. The performance difference between the ASM and APG kernels for CID sentence level relation extraction is not significant. In our evaluation of ASM for the PPI task, ASM

  12. A robust approach to extract biomedical events from literature.

    Science.gov (United States)

    Bui, Quoc-Chinh; Sloot, Peter M A

    2012-10-15

    The abundance of biomedical literature has attracted significant interest in novel methods to automatically extract biomedical relations from the literature. Until recently, most research was focused on extracting binary relations such as protein-protein interactions and drug-disease relations. However, these binary relations cannot fully represent the original biomedical data. Therefore, there is a need for methods that can extract fine-grained and complex relations known as biomedical events. In this article we propose a novel method to extract biomedical events from text. Our method consists of two phases. In the first phase, training data are mapped into structured representations. Based on that, templates are used to extract rules automatically. In the second phase, extraction methods are developed to process the obtained rules. When evaluated against the Genia event extraction abstract and full-text test datasets (Task 1), we obtain results with F-scores of 52.34 and 53.34, respectively, which are comparable to the state-of-the-art systems. Furthermore, our system achieves superior performance in terms of computational efficiency. Our source code is available for academic use at http://dl.dropbox.com/u/10256952/BioEvent.zip.

  13. Electromembrane extraction for pharmaceutical and biomedical analysis

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2018-01-03

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

  15. Logical knowledge representation of regulatory relations in biomedical pathways

    DEFF Research Database (Denmark)

    Zambach, Sine; Hansen, Jens Ulrik

    2010-01-01

    Knowledge on regulatory relations, in for example regulatory pathways in biology, is used widely in experiment design by biomedical researchers and in systems biology. The knowledge has typically either been represented through simple graphs or through very expressive differential equation...... simulations of smaller parts of a pathway. In this work we suggest a knowledge representation of the most basic relations in regulatory processes regulates, positively regulates and negatively regulates in logics based on a semantic analysis. We discuss the usage of these relations in biology and in articial...... intelligence for hypothesis development in drug discovery....

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

    Directory of Open Access Journals (Sweden)

    N. Kanya

    2016-07-01

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

  17. MBA: a literature mining system for extracting biomedical abbreviations.

    Science.gov (United States)

    Xu, Yun; Wang, ZhiHao; Lei, YiMing; Zhao, YuZhong; Xue, Yu

    2009-01-09

    The exploding growth of the biomedical literature presents many challenges for biological researchers. One such challenge is from the use of a great deal of abbreviations. Extracting abbreviations and their definitions accurately is very helpful to biologists and also facilitates biomedical text analysis. Existing approaches fall into four broad categories: rule based, machine learning based, text alignment based and statistically based. State of the art methods either focus exclusively on acronym-type abbreviations, or could not recognize rare abbreviations. We propose a systematic method to extract abbreviations effectively. At first a scoring method is used to classify the abbreviations into acronym-type and non-acronym-type abbreviations, and then their corresponding definitions are identified by two different methods: text alignment algorithm for the former, statistical method for the latter. A literature mining system MBA was constructed to extract both acronym-type and non-acronym-type abbreviations. An abbreviation-tagged literature corpus, called Medstract gold standard corpus, was used to evaluate the system. MBA achieved a recall of 88% at the precision of 91% on the Medstract gold-standard EVALUATION Corpus. We present a new literature mining system MBA for extracting biomedical abbreviations. Our evaluation demonstrates that the MBA system performs better than the others. It can identify the definition of not only acronym-type abbreviations including a little irregular acronym-type abbreviations (e.g., ), but also non-acronym-type abbreviations (e.g., ).

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

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

    2016-04-14

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

  19. A semi-supervised learning framework for biomedical event extraction based on hidden topics.

    Science.gov (United States)

    Zhou, Deyu; Zhong, Dayou

    2015-05-01

    Scientists have devoted decades of efforts to understanding the interaction between proteins or RNA production. The information might empower the current knowledge on drug reactions or the development of certain diseases. Nevertheless, due to the lack of explicit structure, literature in life science, one of the most important sources of this information, prevents computer-based systems from accessing. Therefore, biomedical event extraction, automatically acquiring knowledge of molecular events in research articles, has attracted community-wide efforts recently. Most approaches are based on statistical models, requiring large-scale annotated corpora to precisely estimate models' parameters. However, it is usually difficult to obtain in practice. Therefore, employing un-annotated data based on semi-supervised learning for biomedical event extraction is a feasible solution and attracts more interests. In this paper, a semi-supervised learning framework based on hidden topics for biomedical event extraction is presented. In this framework, sentences in the un-annotated corpus are elaborately and automatically assigned with event annotations based on their distances to these sentences in the annotated corpus. More specifically, not only the structures of the sentences, but also the hidden topics embedded in the sentences are used for describing the distance. The sentences and newly assigned event annotations, together with the annotated corpus, are employed for training. Experiments were conducted on the multi-level event extraction corpus, a golden standard corpus. Experimental results show that more than 2.2% improvement on F-score on biomedical event extraction is achieved by the proposed framework when compared to the state-of-the-art approach. The results suggest that by incorporating un-annotated data, the proposed framework indeed improves the performance of the state-of-the-art event extraction system and the similarity between sentences might be precisely

  20. A study to assess the knowledge and practice on bio-medical waste ...

    African Journals Online (AJOL)

    Background: The proper handling and disposal of bio-medical waste is very imperative. Unfortunately, laxity and lack of adequate knowledge and practice on bio-medical waste disposal leads to staid health and environment apprehension. Aim: To assess the knowledge and practice on bio-medical waste management ...

  1. KNODWAT: a scientific framework application for testing knowledge discovery methods for the biomedical domain.

    Science.gov (United States)

    Holzinger, Andreas; Zupan, Mario

    2013-06-13

    Professionals in the biomedical domain are confronted with an increasing mass of data. Developing methods to assist professional end users in the field of Knowledge Discovery to identify, extract, visualize and understand useful information from these huge amounts of data is a huge challenge. However, there are so many diverse methods and methodologies available, that for biomedical researchers who are inexperienced in the use of even relatively popular knowledge discovery methods, it can be very difficult to select the most appropriate method for their particular research problem. A web application, called KNODWAT (KNOwledge Discovery With Advanced Techniques) has been developed, using Java on Spring framework 3.1. and following a user-centered approach. The software runs on Java 1.6 and above and requires a web server such as Apache Tomcat and a database server such as the MySQL Server. For frontend functionality and styling, Twitter Bootstrap was used as well as jQuery for interactive user interface operations. The framework presented is user-centric, highly extensible and flexible. Since it enables methods for testing using existing data to assess suitability and performance, it is especially suitable for inexperienced biomedical researchers, new to the field of knowledge discovery and data mining. For testing purposes two algorithms, CART and C4.5 were implemented using the WEKA data mining framework.

  2. Semantic transference for enriching multilingual biomedical knowledge resources.

    Science.gov (United States)

    Pérez, María; Berlanga, Rafael

    2015-12-01

    Biomedical knowledge resources (KRs) are mainly expressed in English, and many applications using them suffer from the scarcity of knowledge in non-English languages. The goal of the present work is to take maximum profit from existing multilingual biomedical KRs lexicons to enrich their non-English counterparts. We propose to combine different automatic methods to generate pair-wise language alignments. More specifically, we use two well-known translation methods (GIZA++ and Moses), and we propose a new ad hoc method specially devised for multilingual KRs. Then, resulting alignments are used to transfer semantics between KRs across their languages. Transference quality is ensured by checking the semantic coherence of the generated alignments. Experiments have been carried out over the Spanish, French and German UMLS Metathesaurus counterparts. As a result, the enriched Spanish KR can grow up to 1,514,217 concepts (originally 286,659), the French KR up to 1,104,968 concepts (originally 83,119), and the German KR up to 1,136,020 concepts (originally 86,842). Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Portable blood extraction device integrated with biomedical monitoring system

    Science.gov (United States)

    Khumpuang, S.; Horade, M.; Fujioka, K.; Sugiyama, S.

    2006-01-01

    Painless and portable blood extraction device has been immersed in the world of miniaturization on bio-medical research particularly in manufacturing point-of-care systems. The fabrication of a blood extraction device integrated with an electrolyte-monitoring system is reported in this paper. The device has advantages in precise controlled dosage of blood extracted including the slightly damaged blood vessels and nervous system. The in-house blood diagnostic will become simple for the patients. Main components of the portable system are; the blood extraction device and electrolyte-monitoring system. The monitoring system consists of ISFET (Ion Selective Field Effect Transistor) for measuring the concentration level of minerals in blood. In this work, we measured the level of 3 ions; Na+, K+ and Cl-. The mentioned ions are frequently required the measurement since their concentration levels in the blood can indicate whether the kidney, pancreas, liver or heart is being malfunction. The fabrication of the whole system and experimentation on each ISM (Ion Sensitive Membrane) will be provided. Taking the advantages of LIGA technology, the 100 hollow microneedles fabricated by Synchrotron Radiation deep X-ray lithography through PCT (Plane-pattern to Cross-section Transfer) technique have been consisted in 5x5 mm2 area. The microneedle is 300 μm in base-diameter, 500 μm-pitch, 800 μm-height and 50 μm hole-diameter. The total size of the blood extraction device is 2x2x2 cm 3. The package is made from a plastic socket including slots for inserting microneedle array and ISFET connecting to an electrical circuit for the monitoring. Through the dimensional design for simply handling and selection of disposable material, the patients can self-evaluate the critical level of the body minerals in anywhere and anytime.

  4. Systematic integration of biomedical knowledge prioritizes drugs for repurposing.

    Science.gov (United States)

    Himmelstein, Daniel Scott; Lizee, Antoine; Hessler, Christine; Brueggeman, Leo; Chen, Sabrina L; Hadley, Dexter; Green, Ari; Khankhanian, Pouya; Baranzini, Sergio E

    2017-09-22

    The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval. This study describes Project Rephetio to systematically model drug efficacy based on 755 existing treatments. First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. Data were integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects, and symptoms. Next, we identified network patterns that distinguish treatments from non-treatments. Then, we predicted the probability of treatment for 209,168 compound-disease pairs (het.io/repurpose). Our predictions validated on two external sets of treatment and provided pharmacological insights on epilepsy, suggesting they will help prioritize drug repurposing candidates. This study was entirely open and received realtime feedback from 40 community members.

  5. A knowledge representation view on biomedical structure and function.

    Science.gov (United States)

    Schulz, Stefan; Hahn, Udo

    2002-01-01

    In biomedical ontologies, structural and functional considerations are of outstanding importance, and concepts which belong to these two categories are highly interdependent. At the representational level both axes must be clearly kept separate in order to support disciplined ontology engineering. Furthermore, the biaxial organization of physical structure (both by a taxonomic and partonomic order) entails intricate patterns of inference. We here propose a layered encoding of taxonomic, partonomic and functional aspects of biomedical concepts using description logics. PMID:12463912

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

    Directory of Open Access Journals (Sweden)

    Abdul Wahab Muzaffar

    2015-01-01

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

  7. Knowledge-based biomedical word sense disambiguation: comparison of approaches

    Directory of Open Access Journals (Sweden)

    Aronson Alan R

    2010-11-01

    Full Text Available Abstract Background Word sense disambiguation (WSD algorithms attempt to select the proper sense of ambiguous terms in text. Resources like the UMLS provide a reference thesaurus to be used to annotate the biomedical literature. Statistical learning approaches have produced good results, but the size of the UMLS makes the production of training data infeasible to cover all the domain. Methods We present research on existing WSD approaches based on knowledge bases, which complement the studies performed on statistical learning. We compare four approaches which rely on the UMLS Metathesaurus as the source of knowledge. The first approach compares the overlap of the context of the ambiguous word to the candidate senses based on a representation built out of the definitions, synonyms and related terms. The second approach collects training data for each of the candidate senses to perform WSD based on queries built using monosemous synonyms and related terms. These queries are used to retrieve MEDLINE citations. Then, a machine learning approach is trained on this corpus. The third approach is a graph-based method which exploits the structure of the Metathesaurus network of relations to perform unsupervised WSD. This approach ranks nodes in the graph according to their relative structural importance. The last approach uses the semantic types assigned to the concepts in the Metathesaurus to perform WSD. The context of the ambiguous word and semantic types of the candidate concepts are mapped to Journal Descriptors. These mappings are compared to decide among the candidate concepts. Results are provided estimating accuracy of the different methods on the WSD test collection available from the NLM. Conclusions We have found that the last approach achieves better results compared to the other methods. The graph-based approach, using the structure of the Metathesaurus network to estimate the relevance of the Metathesaurus concepts, does not perform well

  8. Refining Automatically Extracted Knowledge Bases Using Crowdsourcing

    OpenAIRE

    Li, Chunhua; Zhao, Pengpeng; Sheng, Victor S.; Xian, Xuefeng; Wu, Jian; Cui, Zhiming

    2017-01-01

    Machine-constructed knowledge bases often contain noisy and inaccurate facts. There exists significant work in developing automated algorithms for knowledge base refinement. Automated approaches improve the quality of knowledge bases but are far from perfect. In this paper, we leverage crowdsourcing to improve the quality of automatically extracted knowledge bases. As human labelling is costly, an important research challenge is how we can use limited human resources to maximize the quality i...

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

    Science.gov (United States)

    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.

  10. A study to assess the knowledge and practice on bio-medical waste ...

    African Journals Online (AJOL)

    McRoy

    Practice, Bharathi College of Pharmacy, Mandya 571401, India. 5Department of ... revealed the lack of knowledge and awareness of bio-medical waste .... Female. 43. 77. 36. 64. Qualification. MPBHW/ ANM. DMLTC. D.Pharm. 101. 10. 09. 85.

  11. KnowLife: a versatile approach for constructing a large knowledge graph for biomedical sciences.

    Science.gov (United States)

    Ernst, Patrick; Siu, Amy; Weikum, Gerhard

    2015-05-14

    Biomedical knowledge bases (KB's) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at which new findings are published. Second, for automatic information extraction (IE), the text genre of choice has been scientific publications, neglecting sources like health portals and online communities. Third, most prior work on IE has focused on the molecular level or chemogenomics only, like protein-protein interactions or gene-drug relationships, or solely address highly specific topics such as drug effects. We address these three limitations by a versatile and scalable approach to automatic KB construction. Using a small number of seed facts for distant supervision of pattern-based extraction, we harvest a huge number of facts in an automated manner without requiring any explicit training. We extend previous techniques for pattern-based IE with confidence statistics, and we combine this recall-oriented stage with logical reasoning for consistency constraint checking to achieve high precision. To our knowledge, this is the first method that uses consistency checking for biomedical relations. Our approach can be easily extended to incorporate additional relations and constraints. We ran extensive experiments not only for scientific publications, but also for encyclopedic health portals and online communities, creating different KB's based on different configurations. We assess the size and quality of each KB, in terms of number of facts and precision. The best configured KB, KnowLife, contains more than 500,000 facts at a precision of 93% for 13 relations covering genes, organs, diseases, symptoms, treatments, as well as environmental and lifestyle risk factors. KnowLife is a large knowledge base for health and life sciences, automatically constructed from different Web sources. As a unique feature, KnowLife is harvested from

  12. Extracting microRNA-gene relations from biomedical literature using distant supervision.

    Directory of Open Access Journals (Sweden)

    Andre Lamurias

    Full Text Available Many biomedical relation extraction approaches are based on supervised machine learning, requiring an annotated corpus. Distant supervision aims at training a classifier by combining a knowledge base with a corpus, reducing the amount of manual effort necessary. This is particularly useful for biomedicine because many databases and ontologies have been made available for many biological processes, while the availability of annotated corpora is still limited. We studied the extraction of microRNA-gene relations from text. MicroRNA regulation is an important biological process due to its close association with human diseases. The proposed method, IBRel, is based on distantly supervised multi-instance learning. We evaluated IBRel on three datasets, and the results were compared with a co-occurrence approach as well as a supervised machine learning algorithm. While supervised learning outperformed on two of those datasets, IBRel obtained an F-score 28.3 percentage points higher on the dataset for which there was no training set developed specifically. To demonstrate the applicability of IBRel, we used it to extract 27 miRNA-gene relations from recently published papers about cystic fibrosis. Our results demonstrate that our method can be successfully used to extract relations from literature about a biological process without an annotated corpus. The source code and data used in this study are available at https://github.com/AndreLamurias/IBRel.

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

    Science.gov (United States)

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

    2013-01-01

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

  14. Fuzzy concept analysis for semantic knowledge extraction

    OpenAIRE

    De Maio, Carmen

    2012-01-01

    2010 - 2011 Availability of controlled vocabularies, ontologies, and so on is enabling feature to provide some added values in terms of knowledge management. Nevertheless, the design, maintenance and construction of domain ontologies are a human intensive and time consuming task. The Knowledge Extraction consists of automatic techniques aimed to identify and to define relevant concepts and relations of the domain of interest by analyzing structured (relational databases, XML) and unstructu...

  15. Knowledge, attitude, and practices about biomedical waste management among healthcare personnel: A cross-sectional study

    Directory of Open Access Journals (Sweden)

    Vanesh Mathur

    2011-01-01

    Full Text Available Background: The waste produced in the course of healthcare activities carries a higher potential for infection and injury than any other type of waste. Inadequate and inappropriate knowledge of handling of healthcare waste may have serious health consequences and a significant impact on the environment as well. Objective: The objective was to assess knowledge, attitude, and practices of doctors, nurses, laboratory technicians, and sanitary staff regarding biomedical waste management. Materials and Methods: This was a cross-sectional study. Setting: The study was conducted among hospitals (bed capacity >100 of Allahabad city. Participants: Medical personnel included were doctors (75, nurses (60, laboratory technicians (78, and sanitary staff (70. Results: Doctors, nurses, and laboratory technicians have better knowledge than sanitary staff regarding biomedical waste management. Knowledge regarding the color coding and waste segregation at source was found to be better among nurses and laboratory staff as compared to doctors. Regarding practices related to biomedical waste management, sanitary staff were ignorant on all the counts. However, injury reporting was low across all the groups of health professionals. Conclusion: The importance of training regarding biomedical waste management needs emphasis; lack of proper and complete knowledge about biomedical waste management impacts practices of appropriate waste disposal.

  16. Extracting knowledge from protein structure geometry

    DEFF Research Database (Denmark)

    Røgen, Peter; Koehl, Patrice

    2013-01-01

    potential from geometric knowledge extracted from native and misfolded conformers of protein structures. This new potential, Metric Protein Potential (MPP), has two main features that are key to its success. Firstly, it is composite in that it includes local and nonlocal geometric information on proteins...

  17. An unsupervised text mining method for relation extraction from biomedical literature.

    Directory of Open Access Journals (Sweden)

    Changqin Quan

    Full Text Available The wealth of interaction information provided in biomedical articles motivated the implementation of text mining approaches to automatically extract biomedical relations. This paper presents an unsupervised method based on pattern clustering and sentence parsing to deal with biomedical relation extraction. Pattern clustering algorithm is based on Polynomial Kernel method, which identifies interaction words from unlabeled data; these interaction words are then used in relation extraction between entity pairs. Dependency parsing and phrase structure parsing are combined for relation extraction. Based on the semi-supervised KNN algorithm, we extend the proposed unsupervised approach to a semi-supervised approach by combining pattern clustering, dependency parsing and phrase structure parsing rules. We evaluated the approaches on two different tasks: (1 Protein-protein interactions extraction, and (2 Gene-suicide association extraction. The evaluation of task (1 on the benchmark dataset (AImed corpus showed that our proposed unsupervised approach outperformed three supervised methods. The three supervised methods are rule based, SVM based, and Kernel based separately. The proposed semi-supervised approach is superior to the existing semi-supervised methods. The evaluation on gene-suicide association extraction on a smaller dataset from Genetic Association Database and a larger dataset from publicly available PubMed showed that the proposed unsupervised and semi-supervised methods achieved much higher F-scores than co-occurrence based method.

  18. Refining Automatically Extracted Knowledge Bases Using Crowdsourcing

    Directory of Open Access Journals (Sweden)

    Chunhua Li

    2017-01-01

    Full Text Available Machine-constructed knowledge bases often contain noisy and inaccurate facts. There exists significant work in developing automated algorithms for knowledge base refinement. Automated approaches improve the quality of knowledge bases but are far from perfect. In this paper, we leverage crowdsourcing to improve the quality of automatically extracted knowledge bases. As human labelling is costly, an important research challenge is how we can use limited human resources to maximize the quality improvement for a knowledge base. To address this problem, we first introduce a concept of semantic constraints that can be used to detect potential errors and do inference among candidate facts. Then, based on semantic constraints, we propose rank-based and graph-based algorithms for crowdsourced knowledge refining, which judiciously select the most beneficial candidate facts to conduct crowdsourcing and prune unnecessary questions. Our experiments show that our method improves the quality of knowledge bases significantly and outperforms state-of-the-art automatic methods under a reasonable crowdsourcing cost.

  19. Refining Automatically Extracted Knowledge Bases Using Crowdsourcing.

    Science.gov (United States)

    Li, Chunhua; Zhao, Pengpeng; Sheng, Victor S; Xian, Xuefeng; Wu, Jian; Cui, Zhiming

    2017-01-01

    Machine-constructed knowledge bases often contain noisy and inaccurate facts. There exists significant work in developing automated algorithms for knowledge base refinement. Automated approaches improve the quality of knowledge bases but are far from perfect. In this paper, we leverage crowdsourcing to improve the quality of automatically extracted knowledge bases. As human labelling is costly, an important research challenge is how we can use limited human resources to maximize the quality improvement for a knowledge base. To address this problem, we first introduce a concept of semantic constraints that can be used to detect potential errors and do inference among candidate facts. Then, based on semantic constraints, we propose rank-based and graph-based algorithms for crowdsourced knowledge refining, which judiciously select the most beneficial candidate facts to conduct crowdsourcing and prune unnecessary questions. Our experiments show that our method improves the quality of knowledge bases significantly and outperforms state-of-the-art automatic methods under a reasonable crowdsourcing cost.

  20. Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions.

    Science.gov (United States)

    Mrabet, Yassine; Kilicoglu, Halil; Roberts, Kirk; Demner-Fushman, Dina

    2016-01-01

    Determining the main topics in consumer health questions is a crucial step in their processing as it allows narrowing the search space to a specific semantic context. In this paper we propose a topic recognition approach based on biomedical and open-domain knowledge bases. In the first step of our method, we recognize named entities in consumer health questions using an unsupervised method that relies on a biomedical knowledge base, UMLS, and an open-domain knowledge base, DBpedia. In the next step, we cast topic recognition as a binary classification problem of deciding whether a named entity is the question topic or not. We evaluated our approach on a dataset from the National Library of Medicine (NLM), introduced in this paper, and another from the Genetic and Rare Disease Information Center (GARD). The combination of knowledge bases outperformed the results obtained by individual knowledge bases by up to 16.5% F1 and achieved state-of-the-art performance. Our results demonstrate that combining open-domain knowledge bases with biomedical knowledge bases can lead to a substantial improvement in understanding user-generated health content.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-01-23

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

  2. Knowledge, attitude, and practices about biomedical waste management among healthcare personnel: A cross-sectional study

    OpenAIRE

    Vanesh Mathur; S Dwivedi; M A Hassan; R P Misra

    2011-01-01

    Background: The waste produced in the course of healthcare activities carries a higher potential for infection and injury than any other type of waste. Inadequate and inappropriate knowledge of handling of healthcare waste may have serious health consequences and a significant impact on the environment as well. Objective: The objective was to assess knowledge, attitude, and practices of doctors, nurses, laboratory technicians, and sanitary staff regarding biomedical waste management. Material...

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

    Science.gov (United States)

    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.

  4. The role of biomedical knowledge in echocardiographic interpretation expertise development: a correlation study

    DEFF Research Database (Denmark)

    Nielsen, Dorte Guldbrand; Gøtzsche, Ole; Eika, Berit

    2010-01-01

    Purpose: Little is known about factors of relevance for achieving knowledge of echocardiography (TTE); one of the essential skills defined by the European Society of Cardiology Core Curriculum. Recent research in other fields suggests that biomedical knowledge plays a more prominent role in profe......Purpose: Little is known about factors of relevance for achieving knowledge of echocardiography (TTE); one of the essential skills defined by the European Society of Cardiology Core Curriculum. Recent research in other fields suggests that biomedical knowledge plays a more prominent role...... in professional practice than previously assumed. This study investigates the role of biomedical knowledge represented by physiology knowledge in the development of echocardiographic expertise. Methods: Forty-five physicians (15 novices, 15 intermediates and 15 experts) were evaluated on echocardiography...... interpretation skills. An anatomical focused checklist was developed based on Danish Cardiology Society guidelines for a standard echocardiography of adults. A TTE case of a common and complex clinical presentation was recorded and presented to participants on a portable computer using EchoPac software...

  5. EXTRACTING KNOWLEDGE FROM DATA - DATA MINING

    Directory of Open Access Journals (Sweden)

    DIANA ELENA CODREANU

    2011-04-01

    Full Text Available Managers of economic organizations have at their disposal a large volume of information and practically facing an avalanche of information, but they can not operate studying reports containing detailed data volumes without a correlation because of the good an organization may be decided in fractions of time. Thus, to take the best and effective decisions in real time, managers need to have the correct information is presented quickly, in a synthetic way, but relevant to allow for predictions and analysis.This paper wants to highlight the solutions to extract knowledge from data, namely data mining. With this technology not only has to verify some hypotheses, but aims at discovering new knowledge, so that economic organization to cope with fierce competition in the market.

  6. Students' self-explanations while solving unfamiliar cases: the role of biomedical knowledge.

    Science.gov (United States)

    Chamberland, Martine; Mamede, Sílvia; St-Onge, Christina; Rivard, Marc-Antoine; Setrakian, Jean; Lévesque, Annie; Lanthier, Luc; Schmidt, Henk G; Rikers, Remy M J P

    2013-11-01

    General guidelines for teaching clinical reasoning have received much attention, despite a paucity of instructional approaches with demonstrated effectiveness. As suggested in a recent experimental study, self-explanation while solving clinical cases may be an effective strategy to foster reasoning in clinical clerks dealing with less familiar cases. However, the mechanisms that mediate this benefit have not been specifically investigated. The aim of this study was to explore the types of knowledge used by students when solving familiar and less familiar clinical cases with self-explanation. In a previous study, 36 third-year medical students diagnosed familiar and less familiar clinical cases either by engaging in self-explanation or not. Based on an analysis of previously collected data, the present study compared the content of self-explanation protocols generated by seven randomly selected students while solving four familiar and four less familiar cases. In total, 56 verbal protocols (28 familiar and 28 less familiar) were segmented and coded using the following categories: paraphrases, biomedical inferences, clinical inferences, monitoring statements and errors. Students provided more self-explanation segments from less familiar cases (M = 275.29) than from familiar cases (M = 248.71, p = 0.046). They provided significantly more paraphrases (p = 0.001) and made more errors (p = 0.008). A significant interaction was found between familiarity and the type of inferences (biomedical versus clinical, p = 0.016). When self-explaining less familiar cases, students provided significantly more biomedical inferences than familiar cases. Lack of familiarity with a case seems to stimulate medical students to engage in more extensive thinking during self-explanation. Less familiar cases seem to activate students' biomedical knowledge, which in turn helps them to create new links between biomedical and clinical knowledge, and eventually construct a more coherent mental

  7. Precarious Projects: Conversions of (Biomedical) Knowledge in an East African City

    Science.gov (United States)

    Prince, Ruth J.

    2014-01-01

    This article explores the orientations of lay people in Kenya to science—specifically to biomedical knowledge about HIV—and their struggles to convert this knowledge into meaningful futures. In Kenya, the global response to the HIV-AIDS epidemic has resulted in a highly stratified landscape of intervention. Globally-funded treatment programs and clinical trials, focusing on HIV, channel transnational resources, expertise, and knowledge into specific sites—HIV clinics, NGOs, and research stations—inscribing these spaces as ‘global’ while leaving others decidedly ‘local.’ Rolled out in the form of ‘projects,’ these interventions offer resources and opportunities for a limited time only. Based on ethnographic fieldwork in the city of Kisumu, this article follows the circulation of biomedical knowledge through such projects and its conversion in ways beyond those imagined by policy-makers, as it meets the aspirations of city-dwellers and enters into local livelihoods. Mediated by nongovernmental organizations through workshops and certificates, this knowledge is both fragmentary and ephemeral. I explore the temporal and spatial implications of such knowledge for those who seek to attach themselves to it and shape their identities and futures in relation to it. PMID:24383753

  8. Proposal for a new LEIR slow extraction scheme dedicated to biomedical research

    CERN Document Server

    Garonna, A; Abler, D

    2014-01-01

    A proposal is here presented for a new slow extraction scheme for the Low Energy Ion Ring (LEIR) in the context of the feasibility study for a future biomedical research facility at CERN. The new slow extraction system is based on the third-integer resonance. Two resonance driving mechanisms have been studied: the quadrupole-driven method and the RF-knockout technique. Both were made compatible with the tight constraints imposed by parallel operation of LEIR as heavy ion accumulator and care was taken to maximize the use of the available hardware.

  9. "Exploring knowledge-user experiences in integrated knowledge translation: a biomedical investigation of the causes and consequences of food allergy".

    Science.gov (United States)

    Dixon, Jenna; Elliott, Susan J; Clarke, Ann E

    2016-01-01

    Food allergy is a serious public health problem in Canada and other high-income countries, as it is potentially life threatening and severely impacts the quality of life for individuals and their families. Yet, many questions still remain as to its origins and determinants, and the best practices for treatment. Formed to tackle these very questions, the GET-FACTS research study centers on a novel concept in biomedical research: in order to make this science useful, knowledge creation must include meaningful interactions with knowledge-users. With this, knowledge-users are present at every stage of the research and are crucial, central and equal contributors. This study reflects on the early part of that journey from the perspective of the knowledge-users. We conducted interviews with all non-scientist members of the GET-FACTS steering committee, representing Canadian organizations that deal with patient advocacy and policy with regards to food allergy. Steering committee members had a clear sense that scientists and knowledge-users are equally responsible for putting knowledge into action and the importance of consulting and integrating knowledge-users throughout research. They also have high expectations for the GET-FACTS integrated process; that this model of doing science will create better scientists (e.g. improve communication skills) and make the scientific output more useful and relevant. Our work highlights both the unique contributions that knowledge-users can offer to knowledge creation as well as the challenges of trying to unify members from such different communities (policy/advocacy and biomedical science). There remains a real need to develop more touch points and opportunities for collaboration if true integration is to be achieved. Despite the obstacles, this model can help change the way knowledge is created in the biomedical world. ᅟ. Despite the burden of food allergic disease many questions remain as to its origins, determinants and best

  10. DyKOSMap: A framework for mapping adaptation between biomedical knowledge organization systems.

    Science.gov (United States)

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

    2015-06-01

    Knowledge Organization Systems (KOS) and their associated mappings play a central role in several decision support systems. However, by virtue of knowledge evolution, KOS entities are modified over time, impacting mappings and potentially turning them invalid. This requires semi-automatic methods to maintain such semantic correspondences up-to-date at KOS evolution time. We define a complete and original framework based on formal heuristics that drives the adaptation of KOS mappings. Our approach takes into account the definition of established mappings, the evolution of KOS and the possible changes that can be applied to mappings. This study experimentally evaluates the proposed heuristics and the entire framework on realistic case studies borrowed from the biomedical domain, using official mappings between several biomedical KOSs. We demonstrate the overall performance of the approach over biomedical datasets of different characteristics and sizes. Our findings reveal the effectiveness in terms of precision, recall and F-measure of the suggested heuristics and methods defining the framework to adapt mappings affected by KOS evolution. The obtained results contribute and improve the quality of mappings over time. The proposed framework can adapt mappings largely automatically, facilitating thus the maintenance task. The implemented algorithms and tools support and minimize the work of users in charge of KOS mapping maintenance. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Knowledge and acceptability of alternative HIV prevention bio-medical products among MSM who bareback.

    Science.gov (United States)

    Nodin, N; Carballo-Diéguez, A; Ventuneac, A M; Balan, I C; Remien, R

    2008-01-01

    Condom use is the best available strategy to prevent HIV infection during sexual intercourse. However, since many people choose not to use condoms in circumstances in which HIV risk exists, alternatives to condom use for HIV prevention are needed. Currently there are several alternative bio-medical HIV-prevention products in different stages of development: microbicides, vaccines, post-exposure prophylaxis (PEP) and pre-exposure prophylaxis (PrEP). Seventy-two men who have sex with men (MSM) who took part in a study on Internet use and intentional condomless anal intercourse were asked about these four products during a semi-structured interview. The questions explored knowledge and acceptability of all the products and willingness to participate in microbicide and vaccine trials. Qualitative analysis of the data suggests that these men had virtually no knowledge of PrEP, very limited knowledge of microbicides, some information about PEP and considerably more knowledge about vaccines. Reactions towards the products were generally positive except for PrEP, for which reactions were polarized as either enthusiastic or negative. With the exception of PrEP, many men expressed willingness to use the products in the future. Most men would be willing to participate in trials for microbicides and vaccines if given basic reassurances. Concerns over negative side effects and preoccupation with possible infection were some of the motives given for non-willingness to participate in a vaccine trial. These results should inform the development of future trials of biomedical prevention products.

  12. Proposal for a new LEIR Slow Extraction Scheme dedicated to Biomedical Research

    CERN Document Server

    Garonna, A; Carli, C

    2014-01-01

    This report presents a proposal for a new slow extraction scheme for the Low Energy Ion Ring (LEIR) in the context of the feasibility study for a biomedical research facility at CERN. LEIR has to be maintained as a heavy ion accumulator ring for LHC and for fixed-target experiments with the SPS. In parallel to this on-going operation for physics experiments, an additional secondary use of LEIR for a biomedical research facility was proposed [Dosanjh2013, Holzscheiter2012, PHE2010]. This facility would complement the existing research beam-time available at other laboratories for studies related to ion beam therapy. The new slow extraction [Abler2013] is based on the third-integer resonance. The reference beam is composed of fully stripped carbon ions with extraction energies of 20-440 MeV/u, transverse physical emittances of 5-25 µm and momentum spreads of ±2-9•10-4. Two resonance driving mechanisms have been studied: the quadrupole-driven method and the RF-knockout technique. Both were made compatible...

  13. PIMiner: A web tool for extraction of protein interactions from biomedical literature

    KAUST Repository

    Chowdhary, Rajesh

    2013-01-01

    Information on Protein Interactions (PIs) is valuable for biomedical research, but often lies buried in the scientific literature and cannot be readily retrieved. While much progress has been made over the years in extracting PIs from the literature using computational methods, there is a lack of free, public, user-friendly tools for the discovery of PIs. We developed an online tool for the extraction of PI relationships from PubMed-abstracts, which we name PIMiner. Protein pairs and the words that describe their interactions are reported by PIMiner so that new interactions can be easily detected within text. The interaction likelihood levels are reported too. The option to extract only specific types of interactions is also provided. The PIMiner server can be accessed through a web browser or remotely through a client\\'s command line. PIMiner can process 50,000 PubMed abstracts in approximately 7 min and thus appears suitable for large-scale processing of biological/biomedical literature. Copyright © 2013 Inderscience Enterprises Ltd.

  14. Evaluation on knowledge extraction and machine learning in ...

    African Journals Online (AJOL)

    Evaluation on knowledge extraction and machine learning in resolving Malay word ambiguity. ... No 5S (2017) >. Log in or Register to get access to full text downloads. ... Keywords: ambiguity; lexical knowledge; machine learning; Malay word ...

  15. On importance of impurities, potential leachables and extractables in algal nanocellulose for biomedical use.

    Science.gov (United States)

    Liu, Jun; Willför, Stefan; Mihranyan, Albert

    2017-09-15

    Nanocellulose-based biomaterials for biomedical and pharmaceutical applications have been extensively explored. However, studies on different levels of impurities in the nanocellulose and their potential risks are lacking. This article is the most comprehensive to date survey of the importance and characterization of possible leachables and extractables in nanocellulose for biomedical use. In particular, the (1,3)-β-d-glucan interference in endotoxin detection in algal nanocellulose was addressed. Potential lipophilic and hydrophilic leachables, toxic heavy metals, and microbial contaminants are also monitored. As a model system, nanocellulose from Cladophora sp. algae is investigated. The leachable (1,3)-β-d-glucan and endotoxin, which possess strong immunogenic potential, from the cellulose were minimized to clinically insignificant levels of 4.7μg/g and 2.5EU/g, respectively. The levels of various impurities in the Cladophora cellulose are acceptable for future biomedical applications. The presented approach could be considered as a guideline for other types of nanocellulose. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. KNOWLEDGE AND AWARENESS REGARDING BIOMEDICAL WASTE MANAGEMENT AMONG EMPLOYEES OF A TERTIARY CARE HOSPITAL

    Directory of Open Access Journals (Sweden)

    Manoj Bansal

    2013-05-01

    Full Text Available Background: A hospital is an establishment where the persons suffering with the variety of communicable and non communicable diseases are visiting to take medical care facilities. Hospitals and other healthcare establishments in India produce a significant quantity of waste, posing serious problems for its disposal, an issue that has received scant attention. Objective: To assess the level of knowledge regarding biomedical waste and its management among hospital personnel. Material and Methods: The present study was a cross sectional study carried out in a tertiary care hospital of Gwalior in year 2008. Medical, para-medical and non-medical personnel working at their current position for at least 6 months were included as study participants. Self made scoring system was used to categorize the participants as having Good, Average and Poor knowledge. Statistical Analysis: Percentage and Proportion were applied to interpret the result. Results: The score was highest for medical and least for non-medical staff. Conclusion: The present study concludes that regular training programs should be organized about the guidelines and rules of biomedical waste management at all level.

  17. Knowledge based word-concept model estimation and refinement for biomedical text mining.

    Science.gov (United States)

    Jimeno Yepes, Antonio; Berlanga, Rafael

    2015-02-01

    Text mining of scientific literature has been essential for setting up large public biomedical databases, which are being widely used by the research community. In the biomedical domain, the existence of a large number of terminological resources and knowledge bases (KB) has enabled a myriad of machine learning methods for different text mining related tasks. Unfortunately, KBs have not been devised for text mining tasks but for human interpretation, thus performance of KB-based methods is usually lower when compared to supervised machine learning methods. The disadvantage of supervised methods though is they require labeled training data and therefore not useful for large scale biomedical text mining systems. KB-based methods do not have this limitation. In this paper, we describe a novel method to generate word-concept probabilities from a KB, which can serve as a basis for several text mining tasks. This method not only takes into account the underlying patterns within the descriptions contained in the KB but also those in texts available from large unlabeled corpora such as MEDLINE. The parameters of the model have been estimated without training data. Patterns from MEDLINE have been built using MetaMap for entity recognition and related using co-occurrences. The word-concept probabilities were evaluated on the task of word sense disambiguation (WSD). The results showed that our method obtained a higher degree of accuracy than other state-of-the-art approaches when evaluated on the MSH WSD data set. We also evaluated our method on the task of document ranking using MEDLINE citations. These results also showed an increase in performance over existing baseline retrieval approaches. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. An engineering paradigm in the biomedical sciences: Knowledge as epistemic tool.

    Science.gov (United States)

    Boon, Mieke

    2017-10-01

    In order to deal with the complexity of biological systems and attempts to generate applicable results, current biomedical sciences are adopting concepts and methods from the engineering sciences. Philosophers of science have interpreted this as the emergence of an engineering paradigm, in particular in systems biology and synthetic biology. This article aims at the articulation of the supposed engineering paradigm by contrast with the physics paradigm that supported the rise of biochemistry and molecular biology. This articulation starts from Kuhn's notion of a disciplinary matrix, which indicates what constitutes a paradigm. It is argued that the core of the physics paradigm is its metaphysical and ontological presuppositions, whereas the core of the engineering paradigm is the epistemic aim of producing useful knowledge for solving problems external to the scientific practice. Therefore, the two paradigms involve distinct notions of knowledge. Whereas the physics paradigm entails a representational notion of knowledge, the engineering paradigm involves the notion of 'knowledge as epistemic tool'. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.

    Science.gov (United States)

    Ravikumar, Komandur Elayavilli; Wagholikar, Kavishwar B; Li, Dingcheng; Kocher, Jean-Pierre; Liu, Hongfang

    2015-06-06

    Advances in the next generation sequencing technology has accelerated the pace of individualized medicine (IM), which aims to incorporate genetic/genomic information into medicine. One immediate need in interpreting sequencing data is the assembly of information about genetic variants and their corresponding associations with other entities (e.g., diseases or medications). Even with dedicated effort to capture such information in biological databases, much of this information remains 'locked' in the unstructured text of biomedical publications. There is a substantial lag between the publication and the subsequent abstraction of such information into databases. Multiple text mining systems have been developed, but most of them focus on the sentence level association extraction with performance evaluation based on gold standard text annotations specifically prepared for text mining systems. We developed and evaluated a text mining system, MutD, which extracts protein mutation-disease associations from MEDLINE abstracts by incorporating discourse level analysis, using a benchmark data set extracted from curated database records. MutD achieves an F-measure of 64.3% for reconstructing protein mutation disease associations in curated database records. Discourse level analysis component of MutD contributed to a gain of more than 10% in F-measure when compared against the sentence level association extraction. Our error analysis indicates that 23 of the 64 precision errors are true associations that were not captured by database curators and 68 of the 113 recall errors are caused by the absence of associated disease entities in the abstract. After adjusting for the defects in the curated database, the revised F-measure of MutD in association detection reaches 81.5%. Our quantitative analysis reveals that MutD can effectively extract protein mutation disease associations when benchmarking based on curated database records. The analysis also demonstrates that incorporating

  20. Mining knowledge from text repositories using information extraction ...

    Indian Academy of Sciences (India)

    Information extraction (IE); text mining; text repositories; knowledge discovery from .... general purpose English words. However ... of precision and recall, as extensive experimentation is required due to lack of public tagged corpora. 4. Mining ...

  1. Therapeutic Significance of Loligo vulgaris (Lamarck, 1798) ink Extract: A Biomedical Approach

    Science.gov (United States)

    Nadarajah, Sri Kumaran; Vijayaraj, Radha; Mani, Jayaprakashvel

    2017-01-01

    Background: The squid ink extract is well known for its biomedical properties. Objective: In this study, squid Loligo vulgaris was collected from Tuticorin costal water, Bay of Bengal, India. Materials and Methods: Proximate composition of the crude squid ink was studied and found to have protein as the major component over lipid and carbohydrates. Further, bioactive fractions of squid ink were extracted with ethanol, and therapeutic applications such as hemolytic, antioxidant, antimicrobial, and in vitro anti-inflammatory properties were analyzed using standard methods. Results: In hemolytic assay, the squid ink extract exhibited a maximum hemolytic activity of 128 hemolytic unit against tested erythrocytes. In DPPH assay, the ethanolic extract of squid ink has exhibited an antioxidant activity of 83.5%. The squid ink was found to be potent antibacterial agent against the pathogens tested. 200 μL of L. vulgaris ink extract showed remarkable antibacterial activity as zone of inhibition against Escherichia coli (28 mm), Klebsiella pneumoniae (22 mm), Pseudomonas aeruginosa (21 mm), and Staphylococcus aureus (24 mm). The 68.9% inhibition of protein denaturation by the squid ink extract indicated that it has very good in vitro anti-inflammatory properties. The Fourier transform infrared spectroscopy analysis of the ethanolic extracts of the squid ink indicated the presence of functional groups such as 1° and 2° amines, amides, alkynes (terminal), alkenes, aldehydes, nitriles, alkanes, aliphatic amines, carboxylic acids, and alkyl halides, which complements the biochemical background of therapeutic applications. Conclusion: Hence, results of this study concluded that the ethanolic extract of L. vulgaris has many therapeutic applications such as antimicrobial, antioxidant, and anti-inflammatory activities. SUMMARY Squid ink is very high in a number of important nutrients. It’s particularly high in antioxidants for instance, which as well all know help to protect

  2. Knowledge Extraction from Atomically Resolved Images.

    Science.gov (United States)

    Vlcek, Lukas; Maksov, Artem; Pan, Minghu; Vasudevan, Rama K; Kalinin, Sergei V

    2017-10-24

    Tremendous strides in experimental capabilities of scanning transmission electron microscopy and scanning tunneling microscopy (STM) over the past 30 years made atomically resolved imaging routine. However, consistent integration and use of atomically resolved data with generative models is unavailable, so information on local thermodynamics and other microscopic driving forces encoded in the observed atomic configurations remains hidden. Here, we present a framework based on statistical distance minimization to consistently utilize the information available from atomic configurations obtained from an atomically resolved image and extract meaningful physical interaction parameters. We illustrate the applicability of the framework on an STM image of a FeSe x Te 1-x superconductor, with the segregation of the chalcogen atoms investigated using a nonideal interacting solid solution model. This universal method makes full use of the microscopic degrees of freedom sampled in an atomically resolved image and can be extended via Bayesian inference toward unbiased model selection with uncertainty quantification.

  3. PKDE4J: Entity and relation extraction for public knowledge discovery.

    Science.gov (United States)

    Song, Min; Kim, Won Chul; Lee, Dahee; Heo, Go Eun; Kang, Keun Young

    2015-10-01

    Due to an enormous number of scientific publications that cannot be handled manually, there is a rising interest in text-mining techniques for automated information extraction, especially in the biomedical field. Such techniques provide effective means of information search, knowledge discovery, and hypothesis generation. Most previous studies have primarily focused on the design and performance improvement of either named entity recognition or relation extraction. In this paper, we present PKDE4J, a comprehensive text-mining system that integrates dictionary-based entity extraction and rule-based relation extraction in a highly flexible and extensible framework. Starting with the Stanford CoreNLP, we developed the system to cope with multiple types of entities and relations. The system also has fairly good performance in terms of accuracy as well as the ability to configure text-processing components. We demonstrate its competitive performance by evaluating it on many corpora and found that it surpasses existing systems with average F-measures of 85% for entity extraction and 81% for relation extraction. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. A framework for extracting and representing project knowledge contexts using topic models and dynamic knowledge maps

    Science.gov (United States)

    Xu, Jin; Li, Zheng; Li, Shuliang; Zhang, Yanyan

    2015-07-01

    There is still a lack of effective paradigms and tools for analysing and discovering the contents and relationships of project knowledge contexts in the field of project management. In this paper, a new framework for extracting and representing project knowledge contexts using topic models and dynamic knowledge maps under big data environments is proposed and developed. The conceptual paradigm, theoretical underpinning, extended topic model, and illustration examples of the ontology model for project knowledge maps are presented, with further research work envisaged.

  5. Disparities in HIV knowledge and attitudes toward biomedical interventions among the non-medical HIV workforce in the United States.

    Science.gov (United States)

    Copeland, Raniyah M; Wilson, Phill; Betancourt, Gabriela; Garcia, David; Penner, Murray; Abravanel, Rebecca; Wong, Eric Y; Parisi, Lori D

    2017-12-01

    Non-medical, community-based workers play a critical role in supporting people living with (or at risk of acquiring) HIV along the care continuum. The biomedical nature of promising advances in HIV prevention, such as pre-exposure prophylaxis and treatment-as-prevention, requires frontline workers to be knowledgeable about HIV science and treatment. This study was developed to: measure knowledge of HIV science and treatment within the HIV non-medical workforce, evaluate workers' familiarity with and attitudes toward recent biomedical interventions, and identify factors that may affect HIV knowledge and attitudes. A 62-question, web-based survey was completed in English or Spanish between 2012 and 2014 by 3663 US-based employees, contractors, and volunteers working in AIDS service organizations, state/local health departments, and other community-based organizations in a non-medical capacity. Survey items captured the following: respondent demographics, HIV science and treatment knowledge, and familiarity with and attitudes toward biomedical interventions. An average of 61% of HIV knowledge questions were answered correctly. Higher knowledge scores were associated with higher education levels, work at organizations that serve people living with HIV/AIDS or who are at a high risk of acquiring HIV, and longer tenure in the field. Lower knowledge scores were associated with non-Hispanic Black or Black race/ethnicity and taking the survey in Spanish. Similarly, subgroup analyses showed that respondents who were non-Hispanic Black or Hispanic (versus non-Hispanic white), as well as those located in the South (versus other regions) scored significantly lower. These subpopulations were also less familiar with and had less positive attitudes toward newer biomedical prevention interventions. Respondents who took the survey in Spanish (versus English) had lower knowledge scores and higher familiarity with, but generally less positive attitudes toward, biomedical interventions

  6. Knowledge Dictionary for Information Extraction on the Arabic Text Data

    Directory of Open Access Journals (Sweden)

    Wahyu Jauharis Saputra

    2013-04-01

    Full Text Available Information extraction is an early stage of a process of textual data analysis. Information extraction is required to get information from textual data that can be used for process analysis, such as classification and categorization. A textual data is strongly influenced by the language. Arabic is gaining a significant attention in many studies because Arabic language is very different from others, and in contrast to other languages, tools and research on the Arabic language is still lacking. The information extracted using the knowledge dictionary is a concept of expression. A knowledge dictionary is usually constructed manually by an expert and this would take a long time and is specific to a problem only. This paper proposed a method for automatically building a knowledge dictionary. Dictionary knowledge is formed by classifying sentences having the same concept, assuming that they will have a high similarity value. The concept that has been extracted can be used as features for subsequent computational process such as classification or categorization. Dataset used in this paper was the Arabic text dataset. Extraction result was tested by using a decision tree classification engine and the highest precision value obtained was 71.0% while the highest recall value was 75.0%. 

  7. Automatic Knowledge Extraction and Knowledge Structuring for a National Term Bank

    DEFF Research Database (Denmark)

    Lassen, Tine; Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2011-01-01

    This paper gives an introduction to the plans and ongoing work in a project, the aim of which is to develop methods for automatic knowledge extraction and automatic construction and updating of ontologies. The project also aims at developing methods for automatic merging of terminological data fr...... various existing sources, as well as methods for target group oriented knowledge dissemination. In this paper, we mainly focus on the plans for automatic knowledge extraction and knowledge structuring that will result in ontologies for a national term bank.......This paper gives an introduction to the plans and ongoing work in a project, the aim of which is to develop methods for automatic knowledge extraction and automatic construction and updating of ontologies. The project also aims at developing methods for automatic merging of terminological data from...

  8. Design of Automatic Extraction Algorithm of Knowledge Points for MOOCs

    Directory of Open Access Journals (Sweden)

    Haijian Chen

    2015-01-01

    Full Text Available In recent years, Massive Open Online Courses (MOOCs are very popular among college students and have a powerful impact on academic institutions. In the MOOCs environment, knowledge discovery and knowledge sharing are very important, which currently are often achieved by ontology techniques. In building ontology, automatic extraction technology is crucial. Because the general methods of text mining algorithm do not have obvious effect on online course, we designed automatic extracting course knowledge points (AECKP algorithm for online course. It includes document classification, Chinese word segmentation, and POS tagging for each document. Vector Space Model (VSM is used to calculate similarity and design the weight to optimize the TF-IDF algorithm output values, and the higher scores will be selected as knowledge points. Course documents of “C programming language” are selected for the experiment in this study. The results show that the proposed approach can achieve satisfactory accuracy rate and recall rate.

  9. Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature.

    Directory of Open Access Journals (Sweden)

    Ibrahim Burak Ozyurt

    Full Text Available The NIF Registry developed and maintained by the Neuroscience Information Framework is a cooperative project aimed at cataloging research resources, e.g., software tools, databases and tissue banks, funded largely by governments and available as tools to research scientists. Although originally conceived for neuroscience, the NIF Registry has over the years broadened in the scope to include research resources of general relevance to biomedical research. The current number of research resources listed by the Registry numbers over 13K. The broadening in scope to biomedical science led us to re-christen the NIF Registry platform as SciCrunch. The NIF/SciCrunch Registry has been cataloging the resource landscape since 2006; as such, it serves as a valuable dataset for tracking the breadth, fate and utilization of these resources. Our experience shows research resources like databases are dynamic objects, that can change location and scope over time. Although each record is entered manually and human-curated, the current size of the registry requires tools that can aid in curation efforts to keep content up to date, including when and where such resources are used. To address this challenge, we have developed an open source tool suite, collectively termed RDW: Resource Disambiguator for the (Web. RDW is designed to help in the upkeep and curation of the registry as well as in enhancing the content of the registry by automated extraction of resource candidates from the literature. The RDW toolkit includes a URL extractor from papers, resource candidate screen, resource URL change tracker, resource content change tracker. Curators access these tools via a web based user interface. Several strategies are used to optimize these tools, including supervised and unsupervised learning algorithms as well as statistical text analysis. The complete tool suite is used to enhance and maintain the resource registry as well as track the usage of individual

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

    Directory of Open Access Journals (Sweden)

    Herman H H B M van Haagen

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

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

    OpenAIRE

    Jonnalagadda, Siddhartha; Gonzalez, Graciela

    2011-01-01

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

  12. KNOWLEDGE AND AWARENESS REGARDING BIOMEDICAL WASTE MANAGEMENT AMONG EMPLOYEES OF A TERTIARY CARE HOSPITAL

    Directory of Open Access Journals (Sweden)

    Manoj Bansal

    2013-03-01

    Results: The score was highest for medical and least for non-medical staff. Conclusion: The present study concludes that regular training programs should be organized about the guidelines and rules of biomedical waste management at all level.

  13. MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature

    Directory of Open Access Journals (Sweden)

    Fang Yu-Ching

    2011-12-01

    Full Text Available Abstract Background DNA methylation is regarded as a potential biomarker in the diagnosis and treatment of cancer. The relations between aberrant gene methylation and cancer development have been identified by a number of recent scientific studies. In a previous work, we used co-occurrences to mine those associations and compiled the MeInfoText 1.0 database. To reduce the amount of manual curation and improve the accuracy of relation extraction, we have now developed MeInfoText 2.0, which uses a machine learning-based approach to extract gene methylation-cancer relations. Description Two maximum entropy models are trained to predict if aberrant gene methylation is related to any type of cancer mentioned in the literature. After evaluation based on 10-fold cross-validation, the average precision/recall rates of the two models are 94.7/90.1 and 91.8/90% respectively. MeInfoText 2.0 provides the gene methylation profiles of different types of human cancer. The extracted relations with maximum probability, evidence sentences, and specific gene information are also retrievable. The database is available at http://bws.iis.sinica.edu.tw:8081/MeInfoText2/. Conclusion The previous version, MeInfoText, was developed by using association rules, whereas MeInfoText 2.0 is based on a new framework that combines machine learning, dictionary lookup and pattern matching for epigenetics information extraction. The results of experiments show that MeInfoText 2.0 outperforms existing tools in many respects. To the best of our knowledge, this is the first study that uses a hybrid approach to extract gene methylation-cancer relations. It is also the first attempt to develop a gene methylation and cancer relation corpus.

  14. Disease causality extraction based on lexical semantics and document-clause frequency from biomedical literature.

    Science.gov (United States)

    Lee, Dong-Gi; Shin, Hyunjung

    2017-05-18

    Recently, research on human disease network has succeeded and has become an aid in figuring out the relationship between various diseases. In most disease networks, however, the relationship between diseases has been simply represented as an association. This representation results in the difficulty of identifying prior diseases and their influence on posterior diseases. In this paper, we propose a causal disease network that implements disease causality through text mining on biomedical literature. To identify the causality between diseases, the proposed method includes two schemes: the first is the lexicon-based causality term strength, which provides the causal strength on a variety of causality terms based on lexicon analysis. The second is the frequency-based causality strength, which determines the direction and strength of causality based on document and clause frequencies in the literature. We applied the proposed method to 6,617,833 PubMed literature, and chose 195 diseases to construct a causal disease network. From all possible pairs of disease nodes in the network, 1011 causal pairs of 149 diseases were extracted. The resulting network was compared with that of a previous study. In terms of both coverage and quality, the proposed method showed outperforming results; it determined 2.7 times more causalities and showed higher correlation with associated diseases than the existing method. This research has novelty in which the proposed method circumvents the limitations of time and cost in applying all possible causalities in biological experiments and it is a more advanced text mining technique by defining the concepts of causality term strength.

  15. Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction.

    Science.gov (United States)

    Zhang, Yaoyun; Soysal, Ergin; Moon, Sungrim; Wang, Jingqi; Tao, Cui; Xu, Hua

    2015-01-01

    A computable knowledge base containing relations between diseases and lab tests would be a great resource for many biomedical informatics applications. This paper describes our initial step towards establishing a comprehensive knowledge base of disease and lab tests relations utilizing three public on-line resources. LabTestsOnline, MedlinePlus and Wikipedia are integrated to create a freely available, computable disease-lab test knowledgebase. Disease and lab test concepts are identified using MetaMap and relations between diseases and lab tests are determined based on source-specific rules. Experimental results demonstrate a high precision for relation extraction, with Wikipedia achieving the highest precision of 87%. Combining the three sources reached a recall of 51.40%, when compared with a subset of disease-lab test relations extracted from a reference book. Moreover, we found additional disease-lab test relations from on-line resources, indicating they are complementary to existing reference books for building a comprehensive disease and lab test relation knowledge base.

  16. Commonsense knowledge extraction for Persian language: A combinatory approach

    Directory of Open Access Journals (Sweden)

    Mehdi Moradi

    2015-12-01

    Full Text Available Putting human commonsense knowledge into computers has always been a long standing dream of artificial intelligence (AI. The cost of several tens of millions of dollars and times have been covered so that the computers could know about “objects falling, not rising.”,” running is faster than walking. The large database was built, automated and semi-automated methods were introduced and volunteers’ efforts were utilized to achieve this, but an automated, high-throughput and low-noise method for commonsense collection still remains as the holy grail of AI. The aim of this study was to build commonsense knowledge ontology using three approaches namely Hearst method, machine translation and using structured resources. Using three Persian corpuse and Applying aforementioned methods, we could extract 7 different relations. 70000 assertions have been extracted. Finally, average accuracy of Hearst, MT and structured resource were 75%, 75% and 100% respectively.

  17. Automated extraction of knowledge for model-based diagnostics

    Science.gov (United States)

    Gonzalez, Avelino J.; Myler, Harley R.; Towhidnejad, Massood; Mckenzie, Frederic D.; Kladke, Robin R.

    1990-01-01

    The concept of accessing computer aided design (CAD) design databases and extracting a process model automatically is investigated as a possible source for the generation of knowledge bases for model-based reasoning systems. The resulting system, referred to as automated knowledge generation (AKG), uses an object-oriented programming structure and constraint techniques as well as internal database of component descriptions to generate a frame-based structure that describes the model. The procedure has been designed to be general enough to be easily coupled to CAD systems that feature a database capable of providing label and connectivity data from the drawn system. The AKG system is capable of defining knowledge bases in formats required by various model-based reasoning tools.

  18. PIMiner: A web tool for extraction of protein interactions from biomedical literature

    KAUST Repository

    Chowdhary, Rajesh; Zhang, Jinfeng; Tan, Sinlam; Osborne, Daniel E.; Bajic, Vladimir B.; Liu, Jun

    2013-01-01

    server can be accessed through a web browser or remotely through a client's command line. PIMiner can process 50,000 PubMed abstracts in approximately 7 min and thus appears suitable for large-scale processing of biological/biomedical literature

  19. Designing a mobile augmented reality tool for the locative visualisation of biomedical knowledge.

    Science.gov (United States)

    Kilby, Jess; Gray, Kathleen; Elliott, Kristine; Waycott, Jenny; Sanchez, Fernando Martin; Dave, Bharat

    2013-01-01

    Mobile augmented reality (MAR) may offer new and engaging ways to support consumer participation in health. We report on design-based research into a MAR application for smartphones and tablets, intended to improve public engagement with biomedical research in a specific urban precinct. Following a review of technical capabilities and organizational and locative design considerations, we worked with staff of four research institutes to elicit their ideas about information and interaction functionalities of a shared MAR app. The results were promising, supporting the development of a prototype and initial field testing with these staff. Evidence from this project may point the way toward user-centred design of MAR services that will enable more widespread adoption of the technology in other healthcare and biomedical research contexts.

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

    Directory of Open Access Journals (Sweden)

    A Mitnitski

    2003-01-01

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

  1. Enhancing Media Personalization by Extracting Similarity Knowledge from Metadata

    DEFF Research Database (Denmark)

    Butkus, Andrius

    be seen as a cognitive foundation for modeling concepts. Conceptual Spaces is applied in this thesis to analyze media in terms of its dimensions and knowledge domains, which in return defines properties and concepts. One of the most important domains in terms of describing media is the emotional one...... only “more of the same” type of content which does not necessarily lead to the meaningful personalization. Another way to approach similarity is to find a similar underlying meaning in the content. Aspects of meaning in media can be represented using Gardenfors Conceptual Spaces theory, which can......) using Latent Semantic Analysis (one of the unsupervised machine learning techniques). It presents three separate cases to illustrate the similarity knowledge extraction from the metadata, where the emotional components in each case represents different abstraction levels – genres, synopsis and lyrics...

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

    Science.gov (United States)

    Jonnalagadda, Siddhartha; Gonzalez, Graciela

    2010-11-13

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

  3. Automated Extraction Of Associations Between Methylated Genes and Diseases From Biomedical Literature

    KAUST Repository

    Bin Res, Arwa A.

    2012-01-01

    . Based on this model, we developed a tool that automates extraction of associations between methylated genes and diseases from electronic text. Our study contributed an efficient method for extracting specific types of associations from free text

  4. Dataset on the knowledge, attitude and practices of biomedical wastes management among Neyshabur hospital’s healthcare personnel

    Directory of Open Access Journals (Sweden)

    Mahmood Alimohammadi

    2018-04-01

    Full Text Available The data presented in this article are related to the research article entitled “knowledge, attitude and performance regarding waste management among the HCWs in hospitals affiliated with the Neyshabur City, Iran”. A researcher-made questionnaire (accessible as an attachment containing 4 parts of demographic information, knowledge (24 questions, attitude (6 questions and practices (6 questions was used for data gathering. Kruskal- Wallis test, Mann-Whitney U and Spearman correlation coefficient were used to analyze the data. The significance level was set at 0.05 for the test. Data Analyzing showed the relationship between attitude and Practices with a correlation coefficient of 0.177 was statistically significant (P = 0.01. Also, according to this research, the relationship between the individuals' work experience with knowledge, attitude, and Practices with their correlation coefficients of 0.178, 0.247, and 0.152, respectively were significant (P = 0.018, P = 0.001, P = 0.043. Furthermore, the relationship between age with knowledge and practice was not significant (P = 0.605 and P = 0.102, respectively and its relationship with attitude was significant with a correlation coefficient of 0.154 (P = 0.028. Keywords: Bio-medical waste, Health care worker, Knowledge, Awareness, Attitude

  5. Information extraction and knowledge graph construction from geoscience literature

    Science.gov (United States)

    Wang, Chengbin; Ma, Xiaogang; Chen, Jianguo; Chen, Jingwen

    2018-03-01

    Geoscience literature published online is an important part of open data, and brings both challenges and opportunities for data analysis. Compared with studies of numerical geoscience data, there are limited works on information extraction and knowledge discovery from textual geoscience data. This paper presents a workflow and a few empirical case studies for that topic, with a focus on documents written in Chinese. First, we set up a hybrid corpus combining the generic and geology terms from geology dictionaries to train Chinese word segmentation rules of the Conditional Random Fields model. Second, we used the word segmentation rules to parse documents into individual words, and removed the stop-words from the segmentation results to get a corpus constituted of content-words. Third, we used a statistical method to analyze the semantic links between content-words, and we selected the chord and bigram graphs to visualize the content-words and their links as nodes and edges in a knowledge graph, respectively. The resulting graph presents a clear overview of key information in an unstructured document. This study proves the usefulness of the designed workflow, and shows the potential of leveraging natural language processing and knowledge graph technologies for geoscience.

  6. A STUDY OF THE IMPACT OF THREE DAY TRAINING PROGRAMME ON KNOWLEDGE REGARDING BIOMEDICAL WASTE AMONG PARAMEDICAL STAFF OF DISTRICT HOSPITAL ETAWAH (UP

    Directory of Open Access Journals (Sweden)

    Dhiraj Kumar Srivastava

    2013-09-01

    Full Text Available Introduction: Biomedical waste by definition means “Any waste which is generated during the process of diagnosis, treatment or immunization of human or animal or in research activities pertaining there to in the production or testing of biological”Objectives:•    The level of awareness about various aspect of Bio Medical Waste management among the paramedical staff.•    To study the impact of three day training programme on knowledge of Bio Medical Waste management. Material & Methods: The present study  is a Cross sectional Study carried out to assess the impact of three day training programme on knowledge of Paramedical staff posted at District Hospital, Etawah. The change in knowledge was assessed using pre- test and post- test questionnaire.Result: A total of 72 paramedical staff participated in the study. Majority of the participants were unaware about the hazards associated with the improper handing f Biomedical wastes. The knowledge about the different color codes used for the segregation of biomedical waste was also very low. Similarly, the awareness about the vehicle used for the transportation of biomedical waste was also poor.Conclusion: The present study concludes that there is an urgent need for regular training for paramedical staff posted at District Hospital and other government hospital located in small District & town as awareness about the Biomedical waste among them is very low.

  7. A STUDY OF THE IMPACT OF THREE DAY TRAINING PROGRAMME ON KNOWLEDGE REGARDING BIOMEDICAL WASTE AMONG PARAMEDICAL STAFF OF DISTRICT HOSPITAL ETAWAH (UP

    Directory of Open Access Journals (Sweden)

    Dhiraj Kumar Srivastava

    2013-12-01

    Full Text Available Introduction: Biomedical waste by definition means “Any waste which is generated during the process of diagnosis, treatment or immunization of human or animal or in research activities pertaining there to in the production or testing of biological”Objectives:•    The level of awareness about various aspect of Bio Medical Waste management among the paramedical staff.•    To study the impact of three day training programme on knowledge of Bio Medical Waste management. Material & Methods: The present study  is a Cross sectional Study carried out to assess the impact of three day training programme on knowledge of Paramedical staff posted at District Hospital, Etawah. The change in knowledge was assessed using pre- test and post- test questionnaire.Result: A total of 72 paramedical staff participated in the study. Majority of the participants were unaware about the hazards associated with the improper handing f Biomedical wastes. The knowledge about the different color codes used for the segregation of biomedical waste was also very low. Similarly, the awareness about the vehicle used for the transportation of biomedical waste was also poor.Conclusion: The present study concludes that there is an urgent need for regular training for paramedical staff posted at District Hospital and other government hospital located in small District & town as awareness about the Biomedical waste among them is very low.

  8. An Object-Oriented Approach to Knowledge Representation in a Biomedical Domain

    NARCIS (Netherlands)

    Ensing, M.; Paton, R.; Speel, P.H.W.M.; Speel, P.H.W.M.; Rada, R.

    1994-01-01

    An object-oriented approach has been applied to the different stages involved in developing a knowledge base about insulin metabolism. At an early stage the separation of terminological and assertional knowledge was made. The terminological component was developed by medical experts and represented

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

    Science.gov (United States)

    Jonnalagadda, Siddhartha

    2011-01-01

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

  10. Knowledge discovery: Extracting usable information from large amounts of data

    International Nuclear Information System (INIS)

    Whiteson, R.

    1998-01-01

    The threat of nuclear weapons proliferation is a problem of world wide concern. Safeguards are the key to nuclear nonproliferation and data is the key to safeguards. The safeguards community has access to a huge and steadily growing volume of data. The advantages of this data rich environment are obvious, there is a great deal of information which can be utilized. The challenge is to effectively apply proven and developing technologies to find and extract usable information from that data. That information must then be assessed and evaluated to produce the knowledge needed for crucial decision making. Efficient and effective analysis of safeguards data will depend on utilizing technologies to interpret the large, heterogeneous data sets that are available from diverse sources. With an order-of-magnitude increase in the amount of data from a wide variety of technical, textual, and historical sources there is a vital need to apply advanced computer technologies to support all-source analysis. There are techniques of data warehousing, data mining, and data analysis that can provide analysts with tools that will expedite their extracting useable information from the huge amounts of data to which they have access. Computerized tools can aid analysts by integrating heterogeneous data, evaluating diverse data streams, automating retrieval of database information, prioritizing inputs, reconciling conflicting data, doing preliminary interpretations, discovering patterns or trends in data, and automating some of the simpler prescreening tasks that are time consuming and tedious. Thus knowledge discovery technologies can provide a foundation of support for the analyst. Rather than spending time sifting through often irrelevant information, analysts could use their specialized skills in a focused, productive fashion. This would allow them to make their analytical judgments with more confidence and spend more of their time doing what they do best

  11. Gender Writ Small: Gender Enactments and Gendered Narratives about Lab Organization and Knowledge Transmission in a Biomedical Engineering Research Setting

    Science.gov (United States)

    Malone, Kareen Ror; Nersessian, Nancy J.; Newstetter, Wendy

    This article presents qualitative data and offers some innovative theoretical approaches to frame the analysis of gender in science, technology, engineering, and mathematics (STEM) settings. It begins with a theoretical discussion of a discursive approach to gender that captures how gender is lived "on the ground." The authors argue for a less individualistic approach to gender. Data for this research project was gathered from intensive interviews with lab members and ethnographic observations in a biomedical engineering lab. Data analysis relied on a mixed methodology involving qualitative approaches and dialogues with findings from other research traditions. Three themes are highlighted: lab dynamics in relation to issues of critical mass, the division of labor, and knowledge transmission. The data illustrate how gender is created in interactions and is inflected through forms of social organization.

  12. Minimally-invasive, microneedle-array extraction of interstitial fluid for comprehensive biomedical applications: transcriptomics, proteomics, metabolomics, exosome research, and biomarker identification.

    Science.gov (United States)

    Taylor, Robert M; Miller, Philip R; Ebrahimi, Parwana; Polsky, Ronen; Baca, Justin T

    2018-01-01

    Interstitial fluid (ISF) has recently garnered interest as a biological fluid that could be used as an alternate to blood for biomedical applications, diagnosis, and therapy. ISF extraction techniques are promising because they are less invasive and less painful than venipuncture. ISF is an alternative, incompletely characterized source of physiological data. Here, we describe a novel method of ISF extraction in rats, using microneedle arrays, which provides volumes of ISF that are sufficient for downstream analysis techniques such as proteomics, genomics, and extracellular vesicle purification and analysis. This method is potentially less invasive than previously reported techniques. The limited invasiveness and larger volumes of extracted ISF afforded by this microneedle-assisted ISF extraction method provide a technique that is less stressful and more humane to laboratory animals, while also allowing for a reduction in the numbers of animals needed to acquire sufficient volumes of ISF for biomedical analysis and application.

  13. Medical pluralism and livestock health: ethnomedical and biomedical veterinary knowledge among East African agropastoralists.

    Science.gov (United States)

    Caudell, Mark A; Quinlan, Marsha B; Quinlan, Robert J; Call, Douglas R

    2017-01-21

    Human and animal health are deeply intertwined in livestock dependent areas. Livestock health contributes to food security and can influence human health through the transmission of zoonotic diseases. In low-income countries diagnosis and treatment of livestock diseases is often carried out by household members who draw upon both ethnoveterinary medicine (EVM) and contemporary veterinary biomedicine (VB). Expertise in these knowledge bases, along with their coexistence, informs treatment and thus ultimately impacts animal and human health. The aim of the current study was to determine how socio-cultural and ecological differences within and between two livestock-keeping populations, the Maasai of northern Tanzania and Koore of southwest Ethiopia, impact expertise in EVM and VB and coexistence of the two knowledge bases. An ethnoveterinary research project was conducted to examine dimensions of EVM and VB knowledge among the Maasai (N = 142 households) and the Koore (N = 100). Cultural consensus methods were used to quantify expertise and the level of agreement on EVM and VB knowledge. Ordinary least squares regression was used to model patterns of expertise and consensus across groups and to examine associations between knowledge and demographic/sociocultural attributes. Maasai and Koore informants displayed high consensus on EVM but only the Koore displayed consensus on VB knowledge. EVM expertise in the Koore varied across gender, herd size, and level of VB expertise. EVM expertise was highest in the Maasai but was only associated with age. The only factor associated with VB expertise was EVM expertise in the Koore. Variation in consensus and the correlates of expertise across the Maassi and the Koore are likely related to differences in the cultural transmission of EVM and VB knowledge. Transmission dynamics are established by the integration of livestock within the socioecological systems of the Maasai and Koore and culture historical experiences with

  14. Automated Extraction Of Associations Between Methylated Genes and Diseases From Biomedical Literature

    KAUST Repository

    Bin Res, Arwa A.

    2012-12-01

    Associations between methylated genes and diseases have been investigated in several studies, and it is critical to have such information available for better understanding of diseases and clinical decisions. However, such information is scattered in a large number of electronic publications and it is difficult to manually search for it. Therefore, the goal of the project is to develop a machine learning model that can efficiently extract such information. Twelve machine learning algorithms were applied and compared in application to this problem based on three approaches that involve: document-term frequency matrices, position weight matrices, and a hybrid approach that uses the combination of the previous two. The best results we obtained by the hybrid approach with a random forest model that, in a 10-fold cross-validation, achieved F-score and accuracy of nearly 85% and 84%, respectively. On a completely separate testing set, F-score and accuracy of 89% and 88%, respectively, were obtained. Based on this model, we developed a tool that automates extraction of associations between methylated genes and diseases from electronic text. Our study contributed an efficient method for extracting specific types of associations from free text and the methodology developed here can be extended to other similar association extraction problems.

  15. Machine Learning for Knowledge Extraction from PHR Big Data.

    Science.gov (United States)

    Poulymenopoulou, Michaela; Malamateniou, Flora; Vassilacopoulos, George

    2014-01-01

    Cloud computing, Internet of things (IOT) and NoSQL database technologies can support a new generation of cloud-based PHR services that contain heterogeneous (unstructured, semi-structured and structured) patient data (health, social and lifestyle) from various sources, including automatically transmitted data from Internet connected devices of patient living space (e.g. medical devices connected to patients at home care). The patient data stored in such PHR systems constitute big data whose analysis with the use of appropriate machine learning algorithms is expected to improve diagnosis and treatment accuracy, to cut healthcare costs and, hence, to improve the overall quality and efficiency of healthcare provided. This paper describes a health data analytics engine which uses machine learning algorithms for analyzing cloud based PHR big health data towards knowledge extraction to support better healthcare delivery as regards disease diagnosis and prognosis. This engine comprises of the data preparation, the model generation and the data analysis modules and runs on the cloud taking advantage from the map/reduce paradigm provided by Apache Hadoop.

  16. Biofabrication and characterization of silver nanoparticles using aqueous extract of seaweed Enteromorpha compressa and its biomedical properties

    Directory of Open Access Journals (Sweden)

    Vijayan Sri Ramkumar

    2017-03-01

    Full Text Available Green synthesis of nanoparticles using seaweeds are fascinating high research attention nowadays and also gaining center of attention in biomedical applications. In this work, we have synthesized biocompatible and functionalized silver nanoparticles using an aqueous extract of seaweed Enteromorpha compressa as a reducing as well as stabilizing agent and their efficient antimicrobial and anticancer activity are reported here. The UV–vis spectra of AgNPs showed the characteristics SPR absorption band at 421 nm. The chemical interaction and crystalline nature of the AgNPs were evaluated by FT-IR and XRD studies. The XRD result of AgNPs shows typical Ag reflection peaks at 38.1°, 44.2°, 64.4° and 77.1° corresponding to (111, (200, (220 and (311 Bragg’s planes. The surface morphology and composition of the samples were observed by HRTEM, EDS and SAED pattern analyses. Spherical shaped Ag nano structures were observed in the size ranges between 4 and 24 nm with clear lattice fringes in the HRTEM image. This report reveals that seaweed mediated synthesis of AgNPs and sustained delivery of Ag ions to the bacterial and fungal surface have been reducing their growth rate which was evaluated by well diffusion assay. The synthesized AgNPs showed favorable cytotoxicity against Ehlrich Ascites Carcinoma (EAC cells with IC50 value was recorded at 95.35 μg mL−1. This study showed cost effective silver nanoparticles synthesis with excellent biocompatibility and thus could potentially be utilized in biomedical and pharmaceutical applications.

  17. Butea monosperma bark extract mediated green synthesis of silver nanoparticles: Characterization and biomedical applications

    Directory of Open Access Journals (Sweden)

    Sutanuka Pattanayak

    2017-09-01

    Full Text Available The work deals with an environmentally benign process for the synthesis of silver nanoparticle using Butea monosperma bark extract which is used both as a reducing as well as capping agent at room temperature. The reaction mixture turned brownish yellow after about 24 h and an intense surface plasmon resonance (SPR band at around 424 nm clearly indicates the formation of silver nanoparticles. Fourier transform-Infrared (FT-IR spectroscopy showed that the nanoparticles were capped with compounds present in the plant extract. Formation of crystalline fcc silver nanoparticles is analysed by XRD data and the SAED pattern obtained also confirms the crystalline behaviour of the Ag nanoparticles. The size and morphology of these nanoparticles were studied using High Resolution Transmission Electron Microscopy (HRTEM which showed that the nanoparticles had an average dimension of ∼35 nm. A larger DLS data of ∼98 nm shows the presence of the stabilizer on the nanoparticles surface. The bio-synthesized silver nanoparticles revealed potent antibacterial activity against human bacteria of both Gram types. In addition these biologically synthesized nanoparticles also proved to exhibit excellent cytotoxic effect on human myeloid leukemia cell line, KG-1A with IC50 value of 11.47 μg/mL.

  18. Identification of threats using linguistics-based knowledge extraction.

    Energy Technology Data Exchange (ETDEWEB)

    Chew, Peter A.

    2008-09-01

    One of the challenges increasingly facing intelligence analysts, along with professionals in many other fields, is the vast amount of data which needs to be reviewed and converted into meaningful information, and ultimately into rational, wise decisions by policy makers. The advent of the world wide web (WWW) has magnified this challenge. A key hypothesis which has guided us is that threats come from ideas (or ideology), and ideas are almost always put into writing before the threats materialize. While in the past the 'writing' might have taken the form of pamphlets or books, today's medium of choice is the WWW, precisely because it is a decentralized, flexible, and low-cost method of reaching a wide audience. However, a factor which complicates matters for the analyst is that material published on the WWW may be in any of a large number of languages. In 'Identification of Threats Using Linguistics-Based Knowledge Extraction', we have sought to use Latent Semantic Analysis (LSA) and other similar text analysis techniques to map documents from the WWW, in whatever language they were originally written, to a common language-independent vector-based representation. This then opens up a number of possibilities. First, similar documents can be found across language boundaries. Secondly, a set of documents in multiple languages can be visualized in a graphical representation. These alone offer potentially useful tools and capabilities to the intelligence analyst whose knowledge of foreign languages may be limited. Finally, we can test the over-arching hypothesis--that ideology, and more specifically ideology which represents a threat, can be detected solely from the words which express the ideology--by using the vector-based representation of documents to predict additional features (such as the ideology) within a framework based on supervised learning. In this report, we present the results of a three-year project of the same name. We believe

  19. Impact of a short biostatistics course on knowledge and performance of postgraduate scholars: Implications for training of African doctors and biomedical researchers.

    Science.gov (United States)

    Chima, S C; Nkwanyana, N M; Esterhuizen, T M

    2015-12-01

    This study was designed to evaluate the impact of a short biostatistics course on knowledge and performance of statistical analysis by biomedical researchers in Africa. It is recognized that knowledge of biostatistics is essential for understanding and interpretation of modern scientific literature and active participation in the global research enterprise. Unfortunately, it has been observed that basic education of African scholars may be deficient in applied mathematics including biostatistics. Forty university affiliated biomedical researchers from South Africa volunteered for a 4-day short-course where participants were exposed to lectures on descriptive and inferential biostatistics and practical training on using a statistical software package for data analysis. A quantitative questionnaire was used to evaluate participants' statistical knowledge and performance pre- and post-course. Changes in knowledge and performance were measured using objective and subjective criteria. Data from completed questionnaires were captured and analyzed using Statistical Package for Social Sciences. Participants' pre- and post-course data were compared using nonparametric Wilcoxon signed ranks tests for nonnormally distributed variables. A P researchers in this cohort and highlights the potential benefits of short-courses in biostatistics to improve the knowledge and skills of biomedical researchers and scholars in Africa.

  20. Earth Science Data Analytics: Preparing for Extracting Knowledge from Information

    Science.gov (United States)

    Kempler, Steven; Barbieri, Lindsay

    2016-01-01

    Data analytics is the process of examining large amounts of data of a variety of types to uncover hidden patterns, unknown correlations and other useful information. Data analytics is a broad term that includes data analysis, as well as an understanding of the cognitive processes an analyst uses to understand problems and explore data in meaningful ways. Analytics also include data extraction, transformation, and reduction, utilizing specific tools, techniques, and methods. Turning to data science, definitions of data science sound very similar to those of data analytics (which leads to a lot of the confusion between the two). But the skills needed for both, co-analyzing large amounts of heterogeneous data, understanding and utilizing relevant tools and techniques, and subject matter expertise, although similar, serve different purposes. Data Analytics takes on a practitioners approach to applying expertise and skills to solve issues and gain subject knowledge. Data Science, is more theoretical (research in itself) in nature, providing strategic actionable insights and new innovative methodologies. Earth Science Data Analytics (ESDA) is the process of examining, preparing, reducing, and analyzing large amounts of spatial (multi-dimensional), temporal, or spectral data using a variety of data types to uncover patterns, correlations and other information, to better understand our Earth. The large variety of datasets (temporal spatial differences, data types, formats, etc.) invite the need for data analytics skills that understand the science domain, and data preparation, reduction, and analysis techniques, from a practitioners point of view. The application of these skills to ESDA is the focus of this presentation. The Earth Science Information Partners (ESIP) Federation Earth Science Data Analytics (ESDA) Cluster was created in recognition of the practical need to facilitate the co-analysis of large amounts of data and information for Earth science. Thus, from a to

  1. Knowledge extraction from evolving spiking neural networks with rank order population coding.

    Science.gov (United States)

    Soltic, Snjezana; Kasabov, Nikola

    2010-12-01

    This paper demonstrates how knowledge can be extracted from evolving spiking neural networks with rank order population coding. Knowledge discovery is a very important feature of intelligent systems. Yet, a disproportionally small amount of research is centered on the issue of knowledge extraction from spiking neural networks which are considered to be the third generation of artificial neural networks. The lack of knowledge representation compatibility is becoming a major detriment to end users of these networks. We show that a high-level knowledge can be obtained from evolving spiking neural networks. More specifically, we propose a method for fuzzy rule extraction from an evolving spiking network with rank order population coding. The proposed method was used for knowledge discovery on two benchmark taste recognition problems where the knowledge learnt by an evolving spiking neural network was extracted in the form of zero-order Takagi-Sugeno fuzzy IF-THEN rules.

  2. Biomedical potentialities of Taraxacum officinale-based nanoparticles biosynthesized using methanolic leaf extract.

    Science.gov (United States)

    Rasheed, Tahir; Bilal, Muhammad; Li, Chuanlong; Iqbal, Hafiz M N

    2018-02-14

    In the present study, the potential of methanolic leaf extract of Taraxacum officinale plant as a function of bio-inspired green synthesis for the fabrication of silver nanoparticles (AgNPs) has been explored. The bio-reduction of aqueous silver nitrate (AgNO3) solution was confirmed by visually detecting the color change from pale yellow to blackish-brown. Maximum absorbance was observed at 420 nm due to the presence of characteristic surface Plasmon resonance of nano silver by UV-visible spectroscopy. The role of various functional groups in the bio-reduction of silver and chemical transformation was verified by Fourier transform infrared spectroscopy (FTIR). Scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDX) predicts the shape (rocky, flack type, ellipsoidal, etc.), size (68 nm) and elemental composition (Ag as a major constituent) of the biosynthesized AgNPs, respectively. Transmission electron microscopy (TEM) analysis further corroborated the morphology of the AgNPs. Color mapping and atomic force microscopy (AFM) confirmed the nano-sized topography. The dynamic light scattering (DLS) showed the charge, stability, and size of the AgNPs. The generated AgNPs presented potential antibacterial activities against Gram-positive and Gram-negative bacterial strains including Staphylococcus aureus, Escherichia coli, and Haemophilus influenzae. The biosynthesized AgNPs also showed antiproliferative activity against MCF-7 breast cancer cell line in a dose-dependent manner. In conclusion, results clearly indicate that biosynthesized AgNPs could be used as effective nano drug for treating infectious diseases caused by multidrug resistant bacterial strains in the near future. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

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

    African Journals Online (AJOL)

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

  4. artery disease guidelines with extracted knowledge from data mining

    Directory of Open Access Journals (Sweden)

    Peyman Rezaei-Hachesu

    2017-06-01

    Conclusion: Guidelines confirm the achieved results from data mining (DM techniques and help to rank important risk factors based on national and local information. Evaluation of extracted rules determined new patterns for CAD patients.

  5. Facile synthesis of silver nanoparticles using Euphorbia antiquorum L. latex extract and evaluation of their biomedical perspectives as anticancer agents

    Directory of Open Access Journals (Sweden)

    Chandrasekaran Rajkuberan

    2017-12-01

    Full Text Available This study reveals the rapid biosynthesis of silver nanoparticles (EAAgNPs using aqueous latex extract of Euphorbia antiquorum L as a potential bioreductant. Synthesized EAAgNPs generate the surface plasmonic resonance peak at 438 nm in UV–Vis spectrophotometer. Size and shape of EAAgNPs were further characterized through transmission electron microscope (TEM which shows well-dispersed spherical nanoparticles with size ranging from 10 to 50 nm. Energy dispersive X-ray spectroscopic analysis (EDAX confirms the presence of silver (Ag as the major constituent element. X-ray diffraction (XRD pattern of EAAgNPs corresponding to (111, (200, (220 and (311 planes, reveals that the generated nanoparticles were face centered cubic crystalline in nature. Interestingly, fourier-transform infrared spectroscopy (FTIR analysis shows the major role of active phenolic constituents in reduction and stabilization of EAAgNPs. Phyto-fabricated EAAgNPs exhibits significant antimicrobial and larvicidal activity against bacterial human pathogens as well as disease transmitting blood sucking parasites such as Culex quinquefasciatus and Aedes aegypti (IIIrd instar larvae. On the other hand, in vitro cytotoxicity assessment of bioformulated EAAgNPs has shown potential anticancer activity against human cervical carcinoma cells (HeLa. The preliminary biochemical (MTT assay and microscopic studies depict that the synthesized EAAgNPs at minimal dosage (IC50 = 28 μg triggers cellular toxicity response. Hence, the EAAgNPs can be considered as an environmentally benign and non-toxic nanobiomaterial for biomedical applications. Keywords: Crystal structure, Euphorbia antiquorum L., Silver nanoparticles, Anticancer, Human pathogens

  6. Towards an information extraction and knowledge formation framework based on Shannon entropy

    Directory of Open Access Journals (Sweden)

    Iliescu Dragoș

    2017-01-01

    Full Text Available Information quantity subject is approached in this paperwork, considering the specific domain of nonconforming product management as information source. This work represents a case study. Raw data were gathered from a heavy industrial works company, information extraction and knowledge formation being considered herein. Involved method for information quantity estimation is based on Shannon entropy formula. Information and entropy spectrum are decomposed and analysed for extraction of specific information and knowledge-that formation. The result of the entropy analysis point out the information needed to be acquired by the involved organisation, this being presented as a specific knowledge type.

  7. A STUDY OF THE IMPACT OF THREE DAY TRAINING PROGRAMME ON KNOWLEDGE REGARDING BIOMEDICAL WASTE AMONG PARAMEDICAL STAFF OF DISTRICT HOSPITAL ETAWAH (UP)

    OpenAIRE

    Dhiraj Kumar Srivastava; Manoj ansal; Neeraj Gour; Pooja Chaduary; Pankaj Kumar Jain; Mahendra Chouksey; Pawan pathak

    2013-01-01

    Introduction: Biomedical waste by definition means “Any waste which is generated during the process of diagnosis, treatment or immunization of human or animal or in research activities pertaining there to in the production or testing of biological”Objectives:•    The level of awareness about various aspect of Bio Medical Waste management among the paramedical staff.•    To study the impact of three day training programme on knowledge of Bio Medical Waste management. Material & Methods: The pr...

  8. A STUDY OF THE IMPACT OF THREE DAY TRAINING PROGRAMME ON KNOWLEDGE REGARDING BIOMEDICAL WASTE AMONG PARAMEDICAL STAFF OF DISTRICT HOSPITAL ETAWAH (UP)

    OpenAIRE

    Dhiraj Kumar Srivastava; Manoj ansal; Neeraj Gour; Pooja Chaduary; Pankaj Kumar Jain; Mahendra Chouksey; Pawan pathak

    2013-01-01

    Introduction: Biomedical waste by definition means “Any waste which is generated during the process of diagnosis, treatment or immunization of human or animal or in research activities pertaining there to in the production or testing of biological”Objectives:•    The level of awareness about various aspect of Bio Medical Waste management among the paramedical staff.•    To study the impact of three day training programme on knowledge of Bio Medical Waste management. Material & Methods: Th...

  9. Citizen Science for Mining the Biomedical Literature

    Directory of Open Access Journals (Sweden)

    Ginger Tsueng

    2016-12-01

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

  10. A study on knowledge and practice regarding biomedical waste management among staff nurses and nursing students of Rajendra Institute of Medical Sciences, Ranchi

    Directory of Open Access Journals (Sweden)

    Shamim Haider

    2015-03-01

    Full Text Available Background: Hospitals are the centre of cure and also the important centres of infectious waste generation. Effective management of Biomedical Waste (BMW is not only a legal necessity but also a social responsibility. Aims and Objectives: To assess the knowledge and practice in managing the biomedical wastes among nursing staff and student nurses in RIMS, Ranchi. Materials and methods: The study was conducted at RIMS, Ranchi from Oct 2013 to March 2014 (6 months. It was a descriptive, hospital based, cross-sectional study. A total of 240 nurses participated in the present study, randomly chosen from various departments A pre-designed, pre-tested, structured proforma was used for data collection after getting their informed consent. Self-made scoring system was used to categorize the participants as having good, average and poor scores. Data was tabulated and analyzed using percentages and chi-square test. Results: The knowledge regarding general information about BMW management was assessed(with scores 0-8,it was found  that level of knowledge was better in student nurses than staff nurses as student nurses scored good(6-8correct answers in more than half of the questions (65%.Whereas staff nurses scored good in only 33.33% questions. When the practical information regarding the BMW management is assessed (with scores 0-8, it was found that staff nurses had relatively better practice regarding BMW management than students as they scored good(6-8correct answers in 40% and 30% respectively. Conclusion: Though overall knowledge of study participants was good but still they need good quality training to improve their current knowledge about BMW. 

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

    Science.gov (United States)

    Renganathan, Vinaitheerthan

    2017-07-01

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

  12. Using decision-tree classifier systems to extract knowledge from databases

    Science.gov (United States)

    St.clair, D. C.; Sabharwal, C. L.; Hacke, Keith; Bond, W. E.

    1990-01-01

    One difficulty in applying artificial intelligence techniques to the solution of real world problems is that the development and maintenance of many AI systems, such as those used in diagnostics, require large amounts of human resources. At the same time, databases frequently exist which contain information about the process(es) of interest. Recently, efforts to reduce development and maintenance costs of AI systems have focused on using machine learning techniques to extract knowledge from existing databases. Research is described in the area of knowledge extraction using a class of machine learning techniques called decision-tree classifier systems. Results of this research suggest ways of performing knowledge extraction which may be applied in numerous situations. In addition, a measurement called the concept strength metric (CSM) is described which can be used to determine how well the resulting decision tree can differentiate between the concepts it has learned. The CSM can be used to determine whether or not additional knowledge needs to be extracted from the database. An experiment involving real world data is presented to illustrate the concepts described.

  13. [Biomedical informatics].

    Science.gov (United States)

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

    2011-12-01

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

  14. Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task.

    Science.gov (United States)

    Wei, Chih-Hsuan; Peng, Yifan; Leaman, Robert; Davis, Allan Peter; Mattingly, Carolyn J; Li, Jiao; Wiegers, Thomas C; Lu, Zhiyong

    2016-01-01

    Manually curating chemicals, diseases and their relationships is significantly important to biomedical research, but it is plagued by its high cost and the rapid growth of the biomedical literature. In recent years, there has been a growing interest in developing computational approaches for automatic chemical-disease relation (CDR) extraction. Despite these attempts, the lack of a comprehensive benchmarking dataset has limited the comparison of different techniques in order to assess and advance the current state-of-the-art. To this end, we organized a challenge task through BioCreative V to automatically extract CDRs from the literature. We designed two challenge tasks: disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. To assist system development and assessment, we created a large annotated text corpus that consisted of human annotations of chemicals, diseases and their interactions from 1500 PubMed articles. 34 teams worldwide participated in the CDR task: 16 (DNER) and 18 (CID). The best systems achieved an F-score of 86.46% for the DNER task--a result that approaches the human inter-annotator agreement (0.8875)--and an F-score of 57.03% for the CID task, the highest results ever reported for such tasks. When combining team results via machine learning, the ensemble system was able to further improve over the best team results by achieving 88.89% and 62.80% in F-score for the DNER and CID task, respectively. Additionally, another novel aspect of our evaluation is to test each participating system's ability to return real-time results: the average response time for each team's DNER and CID web service systems were 5.6 and 9.3 s, respectively. Most teams used hybrid systems for their submissions based on machining learning. Given the level of participation and results, we found our task to be successful in engaging the text-mining research community, producing a large annotated corpus and improving the results of

  15. Knowledge, Attitude And Practices of Healthcare Workers (HCWs Regarding Biomedical Waste (BMW Management: A Multispeciality Hospital Based CrossSectional Study In Eastern India

    Directory of Open Access Journals (Sweden)

    Ravishekar N. Hiremath

    2016-10-01

    Full Text Available Background: The evolving health care system of India, in its goal of solving health issues and minimizing possible health risks, has unavoidably created waste, which itself may be harmful for health. Inefficient and inadequate knowledge of managing health care waste may have detrimental effects on health and environment. Aim and Objectives: To asses level of Knowledge, Attitude, Practices (KAP about Biomedical Waste (BMW management among Health Care Workers (HCWs with an endeavor to improve the standards and protect the health of HCWs and the environment. Methodology: A Hospital- based cross sectional descriptive study was carried out at one of the Multispecialty Hospital in Eastern India. A total of 80 HCWs who were available at the time of study were included and the data were collected by means of 'personal interview technique' by using a pre-designed semi-structured questionnaire in Hindi (local language. The relevant data was collected, compiled and analyzed using SPSS 17.0 version. Results: Assessment of KAP with pre-decided scoring system showed, 17.5 % had excellent knowledge, 70% with good to average and 12.5% had poor knowledge with respect to BMW management. Knowledge status was not significantly associated with any of the sociodemographic characteristics. When asked about needle stick injuries, 88% felt that needle stick injury was a concern to them and 86% of them were well aware about the consequences of needle-stick injuries. Conclusion: Although the awareness level was high with various aspects of BMW management among HCWs compared to other studies, but still there exists scope for more improvement. Regular awareness capsule with proper BMW committee monitoring is the need of the hour. All measures to sensitize the HCWs against needle stick injuries including both pre and post incident measures need to be taken.

  16. A method for extracting design rationale knowledge based on Text Mining

    Directory of Open Access Journals (Sweden)

    Liu Jihong

    2017-01-01

    Full Text Available Capture design rationale (DR knowledge and presenting it to designers by good form, which have great significance for design reuse and design innovation. Since the 1970s design rationality began to develop, many teams have developed their own design rational system. However, the DR acquisition system is not intelligent enough, and it still requires designers to do a lot of operations. In addition, the existing design documents contain a large number of DR knowledge, but it has not been well excavated. Therefore, a method and system are needed to better extract DR knowledge in design documents. We have proposed a DRKH (design rationale knowledge hierarchy model for DR representation. The DRKH model has three layers, respectively as design intent layer, design decision layer and design basis layer. In this paper, we use text mining method to extract DR from design documents and construct DR model. Finally, the welding robot design specification is taken as an example to demonstrate the system interface.

  17. Towards A Model Of Knowledge Extraction Of Text Mining For Palliative Care Patients In Panama.

    Directory of Open Access Journals (Sweden)

    Denis Cedeno Moreno

    2015-08-01

    Full Text Available Solutions using information technology is an innovative way to manage the information hospice patients in hospitals in Panama. The application of techniques of text mining for the domain of medicine especially information from electronic health records of patients in palliative care is one of the most recent and promising research areas for the analysis of textual data. Text mining is based on new knowledge extraction from unstructured natural language data. We may also create ontologies to describe the terminology and knowledge in a given domain. In an ontology conceptualization of a domain that may be general or specific formalized. Knowledge can be used for decision making by health specialists or can help in research topics for improving the health system.

  18. Careers in biomedical engineering.

    Science.gov (United States)

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

    2010-01-01

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

  19. The unknown-unknowns: Revealing the hidden insights in massive biomedical data using combined artificial intelligence and knowledge networks

    Directory of Open Access Journals (Sweden)

    Chris Yoo

    2017-12-01

    Full Text Available Genomic data is estimated to be doubling every seven months with over 2 trillion bases from whole genome sequence studies deposited in Genbank in just the last 15 years alone. Recent advances in compute and storage have enabled the use of artificial intelligence techniques in areas such as feature recognition in digital pathology and chemical synthesis for drug development. To apply A.I. productively to multidimensional data such as cellular processes and their dysregulation, the data must be transformed into a structured format, using prior knowledge to create contextual relationships and hierarchies upon which computational analysis can be performed. Here we present the organization of complex data into hypergraphs that facilitate the application of A.I. We provide an example use case of a hypergraph containing hundreds of biological data values and the results of several classes of A.I. algorithms applied in a popular compute cloud. While multiple, biologically insightful correlations between disease states, behavior, and molecular features were identified, the insights of scientific import were revealed only when exploration of the data included visualization of subgraphs of represented knowledge. The results suggest that while machine learning can identify known correlations and suggest testable ones, the greater probability of discovering unexpected relationships between seemingly independent variables (unknown-unknowns requires a context-aware system – hypergraphs that impart biological meaning in nodes and edges. We discuss the implications of a combined hypergraph-A.I. analysis approach to multidimensional data and the pre-processing requirements for such a system.

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

    Science.gov (United States)

    Tractenberg, Rochelle E; Gordon, Morris

    2017-01-01

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

  1. Biomedical photonics handbook biomedical diagnostics

    CERN Document Server

    Vo-Dinh, Tuan

    2014-01-01

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

  2. Biomedical ontologies: toward scientific debate.

    Science.gov (United States)

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

    2011-01-01

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

  3. Biomedical nanotechnology.

    Science.gov (United States)

    Hurst, Sarah J

    2011-01-01

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

  4. Analyzing rare diseases terms in biomedical terminologies

    Directory of Open Access Journals (Sweden)

    Erika Pasceri

    2012-03-01

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

  5. Biomedical Engineering

    CERN Document Server

    Suh, Sang C; Tanik, Murat M

    2011-01-01

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

  6. Advanced Methods of Biomedical Signal Processing

    CERN Document Server

    Cerutti, Sergio

    2011-01-01

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

  7. A novel biomedical image indexing and retrieval system via deep preference learning.

    Science.gov (United States)

    Pang, Shuchao; Orgun, Mehmet A; Yu, Zhezhou

    2018-05-01

    The traditional biomedical image retrieval methods as well as content-based image retrieval (CBIR) methods originally designed for non-biomedical images either only consider using pixel and low-level features to describe an image or use deep features to describe images but still leave a lot of room for improving both accuracy and efficiency. In this work, we propose a new approach, which exploits deep learning technology to extract the high-level and compact features from biomedical images. The deep feature extraction process leverages multiple hidden layers to capture substantial feature structures of high-resolution images and represent them at different levels of abstraction, leading to an improved performance for indexing and retrieval of biomedical images. We exploit the current popular and multi-layered deep neural networks, namely, stacked denoising autoencoders (SDAE) and convolutional neural networks (CNN) to represent the discriminative features of biomedical images by transferring the feature representations and parameters of pre-trained deep neural networks from another domain. Moreover, in order to index all the images for finding the similarly referenced images, we also introduce preference learning technology to train and learn a kind of a preference model for the query image, which can output the similarity ranking list of images from a biomedical image database. To the best of our knowledge, this paper introduces preference learning technology for the first time into biomedical image retrieval. We evaluate the performance of two powerful algorithms based on our proposed system and compare them with those of popular biomedical image indexing approaches and existing regular image retrieval methods with detailed experiments over several well-known public biomedical image databases. Based on different criteria for the evaluation of retrieval performance, experimental results demonstrate that our proposed algorithms outperform the state

  8. Using Best Practices to Extract, Organize, and Reuse Embedded Decision Support Content Knowledge Rules from Mature Clinical Systems.

    Science.gov (United States)

    DesAutels, Spencer J; Fox, Zachary E; Giuse, Dario A; Williams, Annette M; Kou, Qing-Hua; Weitkamp, Asli; Neal R, Patel; Bettinsoli Giuse, Nunzia

    2016-01-01

    Clinical decision support (CDS) knowledge, embedded over time in mature medical systems, presents an interesting and complex opportunity for information organization, maintenance, and reuse. To have a holistic view of all decision support requires an in-depth understanding of each clinical system as well as expert knowledge of the latest evidence. This approach to clinical decision support presents an opportunity to unify and externalize the knowledge within rules-based decision support. Driven by an institutional need to prioritize decision support content for migration to new clinical systems, the Center for Knowledge Management and Health Information Technology teams applied their unique expertise to extract content from individual systems, organize it through a single extensible schema, and present it for discovery and reuse through a newly created Clinical Support Knowledge Acquisition and Archival Tool (CS-KAAT). CS-KAAT can build and maintain the underlying knowledge infrastructure needed by clinical systems.

  9. Using Best Practices to Extract, Organize, and Reuse Embedded Decision Support Content Knowledge Rules from Mature Clinical Systems

    Science.gov (United States)

    DesAutels, Spencer J.; Fox, Zachary E.; Giuse, Dario A.; Williams, Annette M.; Kou, Qing-hua; Weitkamp, Asli; Neal R, Patel; Bettinsoli Giuse, Nunzia

    2016-01-01

    Clinical decision support (CDS) knowledge, embedded over time in mature medical systems, presents an interesting and complex opportunity for information organization, maintenance, and reuse. To have a holistic view of all decision support requires an in-depth understanding of each clinical system as well as expert knowledge of the latest evidence. This approach to clinical decision support presents an opportunity to unify and externalize the knowledge within rules-based decision support. Driven by an institutional need to prioritize decision support content for migration to new clinical systems, the Center for Knowledge Management and Health Information Technology teams applied their unique expertise to extract content from individual systems, organize it through a single extensible schema, and present it for discovery and reuse through a newly created Clinical Support Knowledge Acquisition and Archival Tool (CS-KAAT). CS-KAAT can build and maintain the underlying knowledge infrastructure needed by clinical systems. PMID:28269846

  10. Fuzzy Linguistic Knowledge Based Behavior Extraction for Building Energy Management Systems

    Energy Technology Data Exchange (ETDEWEB)

    Dumidu Wijayasekara; Milos Manic

    2013-08-01

    Significant portion of world energy production is consumed by building Heating, Ventilation and Air Conditioning (HVAC) units. Thus along with occupant comfort, energy efficiency is also an important factor in HVAC control. Modern buildings use advanced Multiple Input Multiple Output (MIMO) control schemes to realize these goals. However, since the performance of HVAC units is dependent on many criteria including uncertainties in weather, number of occupants, and thermal state, the performance of current state of the art systems are sub-optimal. Furthermore, because of the large number of sensors in buildings, and the high frequency of data collection, large amount of information is available. Therefore, important behavior of buildings that compromise energy efficiency or occupant comfort is difficult to identify. This paper presents an easy to use and understandable framework for identifying such behavior. The presented framework uses human understandable knowledge-base to extract important behavior of buildings and present it to users via a graphical user interface. The presented framework was tested on a building in the Pacific Northwest and was shown to be able to identify important behavior that relates to energy efficiency and occupant comfort.

  11. Causal knowledge extraction by natural language processing in material science: a case study in chemical vapor deposition

    Directory of Open Access Journals (Sweden)

    Yuya Kajikawa

    2006-11-01

    Full Text Available Scientific publications written in natural language still play a central role as our knowledge source. However, due to the flood of publications, the literature survey process has become a highly time-consuming and tangled process, especially for novices of the discipline. Therefore, tools supporting the literature-survey process may help the individual scientist to explore new useful domains. Natural language processing (NLP is expected as one of the promising techniques to retrieve, abstract, and extract knowledge. In this contribution, NLP is firstly applied to the literature of chemical vapor deposition (CVD, which is a sub-discipline of materials science and is a complex and interdisciplinary field of research involving chemists, physicists, engineers, and materials scientists. Causal knowledge extraction from the literature is demonstrated using NLP.

  12. Character-level neural network for biomedical named entity recognition.

    Science.gov (United States)

    Gridach, Mourad

    2017-06-01

    Biomedical named entity recognition (BNER), which extracts important named entities such as genes and proteins, is a challenging task in automated systems that mine knowledge in biomedical texts. The previous state-of-the-art systems required large amounts of task-specific knowledge in the form of feature engineering, lexicons and data pre-processing to achieve high performance. In this paper, we introduce a novel neural network architecture that benefits from both word- and character-level representations automatically, by using a combination of bidirectional long short-term memory (LSTM) and conditional random field (CRF) eliminating the need for most feature engineering tasks. We evaluate our system on two datasets: JNLPBA corpus and the BioCreAtIvE II Gene Mention (GM) corpus. We obtained state-of-the-art performance by outperforming the previous systems. To the best of our knowledge, we are the first to investigate the combination of deep neural networks, CRF, word embeddings and character-level representation in recognizing biomedical named entities. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Pathophysiologic mechanisms of biomedical nanomaterials

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-05-15

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

  14. Pathophysiologic mechanisms of biomedical nanomaterials

    International Nuclear Information System (INIS)

    Wang, Liming; Chen, Chunying

    2016-01-01

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

  15. Main Road Extraction from ZY-3 Grayscale Imagery Based on Directional Mathematical Morphology and VGI Prior Knowledge in Urban Areas

    Science.gov (United States)

    Liu, Bo; Wu, Huayi; Wang, Yandong; Liu, Wenming

    2015-01-01

    Main road features extracted from remotely sensed imagery play an important role in many civilian and military applications, such as updating Geographic Information System (GIS) databases, urban structure analysis, spatial data matching and road navigation. Current methods for road feature extraction from high-resolution imagery are typically based on threshold value segmentation. It is difficult however, to completely separate road features from the background. We present a new method for extracting main roads from high-resolution grayscale imagery based on directional mathematical morphology and prior knowledge obtained from the Volunteered Geographic Information found in the OpenStreetMap. The two salient steps in this strategy are: (1) using directional mathematical morphology to enhance the contrast between roads and non-roads; (2) using OpenStreetMap roads as prior knowledge to segment the remotely sensed imagery. Experiments were conducted on two ZiYuan-3 images and one QuickBird high-resolution grayscale image to compare our proposed method to other commonly used techniques for road feature extraction. The results demonstrated the validity and better performance of the proposed method for urban main road feature extraction. PMID:26397832

  16. Main Road Extraction from ZY-3 Grayscale Imagery Based on Directional Mathematical Morphology and VGI Prior Knowledge in Urban Areas.

    Science.gov (United States)

    Liu, Bo; Wu, Huayi; Wang, Yandong; Liu, Wenming

    2015-01-01

    Main road features extracted from remotely sensed imagery play an important role in many civilian and military applications, such as updating Geographic Information System (GIS) databases, urban structure analysis, spatial data matching and road navigation. Current methods for road feature extraction from high-resolution imagery are typically based on threshold value segmentation. It is difficult however, to completely separate road features from the background. We present a new method for extracting main roads from high-resolution grayscale imagery based on directional mathematical morphology and prior knowledge obtained from the Volunteered Geographic Information found in the OpenStreetMap. The two salient steps in this strategy are: (1) using directional mathematical morphology to enhance the contrast between roads and non-roads; (2) using OpenStreetMap roads as prior knowledge to segment the remotely sensed imagery. Experiments were conducted on two ZiYuan-3 images and one QuickBird high-resolution grayscale image to compare our proposed method to other commonly used techniques for road feature extraction. The results demonstrated the validity and better performance of the proposed method for urban main road feature extraction.

  17. Main Road Extraction from ZY-3 Grayscale Imagery Based on Directional Mathematical Morphology and VGI Prior Knowledge in Urban Areas.

    Directory of Open Access Journals (Sweden)

    Bo Liu

    Full Text Available Main road features extracted from remotely sensed imagery play an important role in many civilian and military applications, such as updating Geographic Information System (GIS databases, urban structure analysis, spatial data matching and road navigation. Current methods for road feature extraction from high-resolution imagery are typically based on threshold value segmentation. It is difficult however, to completely separate road features from the background. We present a new method for extracting main roads from high-resolution grayscale imagery based on directional mathematical morphology and prior knowledge obtained from the Volunteered Geographic Information found in the OpenStreetMap. The two salient steps in this strategy are: (1 using directional mathematical morphology to enhance the contrast between roads and non-roads; (2 using OpenStreetMap roads as prior knowledge to segment the remotely sensed imagery. Experiments were conducted on two ZiYuan-3 images and one QuickBird high-resolution grayscale image to compare our proposed method to other commonly used techniques for road feature extraction. The results demonstrated the validity and better performance of the proposed method for urban main road feature extraction.

  18. The ethics of biomedical big data

    CERN Document Server

    Mittelstadt, Brent Daniel

    2016-01-01

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

  19. A Method of Extracting Ontology Module Using Concept Relations for Sharing Knowledge in Mobile Cloud Computing Environment

    Directory of Open Access Journals (Sweden)

    Keonsoo Lee

    2014-01-01

    Full Text Available In mobile cloud computing environment, the cooperation of distributed computing objects is one of the most important requirements for providing successful cloud services. To satisfy this requirement, all the members, who are employed in the cooperation group, need to share the knowledge for mutual understanding. Even if ontology can be the right tool for this goal, there are several issues to make a right ontology. As the cost and complexity of managing knowledge increase according to the scale of the knowledge, reducing the size of ontology is one of the critical issues. In this paper, we propose a method of extracting ontology module to increase the utility of knowledge. For the given signature, this method extracts the ontology module, which is semantically self-contained to fulfill the needs of the service, by considering the syntactic structure and semantic relation of concepts. By employing this module, instead of the original ontology, the cooperation of computing objects can be performed with less computing load and complexity. In particular, when multiple external ontologies need to be combined for more complex services, this method can be used to optimize the size of shared knowledge.

  20. A method of extracting ontology module using concept relations for sharing knowledge in mobile cloud computing environment.

    Science.gov (United States)

    Lee, Keonsoo; Rho, Seungmin; Lee, Seok-Won

    2014-01-01

    In mobile cloud computing environment, the cooperation of distributed computing objects is one of the most important requirements for providing successful cloud services. To satisfy this requirement, all the members, who are employed in the cooperation group, need to share the knowledge for mutual understanding. Even if ontology can be the right tool for this goal, there are several issues to make a right ontology. As the cost and complexity of managing knowledge increase according to the scale of the knowledge, reducing the size of ontology is one of the critical issues. In this paper, we propose a method of extracting ontology module to increase the utility of knowledge. For the given signature, this method extracts the ontology module, which is semantically self-contained to fulfill the needs of the service, by considering the syntactic structure and semantic relation of concepts. By employing this module, instead of the original ontology, the cooperation of computing objects can be performed with less computing load and complexity. In particular, when multiple external ontologies need to be combined for more complex services, this method can be used to optimize the size of shared knowledge.

  1. A semantic-based method for extracting concept definitions from scientific publications: evaluation in the autism phenotype domain

    OpenAIRE

    Hassanpour, Saeed; O?Connor, Martin J; Das, Amar K

    2013-01-01

    Background A variety of informatics approaches have been developed that use information retrieval, NLP and text-mining techniques to identify biomedical concepts and relations within scientific publications or their sentences. These approaches have not typically addressed the challenge of extracting more complex knowledge such as biomedical definitions. In our efforts to facilitate knowledge acquisition of rule-based definitions of autism phenotypes, we have developed a novel semantic-based t...

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

    NARCIS (Netherlands)

    Trieschnigg, Rudolf Berend

    2010-01-01

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

  3. Function and Phenotype prediction through Data and Knowledge Fusion

    KAUST Repository

    Vespoor, Karen

    2016-01-27

    The biomedical literature captures the most current biomedical knowledge and is a tremendously rich resource for research. With over 24 million publications currently indexed in the US National Library of Medicine’s PubMed index, however, it is becoming increasingly challenging for biomedical researchers to keep up with this literature. Automated strategies for extracting information from it are required. Large-scale processing of the literature enables direct biomedical knowledge discovery. In this presentation, I will introduce the use of text mining techniques to support analysis of biological data sets, and will specifically discuss applications in protein function and phenotype prediction, as well as analysis of genetic variants that are supported by analysis of the literature and integration with complementary structured resources.

  4. Biomedical engineering and nanotechnology

    International Nuclear Information System (INIS)

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

    2009-01-01

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

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

    Science.gov (United States)

    Warren, Amy L; Donnon, Tyrone

    2013-01-01

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

  6. Customization of biomedical terminologies.

    Science.gov (United States)

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

    2012-01-01

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

  7. Knowledges

    DEFF Research Database (Denmark)

    Berling, Trine Villumsen

    2012-01-01

    Scientific knowledge in international relations has generally focused on an epistemological distinction between rationalism and reflectivism over the last 25 years. This chapter argues that this distinction has created a double distinction between theory/reality and theory/practice, which works...... and reflectivism. Bourdieu, on the contrary, lets the challenge to the theory/reality distinction spill over into a challenge to the theory/practice distinction by thrusting the scientist in the foreground as not just a factor (discourse/genre) but as an actor. In this way, studies of IR need to include a focus...... as a ghost distinction structuring IR research. While reflectivist studies have emphasised the impossibility of detached, objective knowledge production through a dissolution of the theory/reality distinction, the theory/practice distinction has been left largely untouched by both rationalism...

  8. Analysis Methods for Extracting Knowledge from Large-Scale WiFi Monitoring to Inform Building Facility Planning

    DEFF Research Database (Denmark)

    Ruiz-Ruiz, Antonio; Blunck, Henrik; Prentow, Thor Siiger

    2014-01-01

    realistic data to inform facility planning. In this paper, we propose analysis methods to extract knowledge from large sets of network collected WiFi traces to better inform facility management and planning in large building complexes. The analysis methods, which build on a rich set of temporal and spatial......The optimization of logistics in large building com- plexes with many resources, such as hospitals, require realistic facility management and planning. Current planning practices rely foremost on manual observations or coarse unverified as- sumptions and therefore do not properly scale or provide....... Spatio-temporal visualization tools built on top of these methods enable planners to inspect and explore extracted information to inform facility-planning activities. To evaluate the methods, we present results for a large hospital complex covering more than 10 hectares. The evaluation is based on Wi...

  9. EXTRACT

    DEFF Research Database (Denmark)

    Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra

    2016-01-01

    The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have the...... and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed.Database URL: https://extract.hcmr.gr/......., organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual...

  10. Using Web-Based Knowledge Extraction Techniques to Support Cultural Modeling

    Science.gov (United States)

    Smart, Paul R.; Sieck, Winston R.; Shadbolt, Nigel R.

    The World Wide Web is a potentially valuable source of information about the cognitive characteristics of cultural groups. However, attempts to use the Web in the context of cultural modeling activities are hampered by the large-scale nature of the Web and the current dominance of natural language formats. In this paper, we outline an approach to support the exploitation of the Web for cultural modeling activities. The approach begins with the development of qualitative cultural models (which describe the beliefs, concepts and values of cultural groups), and these models are subsequently used to develop an ontology-based information extraction capability. Our approach represents an attempt to combine conventional approaches to information extraction with epidemiological perspectives of culture and network-based approaches to cultural analysis. The approach can be used, we suggest, to support the development of models providing a better understanding of the cognitive characteristics of particular cultural groups.

  11. Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing.

    Science.gov (United States)

    González, Roberto; Zato, Carolina; Benito, Rocío; Bajo, Javier; Hernández, Jesús M; De Paz, Juan F; Vera, Vicente; Corchado, Juan M

    2012-12-01

    Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.

  12. Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing

    Directory of Open Access Journals (Sweden)

    González Roberto

    2012-12-01

    Full Text Available Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.

  13. Extracting Product Features and Opinion Words Using Pattern Knowledge in Customer Reviews

    Directory of Open Access Journals (Sweden)

    Su Su Htay

    2013-01-01

    Full Text Available Due to the development of e-commerce and web technology, most of online Merchant sites are able to write comments about purchasing products for customer. Customer reviews expressed opinion about products or services which are collectively referred to as customer feedback data. Opinion extraction about products from customer reviews is becoming an interesting area of research and it is motivated to develop an automatic opinion mining application for users. Therefore, efficient method and techniques are needed to extract opinions from reviews. In this paper, we proposed a novel idea to find opinion words or phrases for each feature from customer reviews in an efficient way. Our focus in this paper is to get the patterns of opinion words/phrases about the feature of product from the review text through adjective, adverb, verb, and noun. The extracted features and opinions are useful for generating a meaningful summary that can provide significant informative resource to help the user as well as merchants to track the most suitable choice of product.

  14. Extracting product features and opinion words using pattern knowledge in customer reviews.

    Science.gov (United States)

    Htay, Su Su; Lynn, Khin Thidar

    2013-01-01

    Due to the development of e-commerce and web technology, most of online Merchant sites are able to write comments about purchasing products for customer. Customer reviews expressed opinion about products or services which are collectively referred to as customer feedback data. Opinion extraction about products from customer reviews is becoming an interesting area of research and it is motivated to develop an automatic opinion mining application for users. Therefore, efficient method and techniques are needed to extract opinions from reviews. In this paper, we proposed a novel idea to find opinion words or phrases for each feature from customer reviews in an efficient way. Our focus in this paper is to get the patterns of opinion words/phrases about the feature of product from the review text through adjective, adverb, verb, and noun. The extracted features and opinions are useful for generating a meaningful summary that can provide significant informative resource to help the user as well as merchants to track the most suitable choice of product.

  15. Extracting Product Features and Opinion Words Using Pattern Knowledge in Customer Reviews

    Science.gov (United States)

    Lynn, Khin Thidar

    2013-01-01

    Due to the development of e-commerce and web technology, most of online Merchant sites are able to write comments about purchasing products for customer. Customer reviews expressed opinion about products or services which are collectively referred to as customer feedback data. Opinion extraction about products from customer reviews is becoming an interesting area of research and it is motivated to develop an automatic opinion mining application for users. Therefore, efficient method and techniques are needed to extract opinions from reviews. In this paper, we proposed a novel idea to find opinion words or phrases for each feature from customer reviews in an efficient way. Our focus in this paper is to get the patterns of opinion words/phrases about the feature of product from the review text through adjective, adverb, verb, and noun. The extracted features and opinions are useful for generating a meaningful summary that can provide significant informative resource to help the user as well as merchants to track the most suitable choice of product. PMID:24459430

  16. Biomedical engineering fundamentals

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

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

  17. Textural Properties of Hybrid Biomedical Materials Made from Extracts of Tournefortia hirsutissima L. Imbibed and Deposited on Mesoporous and Microporous Materials

    Directory of Open Access Journals (Sweden)

    Miguel Ángel Hernández

    2016-01-01

    Full Text Available Our research group has developed a group of hybrid biomedical materials potentially useful in the healing of diabetic foot ulcerations. The organic part of this type of hybrid materials consists of nanometric deposits, proceeding from the Mexican medicinal plant Tournefortia hirsutissima L., while the inorganic part is composed of a zeolite mixture that includes LTA, ZSM-5, clinoptilolite, and montmorillonite (PZX as well as a composite material, made of CaCO3 and montmorillonite (NABE. The organic part has been analyzed by GC-MS to detect the most abundant components present therein. In turn, the inorganic supports were characterized by XRD, SEM, and High Resolution Adsorption (HRADS of N2 at 76 K. Through this latter methodology, the external surface area of the hybrid materials was evaluated; besides, the most representative textural properties of each substrate such as total pore volume, pore size distribution, and, in some cases, the volume of micropores were calculated. The formation and stabilization of nanodeposits on the inorganic segments of the hybrid supports led to a partial blockage of the microporosity of the LTA and ZSM5 zeolites; this same effect occurred with the NABE and PZX substrates.

  18. Automated Extraction of Cranial Landmarks from Computed Tomography Data using a Combined Method of Knowledge and Pattern Based Approaches

    Directory of Open Access Journals (Sweden)

    Roshan N. RAJAPAKSE

    2016-03-01

    Full Text Available Accurate identification of anatomical structures from medical imaging data is a significant and critical function in the medical domain. Past studies in this context have mainly utilized two main approaches, the knowledge and learning methodologies based methods. Further, most of previous reported studies have focused on identification of landmarks from lateral X-ray Computed Tomography (CT data, particularly in the field of orthodontics. However, this study focused on extracting cranial landmarks from large sets of cross sectional CT slices using a combined method of the two aforementioned approaches. The proposed method of this study is centered mainly on template data sets, which were created using the actual contour patterns extracted from CT cases for each of the landmarks in consideration. Firstly, these templates were used to devise rules which are a characteristic of the knowledge based method. Secondly, the same template sets were employed to perform template matching related to the learning methodologies approach. The proposed method was tested on two landmarks, the Dorsum sellae and the Pterygoid plate, using CT cases of 5 subjects. The results indicate that, out of the 10 tests, the output images were within the expected range (desired accuracy in 7 instances and acceptable range (near accuracy for 2 instances, thus verifying the effectiveness of the combined template sets centric approach proposed in this study.

  19. Sustainable rehabilitation of mining waste and acid mine drainage using geochemistry, mine type, mineralogy, texture, ore extraction and climate knowledge.

    Science.gov (United States)

    Anawar, Hossain Md

    2015-08-01

    The oxidative dissolution of sulfidic minerals releases the extremely acidic leachate, sulfate and potentially toxic elements e.g., As, Ag, Cd, Cr, Cu, Hg, Ni, Pb, Sb, Th, U, Zn, etc. from different mine tailings and waste dumps. For the sustainable rehabilitation and disposal of mining waste, the sources and mechanisms of contaminant generation, fate and transport of contaminants should be clearly understood. Therefore, this study has provided a critical review on (1) recent insights in mechanisms of oxidation of sulfidic minerals, (2) environmental contamination by mining waste, and (3) remediation and rehabilitation techniques, and (4) then developed the GEMTEC conceptual model/guide [(bio)-geochemistry-mine type-mineralogy- geological texture-ore extraction process-climatic knowledge)] to provide the new scientific approach and knowledge for remediation of mining wastes and acid mine drainage. This study has suggested the pre-mining geological, geochemical, mineralogical and microtextural characterization of different mineral deposits, and post-mining studies of ore extraction processes, physical, geochemical, mineralogical and microbial reactions, natural attenuation and effect of climate change for sustainable rehabilitation of mining waste. All components of this model should be considered for effective and integrated management of mining waste and acid mine drainage. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. A Generic Framework for Extraction of Knowledge from Social Web Sources (Social Networking Websites for an Online Recommendation System

    Directory of Open Access Journals (Sweden)

    Javubar Sathick

    2015-04-01

    Full Text Available Mining social web data is a challenging task and finding user interest for personalized and non-personalized recommendation systems is another important task. Knowledge sharing among web users has become crucial in determining usage of web data and personalizing content in various social websites as per the user’s wish. This paper aims to design a framework for extracting knowledge from web sources for the end users to take a right decision at a crucial juncture. The web data is collected from various web sources and structured appropriately and stored as an ontology based data repository. The proposed framework implements an online recommender application for the learners online who pursue their graduation in an open and distance learning environment. This framework possesses three phases: data repository, knowledge engine, and online recommendation system. The data repository possesses common data which is attained by the process of acquiring data from various web sources. The knowledge engine collects the semantic data from the ontology based data repository and maps it to the user through the query processor component. Establishment of an online recommendation system is used to make recommendations to the user for a decision making process. This research work is implemented with the help of an experimental case study which deals with an online recommendation system for the career guidance of a learner. The online recommendation application is implemented with the help of R-tool, NLP parser and clustering algorithm.This research study will help users to attain semantic knowledge from heterogeneous web sources and to make decisions.

  1. Introduction to biomedical engineering

    CERN Document Server

    Enderle, John D; Blanchard, Susan M

    2005-01-01

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

  2. The Ontology for Biomedical Investigations.

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2013-01-16

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

  4. Green synthesis of NiO nanoparticles using Moringa oleifera extract and their biomedical applications: Cytotoxicity effect of nanoparticles against HT-29 cancer cells.

    Science.gov (United States)

    Ezhilarasi, A Angel; Vijaya, J Judith; Kaviyarasu, K; Maaza, M; Ayeshamariam, A; Kennedy, L John

    2016-11-01

    Green protocols for the synthesis of nickel oxide nanoparticles using Moringa oleifera plant extract has been reported in the present study as they are cost effective and ecofriendly, moreover this paper records that the nickel oxide (NiO) nanoparticles prepared from green method shows better cytotoxicity and antibacterial activity. The NiO nanoparticles were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), High resolution transmission electron microscopy (HRTEM), Energy dispersive X-ray analysis (EDX), and Photoluminescence spectroscopy (PL). The formation of a pure nickel oxide phase was confirmed by XRD and FTIR. The synthesized NiO nanoparticles was single crystalline having face centered cubic phase and has two intense photoluminescence emissions at 305.46nm and 410nm. The formation of nano- and micro-structures was confirmed by HRTEM. The in-vitro cytotoxicity and cell viability of human cancer cell HT-29 (Colon Carcinoma cell lines) and antibacterial studies against various bacterial strains were studied with various concentrations of nickel oxide nanoparticles prepared from Moringa oleifera plant extract. MTT assay measurements on cell viability and morphological studies proved that the synthesized NiO nanoparticles posses cytotoxic activity against human cancer cells and the various zones of inhibition (mm), obtained revealed the effective antibacterial activity of NiO nanoparticles against various Gram positive and Gram negative bacterial pathogens. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction.

    Science.gov (United States)

    Thiele, Herbert; Glandorf, Jörg; Hufnagel, Peter

    2010-05-27

    With the large variety of Proteomics workflows, as well as the large variety of instruments and data-analysis software available, researchers today face major challenges validating and comparing their Proteomics data. Here we present a new generation of the ProteinScape bioinformatics platform, now enabling researchers to manage Proteomics data from the generation and data warehousing to a central data repository with a strong focus on the improved accuracy, reproducibility and comparability demanded by many researchers in the field. It addresses scientists; current needs in proteomics identification, quantification and validation. But producing large protein lists is not the end point in Proteomics, where one ultimately aims to answer specific questions about the biological condition or disease model of the analyzed sample. In this context, a new tool has been developed at the Spanish Centro Nacional de Biotecnologia Proteomics Facility termed PIKE (Protein information and Knowledge Extractor) that allows researchers to control, filter and access specific information from genomics and proteomic databases, to understand the role and relationships of the proteins identified in the experiments. Additionally, an EU funded project, ProDac, has coordinated systematic data collection in public standards-compliant repositories like PRIDE. This will cover all aspects from generating MS data in the laboratory, assembling the whole annotation information and storing it together with identifications in a standardised format.

  6. Bioinformatics Strategies in Life Sciences: From Data Processing and Data Warehousing to Biological Knowledge Extraction

    Directory of Open Access Journals (Sweden)

    Thiele Herbert

    2010-03-01

    Full Text Available With the large variety of Proteomics workflows, as well as the large variety of instruments and data-analysis software available, researchers today face major challenges validating and comparing their Proteomics data. Here we present a new generation of the ProteinScapeTM bioinformatics platform, now enabling researchers to manage Proteomics data from the generation and data warehousing to a central data repository with a strong focus on the improved accuracy, reproducibility and comparability demanded by many researchers in the field. It addresses scientists` current needs in proteomics identification, quantification and validation. But producing large protein lists is not the end point in Proteomics, where one ultimately aims to answer specific questions about the biological condition or disease model of the analyzed sample. In this context, a new tool has been developed at the Spanish Centro Nacional de Biotecnologia Proteomics Facility termed PIKE (Protein information and Knowledge Extractor that allows researchers to control, filter and access specific information from genomics and proteomic databases, to understand the role and relationships of the proteins identified in the experiments. Additionally, an EU funded project, ProDac, has coordinated systematic data collection in public standards-compliant repositories like PRIDE. This will cover all aspects from generating MS data in the laboratory, assembling the whole annotation information and storing it together with identifications in a standardised format.

  7. Extraction of tacit knowledge from large ADME data sets via pairwise analysis.

    Science.gov (United States)

    Keefer, Christopher E; Chang, George; Kauffman, Gregory W

    2011-06-15

    Pharmaceutical companies routinely collect data across multiple projects for common ADME endpoints. Although at the time of collection the data is intended for use in decision making within a specific project, knowledge can be gained by data mining the entire cross-project data set for patterns of structure-activity relationships (SAR) that may be applied to any project. One such data mining method is pairwise analysis. This method has the advantage of being able to identify small structural changes that lead to significant changes in activity. In this paper, we describe the process for full pairwise analysis of our high-throughput ADME assays routinely used for compound discovery efforts at Pfizer (microsomal clearance, passive membrane permeability, P-gp efflux, and lipophilicity). We also describe multiple strategies for the application of these transforms in a prospective manner during compound design. Finally, a detailed analysis of the activity patterns in pairs of compounds that share the same molecular transformation reveals multiple types of transforms from an SAR perspective. These include bioisosteres, additives, multiplicatives, and a type we call switches as they act to either turn on or turn off an activity. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. From Biomedical to Psychosomatic Reasoning: A Theoretical Framework

    Directory of Open Access Journals (Sweden)

    Alireza Monajemi

    2014-01-01

    Full Text Available Despite a general acceptance of the biopsychosocial model, medical education and patient care are still largely biomedical in focus, and physicians have many deficiencies in biopsychosocial formulations and care. Education in medical schools puts more emphasis on providing biomedical education (BM than biopsychosocial education (BPS; the initial knowledge formed in medical students is mainly with a biomedical approach. Therefore, it seems that psychosocial aspects play a minor role at this level and PSM knowledge will lag behind BM knowledge. However, it seems that the integration of biomedical and psychosocial-knowledge is crucial for a successful and efficient patient encounter. In this paper, based on the theory of medical expertise development, the steps through which biomedical reasoning transforms to psychosomatic reasoning will be discussed.

  9. Using Data Warehouses to extract knowledge from Agro-Hydrological simulations

    Science.gov (United States)

    Bouadi, Tassadit; Gascuel-Odoux, Chantal; Cordier, Marie-Odile; Quiniou, René; Moreau, Pierre

    2013-04-01

    In recent years, simulation models have been used more and more in hydrology to test the effect of scenarios and help stakeholders in decision making. Agro-hydrological models have oriented agricultural water management, by testing the effect of landscape structure and farming system changes on water and chemical emission in rivers. Such models generate a large amount of data while few of them, such as daily concentrations at the outlet of the catchment, or annual budgets regarding soil, water and atmosphere emissions, are stored and analyzed. Thus, a great amount of information is lost from the simulation process. This is due to the large volumes of simulated data, but also to the difficulties in analyzing and transforming the data in an usable information. In this talk we illustrate a data warehouse which has been built to store and manage simulation data coming from the agro-hydrological model TNT (Topography-based nitrogen transfer and transformations, (Beaujouan et al., 2002)). This model simulates the transfer and transformation of nitrogen in agricultural catchments. TNT was used over 10 years on the Yar catchment (western France), a 50 km2 square area which present a detailed data set and have to facing to environmental issue (coastal eutrophication). 44 output key simulated variables are stored at a daily time step, i.e, 8 GB of storage size, which allows the users to explore the N emission in space and time, to quantify all the processes of transfer and transformation regarding the cropping systems, their location within the catchment, the emission in water and atmosphere, and finally to get new knowledge and help in making specific and detailed decision in space and time. We present the dimensional modeling process of the Nitrogen in catchment data warehouse (i.e. the snowflake model). After identifying the set of multileveled dimensions with complex hierarchical structures and relationships among related dimension levels, we chose the snowflake model to

  10. THE EFFECT OF CICHORIUM INTYBUS L. ETHANOL EXTRACTION ON THE PATHOLOGICAL AND BIOMEDICAL INDEXES OF THE LIVER AND KIDNEY OF BROILERS REARED UNDER HEAT STRESS

    Directory of Open Access Journals (Sweden)

    M Khodadadi

    Full Text Available ABSTRACT The use of compounds with antioxidant properties as a source of phelanoeid compounds is highly recommendable in the poultry industry. Therefore, the effect of Cichorium intybus L. herb on pathobiochemical indexes of chicken under heat stress was studied. After exposure to heat stress (from day 21 to day 42 of growth, hydroalcoholic extraction was provided to 270 broiler chicks randomly divided into six groups and placed in two distinct poultry houses (heat stress and normal conditions. The three groups were recipient group of Cichorium intybus L. (1; recipient group of vitamin C (2 and control group (3. The birds in one of the houses were exposed to heat stress conditions (35 °C for 8 hours for a time period between 22 to 42 days and the birds in the other house were reared under normal conditions (20-22°C for the same time period. Blood samples collected from the birds showed that Cichorium intybus L. herb caused significant decrease in uric acid, Triglyceride, Alanine aminotransferase (ALT, total body clearance factors (CL- factors and right ventricular failure index (RVF and significant increase in K+ under heat stress condition (p< 0.05. Vitamin C caused significant decrease in uric acid, ALT, CL- factors and RVF index and significant increase in K+ and Na+ under heat stress condition (p< 0.05. A significant decrease in cholesterol and triglyceride in recipient group of Cichorium intybus L was observed compared to the recipient group of vitamin C under heat stress condition (p< 0.05. In a pathologic examination normal observations were in recipient group of Cichorium intybus L and recipient group of vitamin C compared to the control group. According to this study, use of Cichorium intybus L extract and vitamin C in chicken under heat stress induced improvement in liver, kidney activity and fat metabolism.

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

    Directory of Open Access Journals (Sweden)

    Thompson Paul

    2011-10-01

    Full Text Available Abstract Background Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events. Results This article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is

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

    Science.gov (United States)

    2011-01-01

    Background Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events) involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events. Results This article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized) together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is modelled using the Lexical

  13. Biomedical text mining and its applications in cancer research.

    Science.gov (United States)

    Zhu, Fei; Patumcharoenpol, Preecha; Zhang, Cheng; Yang, Yang; Chan, Jonathan; Meechai, Asawin; Vongsangnak, Wanwipa; Shen, Bairong

    2013-04-01

    Cancer is a malignant disease that has caused millions of human deaths. Its study has a long history of well over 100years. There have been an enormous number of publications on cancer research. This integrated but unstructured biomedical text is of great value for cancer diagnostics, treatment, and prevention. The immense body and rapid growth of biomedical text on cancer has led to the appearance of a large number of text mining techniques aimed at extracting novel knowledge from scientific text. Biomedical text mining on cancer research is computationally automatic and high-throughput in nature. However, it is error-prone due to the complexity of natural language processing. In this review, we introduce the basic concepts underlying text mining and examine some frequently used algorithms, tools, and data sets, as well as assessing how much these algorithms have been utilized. We then discuss the current state-of-the-art text mining applications in cancer research and we also provide some resources for cancer text mining. With the development of systems biology, researchers tend to understand complex biomedical systems from a systems biology viewpoint. Thus, the full utilization of text mining to facilitate cancer systems biology research is fast becoming a major concern. To address this issue, we describe the general workflow of text mining in cancer systems biology and each phase of the workflow. We hope that this review can (i) provide a useful overview of the current work of this field; (ii) help researchers to choose text mining tools and datasets; and (iii) highlight how to apply text mining to assist cancer systems biology research. Copyright © 2012 Elsevier Inc. All rights reserved.

  14. [Ginkgo biloba extract (EGb 761). State of knowledge in the dawn of the year 2000].

    Science.gov (United States)

    Clostre, F

    1999-07-01

    EGb 761 is a standardized extract of dried leaves of Ginkgo biloba containing 24% ginkgo-flavonol glycosides, 6% terpene lactones such as ginkgolides A, B, C, J and bilobalide. Its broad spectrum of pharmacological activities allows it to be in adequacy to the numerous pathological requirements--hemodynamic, hemorheological, metabolic--which occur in cerebral, retinal, cochleovestibular, cardiac or peripheral ischemia. Moreover, EGb 761 has direct effects against necrosis and apoptosis of neurons and improves neural plasticity as evidenced in vestibular compensation. At the molecular and the cellular levels, some evidence obtained with animal models indicates that EGb 761 can interact as a free radical-scavenger and a inhibitor of lipid peroxidation with all, or nearly all reactive oxygen species; maintains ATP content by a protection of mitochondrial respiration and preservation of oxidative phosphorylations; exerts arterial and venous vasoregulator effects involving the release of endothelial factors and the catecholaminergic system. Moreover, EGb 761 regulates ionic balance in damaged cells and exerts a specific and potent Platelet-activating factor antagonist activity. Numerous well-controlled clinical studies, realized in Europe and in USA, have revealed that EGb 761 is an effective therapy for a wide variety of disturbances of cerebral function, ranging from cerebral impairment of ischemic vascular origins (i.e. multi infarct dementia), early cognitive decline to mild-to-moderate cases of the more severe types of senile dementias (including Alzheimer's disease) or mixed origins (i.e. psychoorganic origin). Improvement of signs and symptoms have been demonstrated for cognitive functions, particularly for memory loss, attention, alertness, vigilance, arousal and mental fluidity. Some clinical studies have showed that EGb 761 treatment may improve the capacity of geriatric patients to cope with the stressful demands of daily life. The explanation is a dual

  15. Biomedical engineering principles

    CERN Document Server

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

    2011-01-01

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

  16. Fundamental of biomedical engineering

    CERN Document Server

    Sawhney, GS

    2007-01-01

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

  17. Conception of Pharmacological Knowledge and Needs Amongst Nigerian Medical Students at Lagos State University College of Medicine: Implication for Future Biomedical Science in Africa.

    Science.gov (United States)

    Agaga, Luther Agbonyegbeni; John, Theresa Adebola

    2016-08-30

    In Nigeria, medical students are trained in more didactic environments than their counterparts in researchintensive academic medical centers. Their conception of pharmacology was thus sought. Students who are taking/have takenthe medical pharmacology course completed an 18-question survey within 10min by marking one/more choices fromalternatives. Instructions were: "Dear Participant, Please treat as confidential, give your true view, avoid influences, avoidcrosstalk, return survey promptly." Out of 301 students, 188 (62.46%) participated. Simple statistics showed: 61.3%respondents associated pharmacology with medicine, 24.9% with science, 16.8 % with industry, and 11.1% with government;32.8% want to know clinical pharmacology, 7.1% basic pharmacology, 6.7% pharmacotherapy, and 34.2% want a blend ofall three; 57.8% want to know clinical uses of drugs, 44.8% mechanisms of action, 44.4% side effects, and 31.1% differentdrugs in a group; 45.8% prefer to study lecturers' notes, 26.7% textbooks, 9.8% the Internet, and 2.7% journals; 46.7% usestandard textbooks, 11.5% revision texts, 2.66% advanced texts, and 8.4% no textbook; 40.4% study pharmacology to beable to treat patients, 39.1% to complete the requirements for MBBS degree, 8.9% to know this interesting subject, and 3.1%to make money. Respondents preferring aspects of pharmacology were: 42.7, 16, 16, and 10 (%) respectively for mechanismsof action, pharmacokinetics, side effects, and drug lists. Medical students' conception and need for pharmacology werebased on MBBS degree requirements; they lacked knowledge/interest in pharmacology as a science and may not be thepotential trusts for Africa's future pharmacology.

  18. Extract useful knowledge from agro-hydrological simulations data for decision making

    Science.gov (United States)

    Gascuel-odoux, C.; Bouadi, T.; Cordier, M.; Quiniou, R.

    2013-12-01

    -Catch has been designed using the open source Business Intelligence Platform Pentaho. We show how to use online analytical processing (OLAP) to access and exploit, intuitively and quickly, the multidimensional and aggregated data from the N-Catch data warehouse. We illustrate how the data warehouse can be used to explore spatio-temporal dimensions efficiently and to discover new knowledge at multiple levels of simulation. OLAP tool can be used to synthesize environmental information and understand nitrogen emissions in water bodies by generating comparative and personalized views of historical data. This DWH is currently extended with data mining or information retrieval methods as Skyline queries to perform advanced analyses (Bouadi et al., 2012). Bouadi et al. N-Catch: A Data Warehouse for Multilevel Analysis of Simulated Nitrogen Data from an Agro-hydrological Model. Submitted. Bouadi et al., 2012) Bouadi, T., Cordier, M., and Quiniou, R. (2012). Incremental computation of skyline queries with dynamic preferences. In DEXA (1), pages 219-233. Trepos et al. 2012. Mining simulation data by rule induction to determine critical source areas of stream water pollution by herbicides. Computers and Electronics in Agriculture 86, 75-88.

  19. Biomedical signal and image processing

    CERN Document Server

    Najarian, Kayvan

    2012-01-01

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

  20. Magnetic nanoparticles for biomedical applications

    International Nuclear Information System (INIS)

    Krustev, P.; Ruskov, T.

    2007-01-01

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

  1. CONAN : Text Mining in the Biomedical Domain

    NARCIS (Netherlands)

    Malik, R.

    2006-01-01

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

  2. SemaTyP: a knowledge graph based literature mining method for drug discovery.

    Science.gov (United States)

    Sang, Shengtian; Yang, Zhihao; Wang, Lei; Liu, Xiaoxia; Lin, Hongfei; Wang, Jian

    2018-05-30

    Drug discovery is the process through which potential new medicines are identified. High-throughput screening and computer-aided drug discovery/design are the two main drug discovery methods for now, which have successfully discovered a series of drugs. However, development of new drugs is still an extremely time-consuming and expensive process. Biomedical literature contains important clues for the identification of potential treatments. It could support experts in biomedicine on their way towards new discoveries. Here, we propose a biomedical knowledge graph-based drug discovery method called SemaTyP, which discovers candidate drugs for diseases by mining published biomedical literature. We first construct a biomedical knowledge graph with the relations extracted from biomedical abstracts, then a logistic regression model is trained by learning the semantic types of paths of known drug therapies' existing in the biomedical knowledge graph, finally the learned model is used to discover drug therapies for new diseases. The experimental results show that our method could not only effectively discover new drug therapies for new diseases, but also could provide the potential mechanism of action of the candidate drugs. In this paper we propose a novel knowledge graph based literature mining method for drug discovery. It could be a supplementary method for current drug discovery methods.

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

    Science.gov (United States)

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

    2018-06-01

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

  4. Biomedical applications engineering tasks

    Science.gov (United States)

    Laenger, C. J., Sr.

    1976-01-01

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

  5. Biomedical applications of polymers

    CERN Document Server

    Gebelein, C G

    1991-01-01

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

  6. Handbook of biomedical optics

    CERN Document Server

    Boas, David A

    2011-01-01

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

  7. Biomedical Engineering Desk Reference

    CERN Document Server

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

    2009-01-01

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

  8. Powering biomedical devices

    CERN Document Server

    Romero, Edwar

    2013-01-01

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

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

    Science.gov (United States)

    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

  10. Facile biological synthetic strategy to morphologically aligned CeO2/ZrO2 core nanoparticles using Justicia adhatoda extract and ionic liquid: Enhancement of its bio-medical properties.

    Science.gov (United States)

    Pandiyan, Nithya; Murugesan, Balaji; Sonamuthu, Jegatheeswaran; Samayanan, Selvam; Mahalingam, Sundrarajan

    2018-01-01

    In this study, a typical green synthesis route has approached for CeO 2 /ZrO 2 core metal oxide nanoparticles using ionic liquid mediated Justicia adhatoda extract. This synthesis method is carried out at simple room temperature condition to obtain the core metal oxide nanoparticles. XRD, SEM and TEM studies employed to study the crystalline and surface morphological properties under nucleation, growth, and aggregation processes. CeO 2 /ZrO 2 core metal oxides display agglomerated nano stick-like structure with 20-45nm size. GC-MS spectroscopy confirms the presence of vasicinone and N,N-Dimethylglycine present in the plant extract, which are capable of converting the corresponding metal ion precursor to CeO 2 /ZrO 2 core metal oxide nanoparticles. In FTIR, the corresponding stretching for Ce-O and Zr-O bands indicated at 498 and 416cm -1 and Raman spectroscopy also supports typical stretching frequencies at 463 and 160cm -1 . Band gap energy of the CeO 2 /ZrO 2 core metal oxide is 3.37eV calculated from UV- DRS spectroscopy. The anti-bacterial studies performed against a set of bacterial strains the result showed that core metal oxide nanoparticles more susceptible to gram-positive (G+) bacteria than gram-negative (G-) bacteria. A unique feature of the antioxidant behaviors core metal oxides reduces the concentration of DPPH radical up to 89%. The CeO 2 /ZrO 2 core metal oxide nanoparticles control the S. marcescent bio-film formation and restrict the quorum sensing. The toxicology behavior of CeO 2 /ZrO 2 core metal oxide NPs is found due to the high oxygen site vacancies, ROS formation, smallest particle size and higher surface area. This type of green synthesis route may efficient and the core metal oxide nanoparticles will possess a good bio-medical agent in future. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Dynamic knowledge representation using agent-based modeling: ontology instantiation and verification of conceptual models.

    Science.gov (United States)

    An, Gary

    2009-01-01

    The sheer volume of biomedical research threatens to overwhelm the capacity of individuals to effectively process this information. Adding to this challenge is the multiscale nature of both biological systems and the research community as a whole. Given this volume and rate of generation of biomedical information, the research community must develop methods for robust representation of knowledge in order for individuals, and the community as a whole, to "know what they know." Despite increasing emphasis on "data-driven" research, the fact remains that researchers guide their research using intuitively constructed conceptual models derived from knowledge extracted from publications, knowledge that is generally qualitatively expressed using natural language. Agent-based modeling (ABM) is a computational modeling method that is suited to translating the knowledge expressed in biomedical texts into dynamic representations of the conceptual models generated by researchers. The hierarchical object-class orientation of ABM maps well to biomedical ontological structures, facilitating the translation of ontologies into instantiated models. Furthermore, ABM is suited to producing the nonintuitive behaviors that often "break" conceptual models. Verification in this context is focused at determining the plausibility of a particular conceptual model, and qualitative knowledge representation is often sufficient for this goal. Thus, utilized in this fashion, ABM can provide a powerful adjunct to other computational methods within the research process, as well as providing a metamodeling framework to enhance the evolution of biomedical ontologies.

  12. NDE in biomedical engineering

    International Nuclear Information System (INIS)

    Bhagwat, Aditya; Kumar, Pradeep

    2015-01-01

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

  13. Biomedical signal analysis

    CERN Document Server

    Rangayyan, Rangaraj M

    2015-01-01

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

  14. Clustering cliques for graph-based summarization of the biomedical research literature

    DEFF Research Database (Denmark)

    Zhang, Han; Fiszman, Marcelo; Shin, Dongwook

    2013-01-01

    Background: Graph-based notions are increasingly used in biomedical data mining and knowledge discovery tasks. In this paper, we present a clique-clustering method to automatically summarize graphs of semantic predications produced from PubMed citations (titles and abstracts).Results: Sem......Rep is used to extract semantic predications from the citations returned by a PubMed search. Cliques were identified from frequently occurring predications with highly connected arguments filtered by degree centrality. Themes contained in the summary were identified with a hierarchical clustering algorithm...

  15. Towards precision medicine; a new biomedical cosmology.

    Science.gov (United States)

    Vegter, M W

    2018-02-10

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

  16. MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge

    Directory of Open Access Journals (Sweden)

    Song Min

    2010-04-01

    Full Text Available Abstract Background Since Swanson proposed the Undiscovered Public Knowledge (UPK model, there have been many approaches to uncover UPK by mining the biomedical literature. These earlier works, however, required substantial manual intervention to reduce the number of possible connections and are mainly applied to disease-effect relation. With the advancement in biomedical science, it has become imperative to extract and combine information from multiple disjoint researches, studies and articles to infer new hypotheses and expand knowledge. Methods We propose MKEM, a Multi-level Knowledge Emergence Model, to discover implicit relationships using Natural Language Processing techniques such as Link Grammar and Ontologies such as Unified Medical Language System (UMLS MetaMap. The contribution of MKEM is as follows: First, we propose a flexible knowledge emergence model to extract implicit relationships across different levels such as molecular level for gene and protein and Phenomic level for disease and treatment. Second, we employ MetaMap for tagging biological concepts. Third, we provide an empirical and systematic approach to discover novel relationships. Results We applied our system on 5000 abstracts downloaded from PubMed database. We performed the performance evaluation as a gold standard is not yet available. Our system performed with a good precision and recall and we generated 24 hypotheses. Conclusions Our experiments show that MKEM is a powerful tool to discover hidden relationships residing in extracted entities that were represented by our Substance-Effect-Process-Disease-Body Part (SEPDB model.

  17. SparkText: Biomedical Text Mining on Big Data Framework

    Science.gov (United States)

    He, Karen Y.; Wang, Kai

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Zhan Ye

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

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

    Science.gov (United States)

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

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

  20. Personalized biomedical devices & systems for healthcare applications

    Science.gov (United States)

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

    2011-03-01

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

  1. Biomedical engineering and society: policy and ethics.

    Science.gov (United States)

    Flexman, J A; Lazareck, L

    2007-01-01

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

  2. Building the biomedical data science workforce.

    Science.gov (United States)

    Dunn, Michelle C; Bourne, Philip E

    2017-07-01

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

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

    Science.gov (United States)

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

    2015-06-01

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

  4. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

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

    2011-08-11

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

  5. The importance of Zebrafish in biomedical research.

    Science.gov (United States)

    Tavares, Bárbara; Santos Lopes, Susana

    2013-01-01

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

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

    Science.gov (United States)

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

    2018-04-01

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

  7. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

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

  8. Biomedical enhancements as justice.

    Science.gov (United States)

    Nam, Jeesoo

    2015-02-01

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

  9. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1976-01-01

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

  10. Finding biomedical categories in Medline®

    Directory of Open Access Journals (Sweden)

    Yeganova Lana

    2012-10-01

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

  11. Discovering gene annotations in biomedical text databases

    Directory of Open Access Journals (Sweden)

    Ozsoyoglu Gultekin

    2008-03-01

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

  12. Biomedical Engineering in Modern Society

    Science.gov (United States)

    Attinger, E. O.

    1971-01-01

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

  13. Biomedical Image Registration

    DEFF Research Database (Denmark)

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

  14. Biomedical Data Mining

    NARCIS (Netherlands)

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

    2009-01-01

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

  15. Anatomy for Biomedical Engineers

    Science.gov (United States)

    Carmichael, Stephen W.; Robb, Richard A.

    2008-01-01

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

  16. Biomedical research applications

    International Nuclear Information System (INIS)

    Anon.

    1982-01-01

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

  17. Enhancing acronym/abbreviation knowledge bases with semantic information.

    Science.gov (United States)

    Torii, Manabu; Liu, Hongfang

    2007-10-11

    In the biomedical domain, a terminology knowledge base that associates acronyms/abbreviations (denoted as SFs) with the definitions (denoted as LFs) is highly needed. For the construction such terminology knowledge base, we investigate the feasibility to build a system automatically assigning semantic categories to LFs extracted from text. Given a collection of pairs (SF,LF) derived from text, we i) assess the coverage of LFs and pairs (SF,LF) in the UMLS and justify the need of a semantic category assignment system; and ii) automatically derive name phrases annotated with semantic category and construct a system using machine learning. Utilizing ADAM, an existing collection of (SF,LF) pairs extracted from MEDLINE, our system achieved an f-measure of 87% when assigning eight UMLS-based semantic groups to LFs. The system has been incorporated into a web interface which integrates SF knowledge from multiple SF knowledge bases. Web site: http://gauss.dbb.georgetown.edu/liblab/SFThesurus.

  18. Biomedical signals, imaging, and informatics

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

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

  19. Compound to Extract to Formulation: a knowledge-transmitting approach for metabolites identification of Gegen-Qinlian Decoction, a traditional Chinese medicine formula

    Science.gov (United States)

    Qiao, Xue; Wang, Qi; Wang, Shuang; Miao, Wen-juan; Li, Yan-jiao; Xiang, Cheng; Guo, De-an; Ye, Min

    2016-01-01

    Herbal medicines usually contain a large group of chemical components, which may be transformed into more complex metabolites in vivo. In this study, we proposed a knowledge-transmitting strategy for metabolites identification of compound formulas. Gegen-Qinlian Decoction (GQD) is a classical formula in traditional Chinese medicine (TCM). It is widely used to treat diarrhea and diabetes in clinical practice. However, only tens of metabolites could be detected using conventional approaches. To comprehensively identify the metabolites of GQD, a “compound to extract to formulation” strategy was established in this study. The metabolic pathways of single representative constituents in GQD were studied, and the metabolic rules were transmitted to chemically similar compounds in herbal extracts. After screening diversified metabolites from herb extracts, the knowledge was summarized to identify the metabolites of GQD. Tandem mass spectrometry (MSn), fragment-based scan (NL, PRE), and selected reaction monitoring (SRM) were employed to identify, screen, and monitor the metabolites, respectively. Using this strategy, we detected 131 GQD metabolites (85 were newly generated) in rats biofluids. Among them, 112 metabolites could be detected when GQD was orally administered at a clinical dosage (12.5 g/kg). This strategy could be used for systematic metabolites identification of complex Chinese medicine formulas. PMID:27996040

  20. Advances in biomedical dosimetry

    International Nuclear Information System (INIS)

    1981-01-01

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

  1. Optical Polarizationin Biomedical Applications

    CERN Document Server

    Tuchin, Valery V; Zimnyakov, Dmitry A

    2006-01-01

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

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

    Science.gov (United States)

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

    2012-01-25

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

  3. A Generic Framework for Extraction of Knowledge from Social Web Sources (Social Networking Websites) for an Online Recommendation System

    Science.gov (United States)

    Sathick, Javubar; Venkat, Jaya

    2015-01-01

    Mining social web data is a challenging task and finding user interest for personalized and non-personalized recommendation systems is another important task. Knowledge sharing among web users has become crucial in determining usage of web data and personalizing content in various social websites as per the user's wish. This paper aims to design a…

  4. MOLIERE: Automatic Biomedical Hypothesis Generation System.

    Science.gov (United States)

    Sybrandt, Justin; Shtutman, Michael; Safro, Ilya

    2017-08-01

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

  5. Three-dimensional biomedical imaging

    International Nuclear Information System (INIS)

    Robb, R.A.

    1985-01-01

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

  6. Knowledge discovery in variant databases using inductive logic programming.

    Science.gov (United States)

    Nguyen, Hoan; Luu, Tien-Dao; Poch, Olivier; Thompson, Julie D

    2013-01-01

    Understanding the effects of genetic variation on the phenotype of an individual is a major goal of biomedical research, especially for the development of diagnostics and effective therapeutic solutions. In this work, we describe the use of a recent knowledge discovery from database (KDD) approach using inductive logic programming (ILP) to automatically extract knowledge about human monogenic diseases. We extracted background knowledge from MSV3d, a database of all human missense variants mapped to 3D protein structure. In this study, we identified 8,117 mutations in 805 proteins with known three-dimensional structures that were known to be involved in human monogenic disease. Our results help to improve our understanding of the relationships between structural, functional or evolutionary features and deleterious mutations. Our inferred rules can also be applied to predict the impact of any single amino acid replacement on the function of a protein. The interpretable rules are available at http://decrypthon.igbmc.fr/kd4v/.

  7. Biomedical applications of batteries

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-08-31

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

  8. Advances in biomedical engineering

    CERN Document Server

    Brown, J H U

    1973-01-01

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

  9. Statistics in biomedical research

    Directory of Open Access Journals (Sweden)

    González-Manteiga, Wenceslao

    2007-06-01

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

  10. Biomedical signals and systems

    CERN Document Server

    Tranquillo, Joseph V

    2013-01-01

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

  11. Biomedical photonics handbook

    CERN Document Server

    Vo-Dinh, Tuan

    2003-01-01

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

  12. Radiochemicals in biomedical research

    International Nuclear Information System (INIS)

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

    1988-01-01

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

  13. Normalizing biomedical terms by minimizing ambiguity and variability

    Directory of Open Access Journals (Sweden)

    McNaught John

    2008-04-01

    Full Text Available Abstract Background One of the difficulties in mapping biomedical named entities, e.g. genes, proteins, chemicals and diseases, to their concept identifiers stems from the potential variability of the terms. Soft string matching is a possible solution to the problem, but its inherent heavy computational cost discourages its use when the dictionaries are large or when real time processing is required. A less computationally demanding approach is to normalize the terms by using heuristic rules, which enables us to look up a dictionary in a constant time regardless of its size. The development of good heuristic rules, however, requires extensive knowledge of the terminology in question and thus is the bottleneck of the normalization approach. Results We present a novel framework for discovering a list of normalization rules from a dictionary in a fully automated manner. The rules are discovered in such a way that they minimize the ambiguity and variability of the terms in the dictionary. We evaluated our algorithm using two large dictionaries: a human gene/protein name dictionary built from BioThesaurus and a disease name dictionary built from UMLS. Conclusions The experimental results showed that automatically discovered rules can perform comparably to carefully crafted heuristic rules in term mapping tasks, and the computational overhead of rule application is small enough that a very fast implementation is possible. This work will help improve the performance of term-concept mapping tasks in biomedical information extraction especially when good normalization heuristics for the target terminology are not fully known.

  14. A semantic-based method for extracting concept definitions from scientific publications: evaluation in the autism phenotype domain.

    Science.gov (United States)

    Hassanpour, Saeed; O'Connor, Martin J; Das, Amar K

    2013-08-12

    A variety of informatics approaches have been developed that use information retrieval, NLP and text-mining techniques to identify biomedical concepts and relations within scientific publications or their sentences. These approaches have not typically addressed the challenge of extracting more complex knowledge such as biomedical definitions. In our efforts to facilitate knowledge acquisition of rule-based definitions of autism phenotypes, we have developed a novel semantic-based text-mining approach that can automatically identify such definitions within text. Using an existing knowledge base of 156 autism phenotype definitions and an annotated corpus of 26 source articles containing such definitions, we evaluated and compared the average rank of correctly identified rule definition or corresponding rule template using both our semantic-based approach and a standard term-based approach. We examined three separate scenarios: (1) the snippet of text contained a definition already in the knowledge base; (2) the snippet contained an alternative definition for a concept in the knowledge base; and (3) the snippet contained a definition not in the knowledge base. Our semantic-based approach had a higher average rank than the term-based approach for each of the three scenarios (scenario 1: 3.8 vs. 5.0; scenario 2: 2.8 vs. 4.9; and scenario 3: 4.5 vs. 6.2), with each comparison significant at the p-value of 0.05 using the Wilcoxon signed-rank test. Our work shows that leveraging existing domain knowledge in the information extraction of biomedical definitions significantly improves the correct identification of such knowledge within sentences. Our method can thus help researchers rapidly acquire knowledge about biomedical definitions that are specified and evolving within an ever-growing corpus of scientific publications.

  15. Professional Identification for Biomedical Engineers

    Science.gov (United States)

    Long, Francis M.

    1973-01-01

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

  16. Egyptian Journal of Biomedical Sciences

    African Journals Online (AJOL)

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

  17. African Journal of Biomedical Research

    African Journals Online (AJOL)

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

  18. Journal of Biomedical Investigation: Editorial Policies

    African Journals Online (AJOL)

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

  19. Biomedical informatics and translational medicine

    Directory of Open Access Journals (Sweden)

    Sarkar Indra

    2010-02-01

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

  20. Computational intelligence in biomedical imaging

    CERN Document Server

    2014-01-01

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

  1. Biomedical applications of nanotechnology.

    Science.gov (United States)

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

    2017-04-01

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

  2. Building the biomedical data science workforce.

    Directory of Open Access Journals (Sweden)

    Michelle C Dunn

    2017-07-01

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

  3. IEEE International Symposium on Biomedical Imaging.

    Science.gov (United States)

    2017-01-01

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

  4. Biomedical semantics in the Semantic Web.

    Science.gov (United States)

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

    2011-03-07

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

  5. Mining biomarker information in biomedical literature

    Directory of Open Access Journals (Sweden)

    Younesi Erfan

    2012-12-01

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

  6. Introduction to Statistics for Biomedical Engineers

    CERN Document Server

    Ropella, Kristina

    2007-01-01

    There are many books written about statistics, some brief, some detailed, some humorous, some colorful, and some quite dry. Each of these texts is designed for a specific audience. Too often, texts about statistics have been rather theoretical and intimidating for those not practicing statistical analysis on a routine basis. Thus, many engineers and scientists, who need to use statistics much more frequently than calculus or differential equations, lack sufficient knowledge of the use of statistics. The audience that is addressed in this text is the university-level biomedical engineering stud

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

    Science.gov (United States)

    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.

  8. Entity recognition in the biomedical domain using a hybrid approach.

    Science.gov (United States)

    Basaldella, Marco; Furrer, Lenz; Tasso, Carlo; Rinaldi, Fabio

    2017-11-09

    This article describes a high-recall, high-precision approach for the extraction of biomedical entities from scientific articles. The approach uses a two-stage pipeline, combining a dictionary-based entity recognizer with a machine-learning classifier. First, the OGER entity recognizer, which has a bias towards high recall, annotates the terms that appear in selected domain ontologies. Subsequently, the Distiller framework uses this information as a feature for a machine learning algorithm to select the relevant entities only. For this step, we compare two different supervised machine-learning algorithms: Conditional Random Fields and Neural Networks. In an in-domain evaluation using the CRAFT corpus, we test the performance of the combined systems when recognizing chemicals, cell types, cellular components, biological processes, molecular functions, organisms, proteins, and biological sequences. Our best system combines dictionary-based candidate generation with Neural-Network-based filtering. It achieves an overall precision of 86% at a recall of 60% on the named entity recognition task, and a precision of 51% at a recall of 49% on the concept recognition task. These results are to our knowledge the best reported so far in this particular task.

  9. Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts

    Directory of Open Access Journals (Sweden)

    Spackman K

    2005-04-01

    Full Text Available Abstract Background Text-mining can assist biomedical researchers in reducing information overload by extracting useful knowledge from large collections of text. We developed a novel text-mining method based on analyzing the network structure created by symbol co-occurrences as a way to extend the capabilities of knowledge extraction. The method was applied to the task of automatic gene and protein name synonym extraction. Results Performance was measured on a test set consisting of about 50,000 abstracts from one year of MEDLINE. Synonyms retrieved from curated genomics databases were used as a gold standard. The system obtained a maximum F-score of 22.21% (23.18% precision and 21.36% recall, with high efficiency in the use of seed pairs. Conclusion The method performs comparably with other studied methods, does not rely on sophisticated named-entity recognition, and requires little initial seed knowledge.

  10. Biomedical informatics: we are what we publish.

    Science.gov (United States)

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

    2013-01-01

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

  11. Smart nanomaterials for biomedics.

    Science.gov (United States)

    Choi, Soonmo; Tripathi, Anuj; Singh, Deepti

    2014-10-01

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

  12. Zirconia in biomedical applications.

    Science.gov (United States)

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

    2016-10-01

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

  13. Student engagement in biomedical courses : studies in technology-enhanced seminar learning

    NARCIS (Netherlands)

    Bouwmeester, RAM

    2016-01-01

    Academic medical and biomedical curricula are designed to educate future academics contributing to new developments in science, clinical practice and society. During undergraduate programs student training is typically focused on acquisition of knowledge and understanding of these interdisciplinary

  14. Extraction method

    International Nuclear Information System (INIS)

    Stary, J.; Kyrs, M.; Navratil, J.; Havelka, S.; Hala, J.

    1975-01-01

    Definitions of the basic terms and of relations are given and the knowledge is described of the possibilities of the extraction of elements, oxides, covalent-bound halogenides and heteropolyacids. Greatest attention is devoted to the detailed analysis of the extraction of chelates and ion associates using diverse agents. For both types of compounds detailed conditions are given of the separation and the effects of the individual factors are listed. Attention is also devoted to extractions using mixtures of organic agents, the synergic effects thereof, and to extractions in non-aqueous solvents. The effects of radiation on extraction and the main types of apparatus used for extractions carried out in the laboratory are described. (L.K.)

  15. Bio-medical CMOS ICs

    CERN Document Server

    Yoo, Hoi-Jun

    2011-01-01

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

  16. Functionalized carbon nanotubes: biomedical applications

    Science.gov (United States)

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

    2012-01-01

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

  17. Molecular Biomedical Imaging Laboratory (MBIL)

    Data.gov (United States)

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

  18. New Directions for Biomedical Engineering

    Science.gov (United States)

    Plonsey, Robert

    1973-01-01

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

  19. Summer Biomedical Engineering Institute 1972

    Science.gov (United States)

    Deloatch, E. M.

    1973-01-01

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

  20. Usage of cell nomenclature in biomedical literature

    KAUST Repository

    Kafkas, Senay

    2017-12-21

    Background Cell lines and cell types are extensively studied in biomedical research yielding to a significant amount of publications each year. Identifying cell lines and cell types precisely in publications is crucial for science reproducibility and knowledge integration. There are efforts for standardisation of the cell nomenclature based on ontology development to support FAIR principles of the cell knowledge. However, it is important to analyse the usage of cell nomenclature in publications at a large scale for understanding the level of uptake of cell nomenclature in literature by scientists. In this study, we analyse the usage of cell nomenclature, both in Vivo, and in Vitro in biomedical literature by using text mining methods and present our results. Results We identified 59% of the cell type classes in the Cell Ontology and 13% of the cell line classes in the Cell Line Ontology in the literature. Our analysis showed that cell line nomenclature is much more ambiguous compared to the cell type nomenclature. However, trends indicate that standardised nomenclature for cell lines and cell types are being increasingly used in publications by the scientists. Conclusions Our findings provide an insight to understand how experimental cells are described in publications and may allow for an improved standardisation of cell type and cell line nomenclature as well as can be utilised to develop efficient text mining applications on cell types and cell lines. All data generated in this study is available at https://github.com/shenay/CellNomenclatureStudy.

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

    Science.gov (United States)

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

    2015-04-23

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

  2. Hydroxyapatite coatings for biomedical applications

    CERN Document Server

    Zhang, Sam

    2013-01-01

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

  3. John Glenn Biomedical Engineering Consortium

    Science.gov (United States)

    Nall, Marsha

    2004-01-01

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

  4. A community of practice: librarians in a biomedical research network.

    Science.gov (United States)

    De Jager-Loftus, Danielle P; Midyette, J David; Harvey, Barbara

    2014-01-01

    Providing library and reference services within a biomedical research community presents special challenges for librarians, especially those in historically lower-funded states. These challenges can include understanding needs, defining and communicating the library's role, building relationships, and developing and maintaining general and subject specific knowledge. This article describes a biomedical research network and the work of health sciences librarians at the lead intensive research institution with librarians from primarily undergraduate institutions and tribal colleges. Applying the concept of a community of practice to a collaborative effort suggests how librarians can work together to provide effective reference services to researchers in biomedicine.

  5. RPCs in biomedical applications

    Science.gov (United States)

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

    2006-08-01

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

  6. Core competencies for scientific editors of biomedical journals: consensus statement.

    Science.gov (United States)

    Moher, David; Galipeau, James; Alam, Sabina; Barbour, Virginia; Bartolomeos, Kidist; Baskin, Patricia; Bell-Syer, Sally; Cobey, Kelly D; Chan, Leighton; Clark, Jocalyn; Deeks, Jonathan; Flanagin, Annette; Garner, Paul; Glenny, Anne-Marie; Groves, Trish; Gurusamy, Kurinchi; Habibzadeh, Farrokh; Jewell-Thomas, Stefanie; Kelsall, Diane; Lapeña, José Florencio; MacLehose, Harriet; Marusic, Ana; McKenzie, Joanne E; Shah, Jay; Shamseer, Larissa; Straus, Sharon; Tugwell, Peter; Wager, Elizabeth; Winker, Margaret; Zhaori, Getu

    2017-09-11

    Scientific editors are responsible for deciding which articles to publish in their journals. However, we have not found documentation of their required knowledge, skills, and characteristics, or the existence of any formal core competencies for this role. We describe the development of a minimum set of core competencies for scientific editors of biomedical journals. The 14 key core competencies are divided into three major areas, and each competency has a list of associated elements or descriptions of more specific knowledge, skills, and characteristics that contribute to its fulfillment. We believe that these core competencies are a baseline of the knowledge, skills, and characteristics needed to perform competently the duties of a scientific editor at a biomedical journal.

  7. Diagnostic reasoning and underlying knowledge of students with preclinical patient contacts in PBL

    NARCIS (Netherlands)

    Diemers, Agnes D.; van de Wiel, Margje W. J.; Scherpbier, Albert J. J. A.; Baarveld, Frank; Dolmans, Diana H. J. M.

    2015-01-01

    CONTEXT: Medical experts have access to elaborate and integrated knowledge networks consisting of biomedical and clinical knowledge. These coherent knowledge networks enable them to generate more accurate diagnoses in a shorter time. However, students' knowledge networks are less organised and

  8. Rotation Covariant Image Processing for Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Henrik Skibbe

    2013-01-01

    Full Text Available With the advent of novel biomedical 3D image acquisition techniques, the efficient and reliable analysis of volumetric images has become more and more important. The amount of data is enormous and demands an automated processing. The applications are manifold, ranging from image enhancement, image reconstruction, and image description to object/feature detection and high-level contextual feature extraction. In most scenarios, it is expected that geometric transformations alter the output in a mathematically well-defined manner. In this paper we emphasis on 3D translations and rotations. Many algorithms rely on intensity or low-order tensorial-like descriptions to fulfill this demand. This paper proposes a general mathematical framework based on mathematical concepts and theories transferred from mathematical physics and harmonic analysis into the domain of image analysis and pattern recognition. Based on two basic operations, spherical tensor differentiation and spherical tensor multiplication, we show how to design a variety of 3D image processing methods in an efficient way. The framework has already been applied to several biomedical applications ranging from feature and object detection tasks to image enhancement and image restoration techniques. In this paper, the proposed methods are applied on a variety of different 3D data modalities stemming from medical and biological sciences.

  9. The biomedical discourse relation bank

    Directory of Open Access Journals (Sweden)

    Joshi Aravind

    2011-05-01

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

  10. [Master course in biomedical engineering].

    Science.gov (United States)

    Jobbágy, Akos; Benyó, Zoltán; Monos, Emil

    2009-11-22

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

  11. Anethum Graveolens Linn (Umbelliferae) Extract Attenuates Stress ...

    African Journals Online (AJOL)

    Erah

    College of Biomedical and Health Sciences, Department of Biotechnology, Konkuk University, Chungju, Republic of ... anti-stress and cognition-improving effects of A. graveolens extract in a rat model. ..... This work was supported by Konkuk.

  12. CDIO Experiences in Biomedical Engineering: Preparing Spanish Students for the Future of Medicine and Medical Device Technology

    OpenAIRE

    Díaz Lantada, Andrés; Serrano Olmedo, José Javier; Ros Felip, Antonio; Jiménez Fernández, Javier; Muñoz García, Julio; Claramunt Alonso, Rafael; Carpio Huertas, Jaime

    2016-01-01

    Biomedical engineering is one of the more recent fields of engineering, aimed at the application of engineering principles, methods and design concepts to medicine and biology for healthcare purposes, mainly as a support for preventive, diagnostic or therapeutic tasks. Biomedical engineering professionals are expected to achieve, during their studies and professional practice, considerable knowledge of both health sciences and engineering. Studying biomedical engineering programmes, or combin...

  13. Innovations in Biomedical Engineering 2016

    CERN Document Server

    Tkacz, Ewaryst; Paszenda, Zbigniew; Piętka, Ewa

    2017-01-01

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

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

    Science.gov (United States)

    Schulz, Stefan; López-García, Pablo

    2015-08-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  16. Biomedical Imaging Principles and Applications

    CERN Document Server

    Salzer, Reiner

    2012-01-01

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

  17. Biomedical applications of magnetic particles

    CERN Document Server

    Mefford, Thompson

    2018-01-01

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

  18. Text Mining for Precision Medicine: Bringing structure to EHRs and biomedical literature to understand genes and health

    Science.gov (United States)

    Simmons, Michael; Singhal, Ayush; Lu, Zhiyong

    2018-01-01

    The key question of precision medicine is whether it is possible to find clinically actionable granularity in diagnosing disease and classifying patient risk. The advent of next generation sequencing and the widespread adoption of electronic health records (EHRs) have provided clinicians and researchers a wealth of data and made possible the precise characterization of individual patient genotypes and phenotypes. Unstructured text — found in biomedical publications and clinical notes — is an important component of genotype and phenotype knowledge. Publications in the biomedical literature provide essential information for interpreting genetic data. Likewise, clinical notes contain the richest source of phenotype information in EHRs. Text mining can render these texts computationally accessible and support information extraction and hypothesis generation. This chapter reviews the mechanics of text mining in precision medicine and discusses several specific use cases, including database curation for personalized cancer medicine, patient outcome prediction from EHR-derived cohorts, and pharmacogenomic research. Taken as a whole, these use cases demonstrate how text mining enables effective utilization of existing knowledge sources and thus promotes increased value for patients and healthcare systems. Text mining is an indispensable tool for translating genotype-phenotype data into effective clinical care that will undoubtedly play an important role in the eventual realization of precision medicine. PMID:27807747

  19. Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health.

    Science.gov (United States)

    Simmons, Michael; Singhal, Ayush; Lu, Zhiyong

    2016-01-01

    The key question of precision medicine is whether it is possible to find clinically actionable granularity in diagnosing disease and classifying patient risk. The advent of next-generation sequencing and the widespread adoption of electronic health records (EHRs) have provided clinicians and researchers a wealth of data and made possible the precise characterization of individual patient genotypes and phenotypes. Unstructured text-found in biomedical publications and clinical notes-is an important component of genotype and phenotype knowledge. Publications in the biomedical literature provide essential information for interpreting genetic data. Likewise, clinical notes contain the richest source of phenotype information in EHRs. Text mining can render these texts computationally accessible and support information extraction and hypothesis generation. This chapter reviews the mechanics of text mining in precision medicine and discusses several specific use cases, including database curation for personalized cancer medicine, patient outcome prediction from EHR-derived cohorts, and pharmacogenomic research. Taken as a whole, these use cases demonstrate how text mining enables effective utilization of existing knowledge sources and thus promotes increased value for patients and healthcare systems. Text mining is an indispensable tool for translating genotype-phenotype data into effective clinical care that will undoubtedly play an important role in the eventual realization of precision medicine.

  20. Knowledge Exploration from Big Data in Biomedicine

    KAUST Repository

    Bajic, Vladimir B.

    2016-01-27

    The last few decades have witnessed an enormous accumulation of data and information in various forms in the domain of Biomedicine. To search for accurate and rich information on any particular topic in this domain appears challenging. The main reasons are that a) useful pieces of information are scattered across numerous sources, b) data is contained in a variety of formats, c) data/information are not indexed with standard identifiers, d) a lot of information is in a free text format, and e) frequently the information needed is not explicitly presented in any single data/information source. This situation requires new approaches to search for, extract and explore the desired information. We will present a system developed at KAUST that addresses some of these challenges. This system is a representative of a technological solution to what can be named Next Generation Knowledge Mining Systems for the biomedical domain.

  1. Co-occurrence graphs for word sense disambiguation in the biomedical domain.

    Science.gov (United States)

    Duque, Andres; Stevenson, Mark; Martinez-Romo, Juan; Araujo, Lourdes

    2018-05-01

    Word sense disambiguation is a key step for many natural language processing tasks (e.g. summarization, text classification, relation extraction) and presents a challenge to any system that aims to process documents from the biomedical domain. In this paper, we present a new graph-based unsupervised technique to address this problem. The knowledge base used in this work is a graph built with co-occurrence information from medical concepts found in scientific abstracts, and hence adapted to the specific domain. Unlike other unsupervised approaches based on static graphs such as UMLS, in this work the knowledge base takes the context of the ambiguous terms into account. Abstracts downloaded from PubMed are used for building the graph and disambiguation is performed using the personalized PageRank algorithm. Evaluation is carried out over two test datasets widely explored in the literature. Different parameters of the system are also evaluated to test robustness and scalability. Results show that the system is able to outperform state-of-the-art knowledge-based systems, obtaining more than 10% of accuracy improvement in some cases, while only requiring minimal external resources. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Text mining for traditional Chinese medical knowledge discovery: a survey.

    Science.gov (United States)

    Zhou, Xuezhong; Peng, Yonghong; Liu, Baoyan

    2010-08-01

    Extracting meaningful information and knowledge from free text is the subject of considerable research interest in the machine learning and data mining fields. Text data mining (or text mining) has become one of the most active research sub-fields in data mining. Significant developments in the area of biomedical text mining during the past years have demonstrated its great promise for supporting scientists in developing novel hypotheses and new knowledge from the biomedical literature. Traditional Chinese medicine (TCM) provides a distinct methodology with which to view human life. It is one of the most complete and distinguished traditional medicines with a history of several thousand years of studying and practicing the diagnosis and treatment of human disease. It has been shown that the TCM knowledge obtained from clinical practice has become a significant complementary source of information for modern biomedical sciences. TCM literature obtained from the historical period and from modern clinical studies has recently been transformed into digital data in the form of relational databases or text documents, which provide an effective platform for information sharing and retrieval. This motivates and facilitates research and development into knowledge discovery approaches and to modernize TCM. In order to contribute to this still growing field, this paper presents (1) a comparative introduction to TCM and modern biomedicine, (2) a survey of the related information sources of TCM, (3) a review and discussion of the state of the art and the development of text mining techniques with applications to TCM, (4) a discussion of the research issues around TCM text mining and its future directions. Copyright 2010 Elsevier Inc. All rights reserved.

  3. Enhancing Diversity in Biomedical Data Science.

    Science.gov (United States)

    Canner, Judith E; McEligot, Archana J; Pérez, María-Eglée; Qian, Lei; Zhang, Xinzhi

    2017-01-01

    The gap in educational attainment separating underrepresented minorities from Whites and Asians remains wide. Such a gap has significant impact on workforce diversity and inclusion among cross-cutting Biomedical Data Science (BDS) research, which presents great opportunities as well as major challenges for addressing health disparities. This article provides a brief description of the newly established National Institutes of Health Big Data to Knowledge (BD2K) diversity initiatives at four universities: California State University, Monterey Bay; Fisk University; University of Puerto Rico, Río Piedras Campus; and California State University, Fullerton. We emphasize three main barriers to BDS careers (ie, preparation, exposure, and access to resources) experienced among those pioneer programs and recommendations for possible solutions (ie, early and proactive mentoring, enriched research experience, and data science curriculum development). The diversity disparities in BDS demonstrate the need for educators, researchers, and funding agencies to support evidence-based practices that will lead to the diversification of the BDS workforce.

  4. [Biomedical waste management in five hospitals in Dakar, Senegal].

    Science.gov (United States)

    Ndiaye, M; El Metghari, L; Soumah, M M; Sow, M L

    2012-10-01

    Biomedical waste is currently a real health and environmental concern. In this regard, a study was conducted in 5 hospitals in Dakar to review their management of biomedical waste and to formulate recommendations. This is a descriptive cross-sectional study conducted from 1 April to 31 July 2010 in five major hospitals of Dakar. A questionnaire administered to hospital managers, heads of departments, residents and heads of hospital hygiene departments as well as interviews conducted with healthcare personnel and operators of waste incinerators made it possible to assess mechanisms and knowledge on biomedical waste management. Content analysis of interviews, observations and a data sheet allowed processing the data thus gathered. Of the 150 questionnaires distributed, 98 responses were obtained representing a response rate of 65.3%. An interview was conducted with 75 employees directly involved in the management of biomedical waste and observations were made on biomedical waste management in 86 hospital services. Sharps as well as blood and liquid waste were found in all services except in pharmacies, pharmaceutical waste in 66 services, infectious waste in 49 services and anatomical waste in 11 services. Sorting of biomedical waste was ill-adapted in 53.5% (N = 46) of services and the use of the colour-coding system effective in 31.4% (N = 27) of services. Containers for the safe disposal of sharps were available in 82.5% (N = 71) of services and were effectively utilized in 51.1% (N = 44) of these services. In most services, an illadapted packaging was observed with the use of plastic bottles and bins for waste collection and overfilled containers. With the exception of Hôpital Principal, the main storage area was in open air, unsecured, with biomedical waste littered on the floor and often mixed with waste similar to household refuse. The transfer of biomedical waste to the main storage area was done using trolleys or carts in 67.4% (N = 58) of services and

  5. Biomedical nanomaterials from design to implementation

    CERN Document Server

    Webster, Thomas

    2016-01-01

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

  6. Archives: Journal of Medical and Biomedical Sciences

    African Journals Online (AJOL)

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

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

    Science.gov (United States)

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

  8. Archives: Journal of Medicine and Biomedical Research

    African Journals Online (AJOL)

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

  9. Science gateways for biomedical big data analysis

    NARCIS (Netherlands)

    Shahand, S.

    2015-01-01

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

  10. Integrated Biomaterials for Biomedical Technology

    CERN Document Server

    Ramalingam, Murugan; Ramakrishna, Seeram; Kobayashi, Hisatoshi

    2012-01-01

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

  11. Environmental/Biomedical Terminology Index

    Energy Technology Data Exchange (ETDEWEB)

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

    1976-12-01

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

  12. Biomedical Engineering Education in Perspective

    Science.gov (United States)

    Gowen, Richard J.

    1973-01-01

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

  13. Environmental/Biomedical Terminology Index

    International Nuclear Information System (INIS)

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

    1976-12-01

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

  14. Statistics in three biomedical journals

    Czech Academy of Sciences Publication Activity Database

    Pilčík, Tomáš

    2003-01-01

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

  15. Design of Biomedical Robots for Phenotype Prediction Problems.

    Science.gov (United States)

    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.

  16. Research evaluation support services in biomedical libraries

    Directory of Open Access Journals (Sweden)

    Karen Elizabeth Gutzman

    2018-01-01

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

  17. Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts

    OpenAIRE

    Tulkens, Stéphan; Šuster, Simon; Daelemans, Walter

    2016-01-01

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

  18. Improving the extraction of complex regulatory events from scientific text by using ontology-based inference.

    Science.gov (United States)

    Kim, Jung-Jae; Rebholz-Schuhmann, Dietrich

    2011-10-06

    The extraction of complex events from biomedical text is a challenging task and requires in-depth semantic analysis. Previous approaches associate lexical and syntactic resources with ontologies for the semantic analysis, but fall short in testing the benefits from the use of domain knowledge. We developed a system that deduces implicit events from explicitly expressed events by using inference rules that encode domain knowledge. We evaluated the system with the inference module on three tasks: First, when tested against a corpus with manually annotated events, the inference module of our system contributes 53.2% of correct extractions, but does not cause any incorrect results. Second, the system overall reproduces 33.1% of the transcription regulatory events contained in RegulonDB (up to 85.0% precision) and the inference module is required for 93.8% of the reproduced events. Third, we applied the system with minimum adaptations to the identification of cell activity regulation events, confirming that the inference improves the performance of the system also on this task. Our research shows that the inference based on domain knowledge plays a significant role in extracting complex events from text. This approach has great potential in recognizing the complex concepts of such biomedical ontologies as Gene Ontology in the literature.

  19. Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

    Directory of Open Access Journals (Sweden)

    Kim Jung-jae

    2011-10-01

    Full Text Available Abstract Background The extraction of complex events from biomedical text is a challenging task and requires in-depth semantic analysis. Previous approaches associate lexical and syntactic resources with ontologies for the semantic analysis, but fall short in testing the benefits from the use of domain knowledge. Results We developed a system that deduces implicit events from explicitly expressed events by using inference rules that encode domain knowledge. We evaluated the system with the inference module on three tasks: First, when tested against a corpus with manually annotated events, the inference module of our system contributes 53.2% of correct extractions, but does not cause any incorrect results. Second, the system overall reproduces 33.1% of the transcription regulatory events contained in RegulonDB (up to 85.0% precision and the inference module is required for 93.8% of the reproduced events. Third, we applied the system with minimum adaptations to the identification of cell activity regulation events, confirming that the inference improves the performance of the system also on this task. Conclusions Our research shows that the inference based on domain knowledge plays a significant role in extracting complex events from text. This approach has great potential in recognizing the complex concepts of such biomedical ontologies as Gene Ontology in the literature.

  20. Characteristics desired in clinical data warehouse for biomedical research.

    Science.gov (United States)

    Shin, Soo-Yong; Kim, Woo Sung; Lee, Jae-Ho

    2014-04-01

    Due to the unique characteristics of clinical data, clinical data warehouses (CDWs) have not been successful so far. Specifically, the use of CDWs for biomedical research has been relatively unsuccessful thus far. The characteristics necessary for the successful implementation and operation of a CDW for biomedical research have not clearly defined yet. THREE EXAMPLES OF CDWS WERE REVIEWED: a multipurpose CDW in a hospital, a CDW for independent multi-institutional research, and a CDW for research use in an institution. After reviewing the three CDW examples, we propose some key characteristics needed in a CDW for biomedical research. A CDW for research should include an honest broker system and an Institutional Review Board approval interface to comply with governmental regulations. It should also include a simple query interface, an anonymized data review tool, and a data extraction tool. Also, it should be a biomedical research platform for data repository use as well as data analysis. The proposed characteristics desired in a CDW may have limited transfer value to organizations in other countries. However, these analysis results are still valid in Korea, and we have developed clinical research data warehouse based on these desiderata.

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

    Science.gov (United States)

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

    2017-05-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

  3. International Conference on Bio-Medical Instrumentation and related Engineering and Physical Sciences (BIOMEP 2015)

    Science.gov (United States)

    2015-09-01

    The International Conference on Bio-Medical Instrumentation and related Engineering and Physical Sciences (BIOMEP 2015) took place in the Technological Educational Institute (TEI) of Athens, Greece on June 18-20, 2015 and was organized by the Department of Biomedical Engineering. The scope of the conference was to provide a forum on the latest developments in Biomedical Instrumentation and related principles of Physical and Engineering sciences. Scientists and engineers from academic, industrial and health disciplines were invited to participate in the Conference and to contribute both in the promotion and dissemination of the scientific knowledge.

  4. Biomedical Risk Factors of Achilles Tendinopathy in Physically Active People: a Systematic Review

    OpenAIRE

    Kozlovskaia, Maria; Vlahovich, Nicole; Ashton, Kevin J.; Hughes, David C.

    2017-01-01

    Background 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 physica...

  5. Branding the bio/biomedical engineering degree.

    Science.gov (United States)

    Voigt, Herbert F

    2011-01-01

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

  6. From biomedical-engineering research to clinical application and industrialization

    Science.gov (United States)

    Taguchi, Tetsushi; Aoyagi, Takao

    2012-12-01

    The rising costs and aging of the population due to a low birth rate negatively affect the healthcare system in Japan. In 2011, the Council for Science and Technology Policy released the 4th Japan's Science and Technology Basic Policy Report from 2011 to 2015. This report includes two major innovations, 'Life Innovation' and 'Green Innovation', to promote economic growth. Biomedical engineering research is part of 'Life Innovation' and its outcomes are required to maintain people's mental and physical health. It has already resulted in numerous biomedical products, and new ones should be developed using nanotechnology-based concepts. The combination of accumulated knowledge and experience, and 'nanoarchitechtonics' will result in novel, well-designed functional biomaterials. This focus issue contains three reviews and 19 original papers on various biomedical topics, including biomaterials, drug-delivery systems, tissue engineering and diagnostics. We hope that it demonstrates the importance of collaboration among scientists, engineers and clinicians, and will contribute to the further development of biomedical engineering.

  7. Tacit knowledge.

    Science.gov (United States)

    Walker, Alexander Muir

    2017-04-01

    Information that is not made explicit is nonetheless embedded in most of our standard procedures. In its simplest form, embedded information may take the form of prior knowledge held by the researcher and presumed to be agreed to by consumers of the research product. More interesting are the settings in which the prior information is held unconsciously by both researcher and reader, or when the very form of an "effective procedure" incorporates its creator's (unspoken) understanding of a problem. While it may not be productive to exhaustively detail the embedded or tacit knowledge that manifests itself in creative scientific work, at least at the beginning, we may want to routinize methods for extracting and documenting the ways of thinking that make "experts" expert. We should not back away from both expecting and respecting the tacit knowledge the pervades our work and the work of others.

  8. New biomedical applications of radiocarbon

    International Nuclear Information System (INIS)

    Davis, J.C.

    1990-12-01

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

  9. Figure mining for biomedical research.

    Science.gov (United States)

    Rodriguez-Esteban, Raul; Iossifov, Ivan

    2009-08-15

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

  10. Gold Nanocages for Biomedical Applications**

    OpenAIRE

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

    2007-01-01

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

  11. Biomedical devices and their applications

    CERN Document Server

    2004-01-01

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

  12. [Cluster analysis in biomedical researches].

    Science.gov (United States)

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

    2013-01-01

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

  13. Biomedical applications of nanodiamond (Review)

    Science.gov (United States)

    Turcheniuk, K.; Mochalin, Vadym N.

    2017-06-01

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

  14. Biomedical signal and image processing.

    Science.gov (United States)

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

    2011-01-01

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

  15. Superhydrophobic Materials for Biomedical Applications

    Science.gov (United States)

    Colson, Yolonda L.; Grinstaff, Mark W.

    2016-01-01

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

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

    International Nuclear Information System (INIS)

    Phillips, M; Kalet, I; McNutt, T; Smith, W

    2014-01-01

    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 discussion 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

  17. Repeat: a framework to assess empirical reproducibility in biomedical research

    Directory of Open Access Journals (Sweden)

    Leslie D. McIntosh

    2017-09-01

    Full Text Available Abstract Background The reproducibility of research is essential to rigorous science, yet significant concerns of the reliability and verifiability of biomedical research have been recently highlighted. Ongoing efforts across several domains of science and policy are working to clarify the fundamental characteristics of reproducibility and to enhance the transparency and accessibility of research. Methods The aim of the proceeding work is to develop an assessment tool operationalizing key concepts of research transparency in the biomedical domain, specifically for secondary biomedical data research using electronic health record data. The tool (RepeAT was developed through a multi-phase process that involved coding and extracting recommendations and practices for improving reproducibility from publications and reports across the biomedical and statistical sciences, field testing the instrument, and refining variables. Results RepeAT includes 119 unique variables grouped into five categories (research design and aim, database and data collection methods, data mining and data cleaning, data analysis, data sharing and documentation. Preliminary results in manually processing 40 scientific manuscripts indicate components of the proposed framework with strong inter-rater reliability, as well as directions for further research and refinement of RepeAT. Conclusions The use of RepeAT may allow the biomedical community to have a better understanding of the current practices of research transparency and accessibility among principal investigators. Common adoption of RepeAT may improve reporting of research practices and the availability of research outputs. Additionally, use of RepeAT will facilitate comparisons of research transparency and accessibility across domains and institutions.

  18. Canadian cardiac surgeons' perspectives on biomedical innovation.

    Science.gov (United States)

    Snyman, Gretchen; Tucker, Joseph E L; Cimini, Massimo; Narine, Kishan; Fedak, Paul W M

    2012-01-01

    Barriers to successful innovation can be identified and potentially addressed by exploring the perspectives of key stakeholders in the innovation process. Cardiac surgeons in Canada were surveyed for personal perspectives on biomedical innovation. Quantitative data was obtained by questionnaire and qualitative data via interviews with selected survey participants. Surgeons were asked to self-identify into 1 of 3 categories: "innovator," "early adopter," or "late adopter," and data were compared between groups. Most surgeons viewed innovation favourably and this effect was consistent irrespective of perceived level of innovativeness. Key barriers to the innovation pathway were identified: (1) support from colleagues and institutions; (2) Canada's health system; (3) sufficient investment capital; and (4) the culture of innovation within the local environment. Knowledge of the innovation process was perceived differently based on self-reported innovativeness. The majority of surgeons did not perceive themselves as having the necessary knowledge and skills to effectively translate innovative ideas to clinical practice. In general, responses indicate support for implementation of leadership and training programs focusing on the innovation process in an effort to prepare surgeons and enhance their ability to successfully innovate and translate new therapies. The perspectives of cardiac surgeons provide an intriguing portal into the challenges and opportunities for healthcare innovation in Canada. Copyright © 2012 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.

  19. Facilities available for biomedical science research in the public universities in Lagos, Nigeria.

    Science.gov (United States)

    John, T A

    2010-03-01

    Across the world, basic medical scientists and physician scientists work on common platforms in state-of-the-arts laboratories doing translational research that occasionally results in bedside application. Biotechnology industries capitalise on useful findings for colossal profit.1 In Nigeria and the rest of Africa, biomedical science has not thrived and the contribution of publications to global high impact journals is low.2 This work investigated facilities available for modern biomedical research in Lagos public universities to extract culprit factors. The two public universities in Lagos, Nigeria were investigated by a cross sectional questionnaire survey of the technical staff manning biomedical science departments. They were asked about availability of 47 modern biomedical science research laboratory components such as cold room and microscopes and six research administration components such as director of research and grants administration. For convenient basic laboratory components such as autoclaves and balances, 50% responses indicated "well maintained and always functional" whereas for less convenient complex, high maintenance, state-of-the-arts equipment 19% responses indicated "well maintained and always functional." Respondents indicated that components of modern biomedical science research administration were 44% of expectation. The survey reveal a deficit in state-of the-arts research equipment and also a deficit in high maintenance, expensive equipment indicating that biomedical science in the investigated environment lacks the momentum of global trends and also lacks buoyant funding. In addition, administration supporting biomedical science is below expectation and may also account for the low contributions of research articles to global high impact journals.

  20. Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature

    Directory of Open Access Journals (Sweden)

    Andre Lamurias

    2017-11-01

    Full Text Available Tolerogenic cell therapies provide an alternative to conventional immunosuppressive treatments of autoimmune disease and address, among other goals, the rejection of organ or stem cell transplants. Since various methodologies can be followed to develop tolerogenic therapies, it is important to be aware and up to date on all available studies that may be relevant to their improvement. Recently, knowledge graphs have been proposed to link various sources of information, using text mining techniques. Knowledge graphs facilitate the automatic retrieval of information about the topics represented in the graph. The objective of this work was to automatically generate a knowledge graph for tolerogenic cell therapy from biomedical literature. We developed a system, ICRel, based on machine learning to extract relations between cells and cytokines from abstracts. Our system retrieves related documents from PubMed, annotates each abstract with cell and cytokine named entities, generates the possible combinations of cell–cytokine pairs cooccurring in the same sentence, and identifies meaningful relations between cells and cytokines. The extracted relations were used to generate a knowledge graph, where each edge was supported by one or more documents. We obtained a graph containing 647 cell–cytokine relations, based on 3,264 abstracts. The modules of ICRel were evaluated with cross-validation and manual evaluation of the relations extracted. The relation extraction module obtained an F-measure of 0.789 in a reference database, while the manual evaluation obtained an accuracy of 0.615. Even though the knowledge graph is based on information that was already published in other articles about immunology, the system we present is more efficient than the laborious task of manually reading all the literature to find indirect or implicit relations. The ICRel graph will help experts identify implicit relations that may not be evident in published studies.

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

    Science.gov (United States)

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

    2016-12-01

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

  2. Integrating Ontological Knowledge and Textual Evidence in Estimating Gene and Gene Product Similarity

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-08

    With the rising influence of the Gene On-tology, new approaches have emerged where the similarity between genes or gene products is obtained by comparing Gene Ontology code annotations associ-ated with them. So far, these approaches have solely relied on the knowledge en-coded in the Gene Ontology and the gene annotations associated with the Gene On-tology database. The goal of this paper is to demonstrate that improvements to these approaches can be obtained by integrating textual evidence extracted from relevant biomedical literature.

  3. Matching biomedical ontologies based on formal concept analysis.

    Science.gov (United States)

    Zhao, Mengyi; Zhang, Songmao; Li, Weizhuo; Chen, Guowei

    2018-03-19

    The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign

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

    Science.gov (United States)

    Yu, Hong; Agarwal, Shashank; Frid, Nadya

    2009-11-01

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

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

    Science.gov (United States)

    Huang, Zhong

    2014-01-01

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

  6. Biomedical Impact in Implantable Devices-The Transcatheter Aortic Valve as an example

    Science.gov (United States)

    Anastasiou, Alexandros; Saatsakis, George

    2015-09-01

    Objective: To update of the scientific community about the biomedical engineering involvement in the implantable devices chain. Moreover the transcatheter Aortic Valve (TAV) replacement, in the field of cardiac surgery, will be analyzed as an example of contemporary implantable technology. Methods: A detailed literature review regarding biomedical engineers participating in the implantable medical product chain, starting from the design of the product till the final implantation technique. Results: The scientific role of biomedical engineers has clearly been established. Certain parts of the product chain are implemented almost exclusively by experienced biomedical engineers such as the transcatheter aortic valve device. The successful professional should have a multidisciplinary knowledge, including medicine, in order to pursue the challenges for such intuitive technology. This clearly indicates that biomedical engineers are among the most appropriate scientists to accomplish such tasks. Conclusions: The biomedical engineering involvement in medical implantable devices has been widely accepted by the scientific community, worldwide. Its important contribution, starting from the design and extended to the development, clinical trials, scientific support, education of other scientists (surgeons, cardiologists, technicians etc.), and even to sales, makes biomedical engineers a valuable player in the scientific arena. Notably, the sector of implantable devices is constantly raising, as emerging technologies continuously set up new targets.

  7. The next generation of similarity measures that fully explore the semantics in biomedical ontologies.

    Science.gov (United States)

    Couto, Francisco M; Pinto, H Sofia

    2013-10-01

    There is a prominent trend to augment and improve the formality of biomedical ontologies. For example, this is shown by the current effort on adding description logic axioms, such as disjointness. One of the key ontology applications that can take advantage of this effort is the conceptual (functional) similarity measurement. The presence of description logic axioms in biomedical ontologies make the current structural or extensional approaches weaker and further away from providing sound semantics-based similarity measures. Although beneficial in small ontologies, the exploration of description logic axioms by semantics-based similarity measures is computational expensive. This limitation is critical for biomedical ontologies that normally contain thousands of concepts. Thus in the process of gaining their rightful place, biomedical functional similarity measures have to take the journey of finding how this rich and powerful knowledge can be fully explored while keeping feasible computational costs. This manuscript aims at promoting and guiding the development of compelling tools that deliver what the biomedical community will require in a near future: a next-generation of biomedical similarity measures that efficiently and fully explore the semantics present in biomedical ontologies.

  8. Knowledge about knowledge

    International Nuclear Information System (INIS)

    Ramm, Hans Henrik

    2006-01-01

    Technology and knowledge make up the knowledge capital that has been so essential to the oil and gas industry's value creation, competitiveness and internationalization. Report prepared for the Norwegian Oil Industry Association (OLF) and The Norwegian Society of Chartered Technical and Scientific Professionals (Tekna), on the Norwegian petroleum cluster as an environment for creating knowledge capital from human capital, how fiscal and other framework conditions may influence the building of knowledge capital, the long-term perspectives for the petroleum cluster, what Norwegian society can learn from the experiences in the petroleum cluster, and the importance of gaining more knowledge about the functionality of knowledge for increased value creation (author) (ml)

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

    Science.gov (United States)

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

    2018-01-01

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

  10. Tritium AMS for biomedical applications

    International Nuclear Information System (INIS)

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

    1993-08-01

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

  11. Luminescent nanodiamonds for biomedical applications.

    Science.gov (United States)

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

    2011-12-01

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

  12. Thermoresponsive Polymers for Biomedical Applications

    Directory of Open Access Journals (Sweden)

    Theoni K. Georgiou

    2011-08-01

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

  13. An introduction to biomedical instrumentation

    CERN Document Server

    Dewhurst, D J

    1976-01-01

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

  14. Review of Biomedical Image Processing

    Directory of Open Access Journals (Sweden)

    Ciaccio Edward J

    2011-11-01

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

  15. Introduction to biomedical engineering technology

    CERN Document Server

    Street, Laurence J

    2011-01-01

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

  16. Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.

    Science.gov (United States)

    Müller, H-M; Van Auken, K M; Li, Y; Sternberg, P W

    2018-03-09

    The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. We describe the next generation of the Textpresso information retrieval system, Textpresso Central (TPC). TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C. elegans bibliography. In addition, TPC allows users to create a customized corpus by uploading and processing documents of their choosing. TPC is UIMA compliant, to facilitate compatibility with external processing modules, and takes advantage of Lucene indexing and search technology for efficient handling of millions of full text documents. Like Textpresso, TPC searches can be performed using keywords and/or categories (semantically related groups of terms), but to provide better context for interpreting and validating queries, search results may now be viewed as highlighted passages in the context of full text. To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements

  17. Basics of biomedical ultrasound for engineers

    CERN Document Server

    Azhari, Haim

    2010-01-01

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

  18. Mathematics and physics of emerging biomedical imaging

    National Research Council Canada - National Science Library

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

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

  19. Frontiers in biomedical engineering and biotechnology.

    Science.gov (United States)

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

    2014-01-01

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

  20. Telemedicine optoelectronic biomedical data processing system

    Science.gov (United States)

    Prosolovska, Vita V.

    2010-08-01

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

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

    Science.gov (United States)

    Fu, Jian; Tan, Renbo

    2014-01-01

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

  2. Biomedical information retrieval across languages.

    Science.gov (United States)

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

    2007-06-01

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

  3. Biomedical applications of control engineering

    CERN Document Server

    Hacısalihzade, Selim S

    2013-01-01

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

  4. Reviewing Manuscripts for Biomedical Journals

    Science.gov (United States)

    Garmel, Gus M

    2010-01-01

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

  5. An Overview of Biomolecular Event Extraction from Scientific Documents.

    Science.gov (United States)

    Vanegas, Jorge A; Matos, Sérgio; González, Fabio; Oliveira, José L

    2015-01-01

    This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed.

  6. An Overview of Biomolecular Event Extraction from Scientific Documents

    Directory of Open Access Journals (Sweden)

    Jorge A. Vanegas

    2015-01-01

    Full Text Available This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed.

  7. Visualization and classification in biomedical terahertz pulsed imaging

    International Nuclear Information System (INIS)

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

    2002-01-01

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

  8. A method for named entity normalization in biomedical articles: application to diseases and plants.

    Science.gov (United States)

    Cho, Hyejin; Choi, Wonjun; Lee, Hyunju

    2017-10-13

    In biomedical articles, a named entity recognition (NER) technique that identifies entity names from texts is an important element for extracting biological knowledge from articles. After NER is applied to articles, the next step is to normalize the identified names into standard concepts (i.e., disease names are mapped to the National Library of Medicine's Medical Subject Headings disease terms). In biomedical articles, many entity normalization methods rely on domain-specific dictionaries for resolving synonyms and abbreviations. However, the dictionaries are not comprehensive except for some entities such as genes. In recent years, biomedical articles have accumulated rapidly, and neural network-based algorithms that incorporate a large amount of unlabeled data have shown considerable success in several natural language processing problems. In this study, we propose an approach for normalizing biological entities, such as disease names and plant names, by using word embeddings to represent semantic spaces. For diseases, training data from the National Center for Biotechnology Information (NCBI) disease corpus and unlabeled data from PubMed abstracts were used to construct word representations. For plants, a training corpus that we manually constructed and unlabeled PubMed abstracts were used to represent word vectors. We showed that the proposed approach performed better than the use of only the training corpus or only the unlabeled data and showed that the normalization accuracy was improved by using our model even when the dictionaries were not comprehensive. We obtained F-scores of 0.808 and 0.690 for normalizing the NCBI disease corpus and manually constructed plant corpus, respectively. We further evaluated our approach using a data set in the disease normalization task of the BioCreative V challenge. When only the disease corpus was used as a dictionary, our approach significantly outperformed the best system of the task. The proposed approach shows robust

  9. Journal of Medicine and Biomedical Research - Vol 14, No 1 (2015)

    African Journals Online (AJOL)

    Journal of Medicine and Biomedical Research - Vol 14, No 1 (2015) ... Histopathological effects of oral and subcutaneous administration of Roselle Calyx ... Ameliorative effect of Vitamin C on lead induced hepatotoxicty in rats · EMAIL ... Effect of Hibiscus sabdariffa calyx extract on stressed rabbit plasma cholesterol status ...

  10. Bioethical Principles of Biomedical Research Involving Animals

    Directory of Open Access Journals (Sweden)

    Bakir Mehić

    2011-08-01

    animals for research, testing, or training in different countries. In the few that have done so, the measures adopted vary widely: on the one hand, legally enforceable detailed regulations with licensing of experimenters and their premises together with an official inspectorate; on the other, entirely voluntary self-regulation by the biomedical community, with lay participation. Many variations are possible between these extremes, one intermediate situation being a legal requirement that experiments or other procedures involving the use of animals should be subject to the approval of ethical committees of specified composition.The International Guiding Principles are the product of the collaboration of a representative sample of the international biomedical community, including experts of the World Health Organization, and of consultations with responsible animal welfare groups. The International Guiding Principles have already gained a considerable measure of acceptance internationally. European Medical Research Councils (EMRC, an international association that includes all the West European medical research councils, fully endorsed the Guiding Principles in 1984. Here we bring the basic bioethical principles for using animals in biomedical research[3]: Methods such as mathematical models, computer simulation and in vitro biological systems should be used wherever appropriate,Animal experiments should be undertaken only after due consideration of their relevance for human or animal health and the advancement of biological knowledge,The animals selected for an experiment should be of an appropriate species and quality, and the minimum number required to obtain scientifically valid results,Investigators and other personnel should never fail to treat animals as sentient, and should regard their proper care and use and the avoidance or minimization of discomfort, distress, or pain as ethical imperatives,Procedures with animals that may cause more than momentary or minimal

  11. An unsupervised strategy for biomedical image segmentation

    Directory of Open Access Journals (Sweden)

    Roberto Rodríguez

    2010-09-01

    Full Text Available Roberto Rodríguez1, Rubén Hernández21Digital Signal Processing Group, Institute of Cybernetics, Mathematics, and Physics, Havana, Cuba; 2Interdisciplinary Professional Unit of Engineering and Advanced Technology, IPN, MexicoAbstract: Many segmentation techniques have been published, and some of them have been widely used in different application problems. Most of these segmentation techniques have been motivated by specific application purposes. Unsupervised methods, which do not assume any prior scene knowledge can be learned to help the segmentation process, and are obviously more challenging than the supervised ones. In this paper, we present an unsupervised strategy for biomedical image segmentation using an algorithm based on recursively applying mean shift filtering, where entropy is used as a stopping criterion. This strategy is proven with many real images, and a comparison is carried out with manual segmentation. With the proposed strategy, errors less than 20% for false positives and 0% for false negatives are obtained.Keywords: segmentation, mean shift, unsupervised segmentation, entropy

  12. Open Biomedical Engineering education in Africa.

    Science.gov (United States)

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

    2015-08-01

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

  13. Light Ion Biomedical Research Accelerator LIBRA

    International Nuclear Information System (INIS)

    Gough, R.A.

    1987-01-01

    LIBRA is a concept to place a light-ion, charged-particle facility in a hospital environment, and to dedicate it to applications in biology and medicine. There are two aspects of the program envisaged for LIBRA: a basic research effort coupled with a program in clinical applications of accelerated charged particles. The operational environment to be provided for LIBRA is one in which both of these components can coexist and flourish, and one that will promote the transfer of technology and knowledge from one to the other. In order to further investigate the prospects for a Light Ion Biomedical Research Accelerator (LIBRA), discussions are underway with the Merritt Peralta Medical Center MPMC) in Oakland CA, and the University of California at San Francisco (UCSF). In this paper, a brief discussion of the technical requirements for such a facility is given, together with an outline of the accelerator technology required. While still in a preliminary stage, it is possible nevertheless to develop an adequate working description of the type, size, performance and cost of the accelerator facilities required to meet the preliminary goals for LIBRA

  14. The Light Ion Biomedical Research Accelerator (LIBRA)

    International Nuclear Information System (INIS)

    Gough, R.A.

    1987-03-01

    LIBRA is a concept to place a light-ion, charged-particle facility in a hospital environment, and to dedicate it to applications in biology and medicine. There are two aspects of the program envisaged for LIBRA: a basic research effort coupled with a program in clinical applications of accelerated charged particles. The operational environment to be provided for LIBRA is one in which both of these components can coexist and flourish, and one that will promote the transfer of technology and knowledge from one to the other. In order to further investigate the prospects for a Light Ion Biomedical Research Accelerator (LIBRA), discussions are underway with the Merritt Peralta Medical Center (MPMC) in Oakland, California, and the University of California at San Francisco (UCSF). In this paper, a brief discussion of the technical requirements for such a facility is given, together with an outline of the accelerator technology required. While still in a preliminary stage, it is possible nevertheless to develop an adequate working description of the type, size, performance and cost of the accelerator facilities required to meet the preliminary goals for LIBRA

  15. Biomedical laboratories: architecture and radioprotection principles

    International Nuclear Information System (INIS)

    Lapa, Renata

    2005-01-01

    In institutions where biological research are made and some technologies make use of radioisotope, the radiation protection is an issue of biosecurity for conceptual reasons. In the process of architectural design of Biomedical Laboratories, engineering and architecture reveal interfaces with other areas of knowledge and specific concepts. Exploring the role of architectural design in favor of personal and environmental protection in biological containment laboratories that handle non-sealed sources in research, the work discusses the triad that compose the principle of containment in health environments: best practices, protective equipment, physical facilities, with greater emphasis on the latter component. The shortcomings of the design process are reflected in construction and in use-operation and maintenance of these buildings, with direct consequences on the occupational health and safety, environmental and credibility of work processes. In this context, the importance of adoption of alternatives to improve the design process is confirmed, taking into account the early consideration of several variables involved and providing subsidies to the related laboratories . The research, conducted at FIOCRUZ - a Brazilian health institution, developed from the analysis of the participants in the architectural project, aiming at the formulation of design guidelines which could contribute to the rationalisation of this kind of building construction

  16. Archives of Medical and Biomedical Research

    African Journals Online (AJOL)

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

  17. A new educational program on biomedical engineering

    NARCIS (Netherlands)

    van Alste, Jan A.

    2000-01-01

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

  18. Sierra Leone Journal of Biomedical Research

    African Journals Online (AJOL)

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

  19. KnowEnG: a knowledge engine for genomics.

    Science.gov (United States)

    Sinha, Saurabh; Song, Jun; Weinshilboum, Richard; Jongeneel, Victor; Han, Jiawei

    2015-11-01

    We describe here the vision, motivations, and research plans of the National Institutes of Health Center for Excellence in Big Data Computing at the University of Illinois, Urbana-Champaign. The Center is organized around the construction of "Knowledge Engine for Genomics" (KnowEnG), an E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data. The scientist will come to KnowEnG with their own data sets in the form of spreadsheets and ask KnowEnG to analyze those data sets in the light of a massive knowledge base of community data sets called the "Knowledge Network" that will be at the heart of the system. The Center is undertaking discovery projects aimed at testing the utility of KnowEnG for transforming big data to knowledge. These projects span a broad range of biological enquiry, from pharmacogenomics (in collaboration with Mayo Clinic) to transcriptomics of human behavior. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. Challenges for automatically extracting molecular interactions from full-text articles.

    Science.gov (United States)

    McIntosh, Tara; Curran, James R

    2009-09-24

    The increasing availability of full-text biomedical articles will allow more biomedical knowledge to be extracted automatically with greater reliability. However, most Information Retrieval (IR) and Extraction (IE) tools currently process only abstracts. The lack of corpora has limited the development of tools that are capable of exploiting the knowledge in full-text articles. As a result, there has been little investigation into the advantages of full-text document structure, and the challenges developers will face in processing full-text articles. We manually annotated passages from full-text articles that describe interactions summarised in a Molecular Interaction Map (MIM). Our corpus tracks the process of identifying facts to form the MIM summaries and captures any factual dependencies that must be resolved to extract the fact completely. For example, a fact in the results section may require a synonym defined in the introduction. The passages are also annotated with negated and coreference expressions that must be resolved.We describe the guidelines for identifying relevant passages and possible dependencies. The corpus includes 2162 sentences from 78 full-text articles. Our corpus analysis demonstrates the necessity of full-text processing; identifies the article sections where interactions are most commonly stated; and quantifies the proportion of interaction statements requiring coherent dependencies. Further, it allows us to report on the relative importance of identifying synonyms and resolving negated expressions. We also experiment with an oracle sentence retrieval system using the corpus as a gold-standard evaluation set. We introduce the MIM corpus, a unique resource that maps interaction facts in a MIM to annotated passages within full-text articles. It is an invaluable case study providing guidance to developers of biomedical IR and IE systems, and can be used as a gold-standard evaluation set for full-text IR tasks.

  1. Reusing Design Knowledge Based on Design Cases and Knowledge Map

    Science.gov (United States)

    Yang, Cheng; Liu, Zheng; Wang, Haobai; Shen, Jiaoqi

    2013-01-01

    Design knowledge was reused for innovative design work to support designers with product design knowledge and help designers who lack rich experiences to improve their design capacity and efficiency. First, based on the ontological model of product design knowledge constructed by taxonomy, implicit and explicit knowledge was extracted from some…

  2. Publishing priorities of biomedical research funders

    Science.gov (United States)

    Collins, Ellen

    2013-01-01

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

  3. Applications of computational intelligence in biomedical technology

    CERN Document Server

    Majernik, Jaroslav; Pancerz, Krzysztof; Zaitseva, Elena

    2016-01-01

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

  4. Piezoelectric nanomaterials for biomedical applications

    CERN Document Server

    Menciassi, Arianna

    2012-01-01

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

  5. Magnetite nanoparticles for biomedical applications

    International Nuclear Information System (INIS)

    Sora, Sergiu; Ion, Rodica Mariana

    2010-01-01

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

  6. FULERENIC MATERIALS WITH BIOMEDICAL APPLICATIONS

    Directory of Open Access Journals (Sweden)

    Radu Claudiu FIERASCU

    2010-05-01

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

  7. Biomedical Wireless Ambulatory Crew Monitor

    Science.gov (United States)

    Chmiel, Alan; Humphreys, Brad

    2009-01-01

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

  8. Application of an efficient Bayesian discretization method to biomedical data

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2011-07-01

    Full Text Available Abstract Background Several data mining methods require data that are discrete, and other methods often perform better with discrete data. We introduce an efficient Bayesian discretization (EBD method for optimal discretization of variables that runs efficiently on high-dimensional biomedical datasets. The EBD method consists of two components, namely, a Bayesian score to evaluate discretizations and a dynamic programming search procedure to efficiently search the space of possible discretizations. We compared the performance of EBD to Fayyad and Irani's (FI discretization method, which is commonly used for discretization. Results On 24 biomedical datasets obtained from high-throughput transcriptomic and proteomic studies, the classification performances of the C4.5 classifier and the naïve Bayes classifier were statistically significantly better when the predictor variables were discretized using EBD over FI. EBD was statistically significantly more stable to the variability of the datasets than FI. However, EBD was less robust, though not statistically significantly so, than FI and produced slightly more complex discretizations than FI. Conclusions On a range of biomedical datasets, a Bayesian discretization method (EBD yielded better classification performance and stability but was less robust than the widely used FI discretization method. The EBD discretization method is easy to implement, permits the incorporation of prior knowledge and belief, and is sufficiently fast for application to high-dimensional data.

  9. Titanium nanostructures for biomedical applications

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  10. Titanium nanostructures for biomedical applications

    Science.gov (United States)

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

    2015-02-01

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

  11. An improved rank based disease prediction using web navigation patterns on bio-medical databases

    Directory of Open Access Journals (Sweden)

    P. Dhanalakshmi

    2017-12-01

    Full Text Available Applying machine learning techniques to on-line biomedical databases is a challenging task, as this data is collected from large number of sources and it is multi-dimensional. Also retrieval of relevant document from large repository such as gene document takes more processing time and an increased false positive rate. Generally, the extraction of biomedical document is based on the stream of prior observations of gene parameters taken at different time periods. Traditional web usage models such as Markov, Bayesian and Clustering models are sensitive to analyze the user navigation patterns and session identification in online biomedical database. Moreover, most of the document ranking models on biomedical database are sensitive to sparsity and outliers. In this paper, a novel user recommendation system was implemented to predict the top ranked biomedical documents using the disease type, gene entities and user navigation patterns. In this recommendation system, dynamic session identification, dynamic user identification and document ranking techniques were used to extract the highly relevant disease documents on the online PubMed repository. To verify the performance of the proposed model, the true positive rate and runtime of the model was compared with that of traditional static models such as Bayesian and Fuzzy rank. Experimental results show that the performance of the proposed ranking model is better than the traditional models.

  12. Applying Knowledge on Collagen of CLRI: In Human Health Care

    Indian Academy of Sciences (India)

    Applying Knowledge on Collagen of CLRI: In Human Health Care ... Kollagen & NeuSkin are products in the market based on technologies. ... derived products of biomedical value in tissue remodeling and engineering are in advanced stage ...

  13. Education of biomedical engineering in Taiwan.

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2018-04-10

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

  15. Pattern recognition and expert image analysis systems in biomedical image processing (Invited Paper)

    Science.gov (United States)

    Oosterlinck, A.; Suetens, P.; Wu, Q.; Baird, M.; F. M., C.

    1987-09-01

    This paper gives an overview of pattern recoanition techniques (P.R.) used in biomedical image processing and problems related to the different P.R. solutions. Also the use of knowledge based systems to overcome P.R. difficulties, is described. This is illustrated by a common example ofabiomedical image processing application.

  16. De la extracción al modelado del conocimiento en un Sistema Basado en el Conocimiento. Un enfoque desde el agrupamiento conceptual lógico combinatorio (From the extraction to knowledge modeling in a Knowledge Based System. A logical combinatorial conceptual grouping approach

    Directory of Open Access Journals (Sweden)

    Yunia Reyes González

    2017-10-01

    acquisition process required in a knowledge-based system can be automated or partially automated. The idea is to reduce the working time between the knowledge engineer and the knowledge expert in the intelligent computer system that is to be built. This paper presents the potential of logical combinatorial grouping for both extraction and knowledge modeling in the construction of this type of computer systems. Three specific cases of Knowledge Based Systems are presented in which concepts are used in their essential processes: how to represent the knowledge and method of solving the problem. This approach allows, among other advantages, the automation of knowledge extraction process which makes it possible to separate it from human experts and bring the Knowledge Based Systems theory to more current paradigms where techniques like Big Data are applied.

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

    Directory of Open Access Journals (Sweden)

    J. Rajeswari

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

  18. Enhancing biomedical design with design thinking.

    Science.gov (United States)

    Kemnitzer, Ronald; Dorsa, Ed

    2009-01-01

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

  19. Biomedical Optical Imaging Technologies Design and Applications

    CERN Document Server

    2013-01-01

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

  20. OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

    Directory of Open Access Journals (Sweden)

    Johnson Helen L

    2008-01-01

    Full Text Available Abstract Background Information extraction (IE efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a diverse literature. Here we report on the design, implementation and several evaluations of OpenDMAP, an ontology-driven, integrated concept analysis system. It significantly advances the state of the art in information extraction by leveraging knowledge in ontological resources, integrating diverse text processing applications, and using an expanded pattern language that allows the mixing of syntactic and semantic elements and variable ordering. Results OpenDMAP information extraction systems were produced for extracting protein transport assertions (transport, protein-protein interaction assertions (interaction and assertions that a gene is expressed in a cell type (expression. Evaluations were performed on each system, resulting in F-scores ranging from .26 – .72 (precision .39 – .85, recall .16 – .85. Additionally, each of these systems was run over all abstracts in MEDLINE, producing a total of 72,460 transport instances, 265,795 interaction instances and 176,153 expression instances. Conclusion OpenDMAP advances the performance standards for extracting protein-protein interaction predications from the full texts of biomedical research articles. Furthermore, this level of performance appears to generalize to other information extraction tasks, including extracting information about predicates of more than two arguments. The output of the information extraction system is always constructed from elements of an ontology, ensuring that the knowledge representation is grounded with respect to a carefully constructed model of reality. The results of these efforts can be used to increase the efficiency of manual curation efforts and to provide additional features in systems that integrate multiple sources for

  1. A Pilot Study of Biomedical Text Comprehension using an Attention-Based Deep Neural Reader: Design and Experimental Analysis.

    Science.gov (United States)

    Kim, Seongsoon; Park, Donghyeon; Choi, Yonghwa; Lee, Kyubum; Kim, Byounggun; Jeon, Minji; Kim, Jihye; Tan, Aik Choon; Kang, Jaewoo

    2018-01-05

    With the development of artificial intelligence (AI) technology centered on deep-learning, the computer has evolved to a point where it can read a given text and answer a question based on the context of the text. Such a specific task is known as the task of machine comprehension. Existing machine comprehension tasks mostly use datasets of general texts, such as news articles or elementary school-level storybooks. However, no attempt has been made to determine whether an up-to-date deep learning-based machine comprehension model can also process scientific literature containing expert-level knowledge, especially in the biomedical domain. This study aims to investigate whether a machine comprehension model can process biomedical articles as well as general texts. Since there is no dataset for the biomedical literature comprehension task, our work includes generating a large-scale question answering dataset using PubMed and manually evaluating the generated dataset. We present an attention-based deep neural model tailored to the biomedical domain. To further enhance the performance of our model, we used a pretrained word vector and biomedical entity type embedding. We also developed an ensemble method of combining the results of several independent models to reduce the variance of the answers from the models. The experimental results showed that our proposed deep neural network model outperformed the baseline model by more than 7% on the new dataset. We also evaluated human performance on the new dataset. The human evaluation result showed that our deep neural model outperformed humans in comprehension by 22% on average. In this work, we introduced a new task of machine comprehension in the biomedical domain using a deep neural model. Since there was no large-scale dataset for training deep neural models in the biomedical domain, we created the new cloze-style datasets Biomedical Knowledge Comprehension Title (BMKC_T) and Biomedical Knowledge Comprehension Last

  2. Technical editing of research reports in biomedical journals.

    Science.gov (United States)

    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

  3. Application of an automated natural language processing (NLP) workflow to enable federated search of external biomedical content in drug discovery and development.

    Science.gov (United States)

    McEntire, Robin; Szalkowski, Debbie; Butler, James; Kuo, Michelle S; Chang, Meiping; Chang, Man; Freeman, Darren; McQuay, Sarah; Patel, Jagruti; McGlashen, Michael; Cornell, Wendy D; Xu, Jinghai James

    2016-05-01

    External content sources such as MEDLINE(®), National Institutes of Health (NIH) grants and conference websites provide access to the latest breaking biomedical information, which can inform pharmaceutical and biotechnology company pipeline decisions. The value of the sites for industry, however, is limited by the use of the public internet, the limited synonyms, the rarity of batch searching capability and the disconnected nature of the sites. Fortunately, many sites now offer their content for download and we have developed an automated internal workflow that uses text mining and tailored ontologies for programmatic search and knowledge extraction. We believe such an efficient and secure approach provides a competitive advantage to companies needing access to the latest information for a range of use cases and complements manually curated commercial sources. Copyright © 2016. Published by Elsevier Ltd.

  4. Gold Nanocages for Biomedical Applications**

    Science.gov (United States)

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

    2008-01-01

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

  5. Gold Nanocages for Biomedical Applications.

    Science.gov (United States)

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

    2007-10-17

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

  6. Relational Databases and Biomedical Big Data.

    Science.gov (United States)

    de Silva, N H Nisansa D

    2017-01-01

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

  7. NIH/NSF accelerate biomedical research innovations

    Science.gov (United States)

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

  8. Handbook of photonics for biomedical engineering

    CERN Document Server

    Kim, Donghyun; Somekh, Michael

    2017-01-01

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

  9. VII Latin American Congress on Biomedical Engineering

    CERN Document Server

    Bustamante, John; Sierra, Daniel

    2017-01-01

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

  10. International Journal of Medicine and Biomedical Research

    African Journals Online (AJOL)

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

  11. Sierra Leone Journal of Biomedical Research

    African Journals Online (AJOL)

    MHRL

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

  12. VI Latin American Congress on Biomedical Engineering

    CERN Document Server

    Hadad, Alejandro

    2015-01-01

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

  13. Distributed System for Spaceflight Biomedical Support

    Data.gov (United States)

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

  14. Journal of Medical and Biomedical Sciences

    African Journals Online (AJOL)

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

  15. A Program on Biochemical and Biomedical Engineering.

    Science.gov (United States)

    San, Ka-Yiu; McIntire, Larry V.

    1989-01-01

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

  16. NICHD Biomedical Mass Spectrometry Core Facility

    Data.gov (United States)

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

  17. Computer vision for biomedical image applications. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-07-01

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

  18. A review of extractions of seaweed hydrocolloids: Properties and applications

    Directory of Open Access Journals (Sweden)

    H. P. S. Abdul Khalil

    2018-04-01

    Full Text Available The term hydrocolloid generally refers to substances that form gels or provide viscous dispersion in the presence of water. Alginate, agar, and carrageenan are three commercially valuable hydrocolloids derived from certain brown and red seaweed and each has their distinct physicochemical properties (i.e. functional and bioactive. Various applications of these seaweed hydrocolloids as thickeners, stabilizers, coagulants and salves (in the wound and burn dressings and materials to produce bio-medical impressions in the food, pharmaceutical, and biotechnology industries are highlighted in this review. Although the existing industrial methods of extraction for these seaweed hydrocolloids are well-established, still growing demand has exposed certain limitations of those methods, notably efficiency and product consistency. In order to achieve targeted hydrocolloids for specific purposes and functionalities, some novel and green extraction methods have also been proposed and discussed. Microwave-assisted extraction (MAE, ultrasound-assisted extraction (UAE, enzyme-assisted extraction (EAE, supercritical fluid extraction (SFE, pressurized solvent extractions (PSE, reactive extrusion and photobleaching process are selectively presented as highly promising candidates that can avoid the use of chemicals and provide novel means of access to seaweed hydrocolloids with both economic and environmental benefits. However, this review does not provide the ‘best’ method or procedure as many are still under development. Hence, the review gives ‘food for thought’as to new processes which might be adopted industrially and concluded that further research is required in order to contribute additional new knowledge and refinement to this field of study.

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

    Science.gov (United States)

    Lopes, Pedro; Oliveira, José Luís

    2012-12-17

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

  20. Semiconducting silicon nanowires for biomedical applications

    CERN Document Server

    Coffer, JL

    2014-01-01

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

  1. Statistics and Biomedical Informatics in Forensic Sciences

    Czech Academy of Sciences Publication Activity Database

    Zvárová, Jana

    2009-01-01

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

  2. European virtual campus for biomedical engineering EVICAB.

    Science.gov (United States)

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

    2007-01-01

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

  3. Advanced computational approaches to biomedical engineering

    CERN Document Server

    Saha, Punam K; Basu, Subhadip

    2014-01-01

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

  4. Biomedical Applications of Enzymes From Marine Actinobacteria.

    Science.gov (United States)

    Kamala, K; Sivaperumal, P

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

  5. Biomedical photonics handbook therapeutics and advanced biophotonics

    CERN Document Server

    Vo-Dinh, Tuan

    2014-01-01

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

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

    Science.gov (United States)

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

    2017-02-28

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

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

    Science.gov (United States)

    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.

  8. Exploring subdomain variation in biomedical language

    Directory of Open Access Journals (Sweden)

    Séaghdha Diarmuid Ó

    2011-05-01

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

  9. Writing intelligible English prose for biomedical journals.

    Science.gov (United States)

    Ludbrook, John

    2007-01-01

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

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

    Science.gov (United States)

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

    2009-01-06

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

  11. A methodology for extracting knowledge rules from artificial neural networks applied to forecast demand for electric power; Uma metodologia para extracao de regras de conhecimento a partir de redes neurais artificiais aplicadas para previsao de demanda por energia eletrica

    Energy Technology Data Exchange (ETDEWEB)

    Steinmetz, Tarcisio; Souza, Glauber; Ferreira, Sandro; Santos, Jose V. Canto dos; Valiati, Joao [Universidade do Vale do Rio dos Sinos (PIPCA/UNISINOS), Sao Leopoldo, RS (Brazil). Programa de Pos-Graduacao em Computacao Aplicada], Emails: trsteinmetz@unisinos.br, gsouza@unisinos.br, sferreira, jvcanto@unisinos.br, jfvaliati@unisinos.br

    2009-07-01

    We present a methodology for the extraction of rules from Artificial Neural Networks (ANN) trained to forecast the electric load demand. The rules have the ability to express the knowledge regarding the behavior of load demand acquired by the ANN during the training process. The rules are presented to the user in an easy to read format, such as IF premise THEN consequence. Where premise relates to the input data submitted to the ANN (mapped as fuzzy sets), and consequence appears as a linear equation describing the output to be presented by the ANN, should the premise part holds true. Experimentation demonstrates the method's capacity for acquiring and presenting high quality rules from neural networks trained to forecast electric load demand for several amounts of time in the future. (author)

  12. Eleven quick tips for architecting biomedical informatics workflows with cloud computing.

    Science.gov (United States)

    Cole, Brian S; Moore, Jason H

    2018-03-01

    Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world's largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction.

  13. Current biomedical waste management practices and cross-infection control procedures of dentists in India.

    Science.gov (United States)

    Singh, Balendra Pratap; Khan, Suleman A; Agrawal, Neeraj; Siddharth, Ramashanker; Kumar, Lakshya

    2012-06-01

    To investigate the knowledge, attitudes and behaviour of dentists working in dental clinics and dental hospitals regarding biomedical waste management and cross-infection control. A national survey was conducted. Self-administered questionnaires were sent to 800 dentists across India. A total of 494 dentists responded, giving a response rate of 61.8%. Of these, 228 of 323 (70.6%) general dentists reported using boiling water as a sterilising medium and 339 (68.6%) dentists reported disposing of hazardous waste such as syringes, blades and ampoules in dustbins and emptying these into municipal corporation bins. Dentists should undergo continuing education programmes on biomedical waste management and infection control guidelines. Greater cooperation between dental clinics and hospitals and pollution control boards is needed to ensure the proper handling and disposal of biomedical waste. © 2012 FDI World Dental Federation.

  14. The role of a creative "joint assignment" project in biomedical engineering bachelor degree education.

    Science.gov (United States)

    Jiehui Jiang; Yuting Zhang; Mi Zhou; Xiaosong Zheng; Zhuangzhi Yan

    2017-07-01

    Biomedical Engineering (BME) bachelor education aims to train qualified engineers who devote themselves to addressing biological and medical problems by integrating the technological, medical and biological knowledge. Design thinking and teamwork with other disciplines are necessary for biomedical engineers. In the current biomedical engineering education system of Shanghai University (SHU), however, such design thinking and teamwork through a practical project is lacking. This paper describes a creative "joint assignment" project in Shanghai University, China, which has provided BME bachelor students a two-year practical experience to work with students from multidisciplinary departments including sociology, mechanics, computer sciences, business and art, etc. To test the feasibility of this project, a twenty-month pilot project has been carried out from May 2015 to December 2016. The results showed that this pilot project obviously enhanced competitive power of BME students in Shanghai University, both in the capabilities of design thinking and teamwork.

  15. The structure of surface texture knowledge

    International Nuclear Information System (INIS)

    Yan Wang; Scott, Paul J; Jiang Xiangqian

    2005-01-01

    This research aims to create an intelligent knowledge-based system for engineering and bio-medical engineering surface texture, which will provide expert knowledge of surface texture to link surface function, specification of micro- and nano-geometry through manufacture, and verification. The intelligent knowledge base should be capable of incorporating knowledge from multiple sources (standards, books, experts, etc), adding new knowledge from these sources and still remain a coherent reliable system. A new data model based on category theory will be adopted to construct this system

  16. Prayer Camps and Biomedical Care in Ghana: Is Collaboration in Mental Health Care Possible?

    Science.gov (United States)

    Arias, Daniel; Taylor, Lauren; Ofori-Atta, Angela; Bradley, Elizabeth H

    2016-01-01

    engaging with prayer camps to expand access to clinical care for patients residing in the camps. The findings demonstrate that biomedical care providers are interested in engaging with prayer camps. Key areas where partnerships may best improve conditions for patients at prayer camps include collaborating on creating safe and secure physical spaces and delivering medication for mental illness to patients living in prayer camps. However, while prayer camp staff are willing to engage biomedical knowledge, deeply held beliefs and routine practices of faith and biomedical healers are difficult to reconcile Additional discussion is needed to find the common ground on which the scarce resources for mental health care in Ghana can collaborate most effectively.

  17. BioN∅T: A searchable database of biomedical negated sentences

    Directory of Open Access Journals (Sweden)

    Agarwal Shashank

    2011-10-01

    Full Text Available Abstract Background Negated biomedical events are often ignored by text-mining applications; however, such events carry scientific significance. We report on the development of BioN∅T, a database of negated sentences that can be used to extract such negated events. Description Currently BioN∅T incorporates ≈32 million negated sentences, extracted from over 336 million biomedical sentences from three resources: ≈2 million full-text biomedical articles in Elsevier and the PubMed Central, as well as ≈20 million abstracts in PubMed. We evaluated BioN∅T on three important genetic disorders: autism, Alzheimer's disease and Parkinson's disease, and found that BioN∅T is able to capture negated events that may be ignored by experts. Conclusions The BioN∅T database can be a useful resource for biomedical researchers. BioN∅T is freely available at http://bionot.askhermes.org/. In future work, we will develop semantic web related technologies to enrich BioN∅T.

  18. A Novel Multiple Choice Question Generation Strategy: Alternative Uses for Controlled Vocabulary Thesauri in Biomedical-Sciences Education.

    Science.gov (United States)

    Lopetegui, Marcelo A; Lara, Barbara A; Yen, Po-Yin; Çatalyürek, Ümit V; Payne, Philip R O

    2015-01-01

    Multiple choice questions play an important role in training and evaluating biomedical science students. However, the resource intensive nature of question generation limits their open availability, reducing their contribution to evaluation purposes mainly. Although applied-knowledge questions require a complex formulation process, the creation of concrete-knowledge questions (i.e., definitions, associations) could be assisted by the use of informatics methods. We envisioned a novel and simple algorithm that exploits validated knowledge repositories and generates concrete-knowledge questions by leveraging concepts' relationships. In this manuscript we present the development and validation of a prototype which successfully produced meaningful concrete-knowledge questions, opening new applications for existing knowledge repositories, potentially benefiting students of all biomedical sciences disciplines.

  19. "Tacit Knowledge" versus "Explicit Knowledge"

    DEFF Research Database (Denmark)

    Sanchez, Ron

    creators and carriers. By contrast, the explicit knowledge approach emphasizes processes for articulating knowledge held by individuals, the design of organizational approaches for creating new knowledge, and the development of systems (including information systems) to disseminate articulated knowledge...

  20. Globalizing and crowdsourcing biomedical research.

    Science.gov (United States)

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

    2016-12-01

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

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

    Science.gov (United States)

    Zhu, Yongjun; Yan, Erjia; Wang, Fei

    2017-07-03

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

  2. Astonishing advances in mouse genetic tools for biomedical research.

    Science.gov (United States)

    Kaczmarczyk, Lech; Jackson, Walker S

    2015-01-01

    The humble house mouse has long been a workhorse model system in biomedical research. The technology for introducing site-specific genome modifications led to Nobel Prizes for its pioneers and opened a new era of mouse genetics. However, this technology was very time-consuming and technically demanding. As a result, many investigators continued to employ easier genome manipulation methods, though resulting models can suffer from overlooked or underestimated consequences. Another breakthrough, invaluable for the molecular dissection of disease mechanisms, was the invention of high-throughput methods to measure the expression of a plethora of genes in parallel. However, the use of samples containing material from multiple cell types could obfuscate data, and thus interpretations. In this review we highlight some important issues in experimental approaches using mouse models for biomedical research. We then discuss recent technological advances in mouse genetics that are revolutionising human disease research. Mouse genomes are now easily manipulated at precise locations thanks to guided endonucleases, such as transcription activator-like effector nucleases (TALENs) or the CRISPR/Cas9 system, both also having the potential to turn the dream of human gene therapy into reality. Newly developed methods of cell type-specific isolation of transcriptomes from crude tissue homogenates, followed by detection with next generation sequencing (NGS), are vastly improving gene regulation studies. Taken together, these amazing tools simplify the creation of much more accurate mouse models of human disease, and enable the extraction of hitherto unobtainable data.

  3. Simbody: multibody dynamics for biomedical research.

    Science.gov (United States)

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

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

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

    Science.gov (United States)

    Gutiérrez, José María

    2002-01-01

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

  5. Biomedical engineering education--status and perspectives.

    Science.gov (United States)

    Magjarevic, Ratko; Zequera Diaz, Martha L

    2014-01-01

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

  6. Industry careers for the biomedical engineer.

    Science.gov (United States)

    Munzner, Robert F

    2004-01-01

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

  7. Biomedical engineering for health research and development.

    Science.gov (United States)

    Zhang, X-Y

    2015-01-01

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

  8. Development of polyphenolic nanoparticles for biomedical applications

    Science.gov (United States)

    Cheng, Huaitzung Andrew

    Polymeric nanoparticles have a wide range of applications, particularly as drug delivery and diagnostic agents, and tannins have been regarded as a promising building block for redox and pH responsive systems. Tannins are a class of naturally occurring polyphenols commonly produced by plants and are found in many of our consumables like teas, spices, fresh fruits, and vegetables. Many of the health benefits associated with these foods are a result of their high tannin contents and the many different types of tannins found in various plants have demonstrated therapeutic potentials for conditions ranging from cardiovascular disease and diabetes to ulcers and cancer. Diets rich in tannins have been associated with lower blood pressure in patients with hypertension. The plurality of phenols in tannins also makes them powerful antioxidants and as a result, there is a lot of interest in taking advantage of their self-assembling abilities to make redox and pH responsive drug delivery systems. However, the benefit of natural tannins is limited by their instability in physiological conditions. Furthermore, there is limited control over molecular weight and reactivity of the phenolic content of plant extracts. Herein we report the novel synthesis of pseudotannins with control over molecular weight and reactivity of phenolic moieties. These pseudotannins have can form nanoscale interpolymer complexes under physiological conditions and have demonstrated antioxidative potential. Furthermore, pseudotannin IPCs have been shown to be responsive to physiologically relevant oxidation as well as the ability to easily incorporate cell targeting peptides, fluorescent tags, and MRI contrast agents. The work presented here describes how pseudotannins would be ideally suited to minimally invasive techniques for diagnosing atherosclerotic plaques and targeting triple negative breast cancer. We demonstrate that pseudotannin can very easily and quickly form nanoscale particles that are small

  9. Knowledge representation and management: benefits and challenges of the semantic web for the fields of KRM and NLP.

    Science.gov (United States)

    Rassinoux, A-M

    2011-01-01

    To summarize excellent current research in the field of knowledge representation and management (KRM). A synopsis of the articles selected for the IMIA Yearbook 2011 is provided and an attempt to highlight the current trends in the field is sketched. This last decade, with the extension of the text-based web towards a semantic-structured web, NLP techniques have experienced a renewed interest in knowledge extraction. This trend is corroborated through the five papers selected for the KRM section of the Yearbook 2011. They all depict outstanding studies that exploit NLP technologies whenever possible in order to accurately extract meaningful information from various biomedical textual sources. Bringing semantic structure to the meaningful content of textual web pages affords the user with cooperative sharing and intelligent finding of electronic data. As exemplified by the best paper selection, more and more advanced biomedical applications aim at exploiting the meaningful richness of free-text documents in order to generate semantic metadata and recently to learn and populate domain ontologies. These later are becoming a key piece as they allow portraying the semantics of the Semantic Web content. Maintaining their consistency with documents and semantic annotations that refer to them is a crucial challenge of the Semantic Web for the coming years.

  10. Chemical name extraction based on automatic training data generation and rich feature set.

    Science.gov (United States)

    Yan, Su; Spangler, W Scott; Chen, Ying

    2013-01-01

    The automation of extracting chemical names from text has significant value to biomedical and life science research. A major barrier in this task is the difficulty of getting a sizable and good quality data to train a reliable entity extraction model. Another difficulty is the selection of informative features of chemical names, since comprehensive domain knowledge on chemistry nomenclature is required. Leveraging random text generation techniques, we explore the idea of automatically creating training sets for the task of chemical name extraction. Assuming the availability of an incomplete list of chemical names, called a dictionary, we are able to generate well-controlled, random, yet realistic chemical-like training documents. We statistically analyze the construction of chemical names based on the incomplete dictionary, and propose a series of new features, without relying on any domain knowledge. Compared to state-of-the-art models learned from manually labeled data and domain knowledge, our solution shows better or comparable results in annotating real-world data with less human effort. Moreover, we report an interesting observation about the language for chemical names. That is, both the structural and semantic components of chemical names follow a Zipfian distribution, which resembles many natural languages.

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

    Science.gov (United States)

    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.

  12. Radiation protection in medical and biomedical research

    International Nuclear Information System (INIS)

    Fuente Puch, A.E. de la

    2013-01-01

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

  13. Networked Biomedical System for Ubiquitous Health Monitoring

    Directory of Open Access Journals (Sweden)

    Arjan Durresi

    2008-01-01

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

  14. Practical radiation shielding for biomedical research

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  15. Finding and accessing diagrams in biomedical publications.

    Science.gov (United States)

    Kuhn, Tobias; Luong, ThaiBinh; Krauthammer, Michael

    2012-01-01

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

  16. 15th International Conference on Biomedical Engineering

    CERN Document Server

    2014-01-01

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

  17. Biomedical applications using low temperature plasma technology

    International Nuclear Information System (INIS)

    Dai Xiujuan; Jiang Nan

    2006-01-01

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

  18. Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

    Science.gov (United States)

    Oellrich, Anika; Collier, Nigel; Smedley, Damian; Groza, Tudor

    2015-01-01

    Electronic health records and scientific articles possess differing linguistic characteristics that may impact the performance of natural language processing tools developed for one or the other. In this paper, we investigate the performance of four extant concept recognition tools: the clinical Text Analysis and Knowledge Extraction System (cTAKES), the National Center for Biomedical Ontology (NCBO) Annotator, the Biomedical Concept Annotation System (BeCAS) and MetaMap. Each of the four concept recognition systems is applied to four different corpora: the i2b2 corpus of clinical documents, a PubMed corpus of Medline abstracts, a clinical trails corpus and the ShARe/CLEF corpus. In addition, we assess the individual system performances with respect to one gold standard annotation set, available for the ShARe/CLEF corpus. Furthermore, we built a silver standard annotation set from the individual systems' output and assess the quality as well as the contribution of individual systems to the quality of the silver standard. Our results demonstrate that mainly the NCBO annotator and cTAKES contribute to the silver standard corpora (F1-measures in the range of 21% to 74%) and their quality (best F1-measure of 33%), independent from the type of text investigated. While BeCAS and MetaMap can contribute to the precision of silver standard annotations (precision of up to 42%), the F1-measure drops when combined with NCBO Annotator and cTAKES due to a low recall. In conclusion, the performances of individual systems need to be improved independently from the text types, and the leveraging strategies to best take advantage of individual systems' annotations need to be revised. The textual content of the PubMed corpus, accession numbers for the clinical trials corpus, and assigned annotations of the four concept recognition systems as well as the generated silver standard annotation sets are available from http://purl.org/phenotype/resources. The textual content of the Sh

  19. Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

    Directory of Open Access Journals (Sweden)

    Anika Oellrich

    Full Text Available Electronic health records and scientific articles possess differing linguistic characteristics that may impact the performance of natural language processing tools developed for one or the other. In this paper, we investigate the performance of four extant concept recognition tools: the clinical Text Analysis and Knowledge Extraction System (cTAKES, the National Center for Biomedical Ontology (NCBO Annotator, the Biomedical Concept Annotation System (BeCAS and MetaMap. Each of the four concept recognition systems is applied to four different corpora: the i2b2 corpus of clinical documents, a PubMed corpus of Medline abstracts, a clinical trails corpus and the ShARe/CLEF corpus. In addition, we assess the individual system performances with respect to one gold standard annotation set, available for the ShARe/CLEF corpus. Furthermore, we built a silver standard annotation set from the individual systems' output and assess the quality as well as the contribution of individual systems to the quality of the silver standard. Our results demonstrate that mainly the NCBO annotator and cTAKES contribute to the silver standard corpora (F1-measures in the range of 21% to 74% and their quality (best F1-measure of 33%, independent from the type of text investigated. While BeCAS and MetaMap can contribute to the precision of silver standard annotations (precision of up to 42%, the F1-measure drops when combined with NCBO Annotator and cTAKES due to a low recall. In conclusion, the performances of individual systems need to be improved independently from the text types, and the leveraging strategies to best take advantage of individual systems' annotations need to be revised. The textual content of the PubMed corpus, accession numbers for the clinical trials corpus, and assigned annotations of the four concept recognition systems as well as the generated silver standard annotation sets are available from http://purl.org/phenotype/resources. The textual content

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

    Science.gov (United States)

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Giovanni Aloisio

    2004-06-01

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

  2. Biomedical sensor design using analog compressed sensing

    Science.gov (United States)

    Balouchestani, Mohammadreza; Krishnan, Sridhar

    2015-05-01

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

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

    Science.gov (United States)

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

    2018-02-01

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

  4. Desiderata for ontologies to be used in semantic annotation of biomedical documents.

    Science.gov (United States)

    Bada, Michael; Hunter, Lawrence

    2011-02-01

    A wealth of knowledge valuable to the translational research scientist is contained within the vast biomedical literature, but this knowledge is typically in the form of natural language. Sophisticated natural-language-processing systems are needed to translate text into unambiguous formal representations grounded in high-quality consensus ontologies, and these systems in turn rely on gold-standard corpora of annotated documents for training and testing. To this end, we are constructing the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-text biomedical journal articles that are being manually annotated with the entire sets of terms from select vocabularies, predominantly from the Open Biomedical Ontologies (OBO) library. Our efforts in building this corpus has illuminated infelicities of these ontologies with respect to the semantic annotation of biomedical documents, and we propose desiderata whose implementation could substantially improve their utility in this task; these include the integration of overlapping terms across OBOs, the resolution of OBO-specific ambiguities, the integration of the BFO with the OBOs and the use of mid-level ontologies, the inclusion of noncanonical instances, and the expansion of relations and realizable entities. Copyright © 2010 Elsevier Inc. All rights reserved.

  5. Polymer/metal nanocomposites for biomedical applications.

    Science.gov (United States)

    Zare, Yasser; Shabani, Iman

    2016-03-01

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

  6. Developing biomedical devices design, innovation and protection

    CERN Document Server

    Andreoni, Giuseppe; Colombo, Barbara

    2013-01-01

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

  7. Discrete-Time Biomedical Signal Encryption

    Directory of Open Access Journals (Sweden)

    Victor Grigoraş

    2017-12-01

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

  8. Conference on medical physics and biomedical engineering

    International Nuclear Information System (INIS)

    2013-01-01

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

  9. Biomedical engineering education through global engineering teams.

    Science.gov (United States)

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

    2012-01-01

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

  10. Should biomedical research be like Airbnb?

    Directory of Open Access Journals (Sweden)

    Vivien R Bonazzi

    2017-04-01

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

  11. Should biomedical research be like Airbnb?

    Science.gov (United States)

    Bonazzi, Vivien R; Bourne, Philip E

    2017-04-01

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

  12. Optimization and Data Analysis in Biomedical Informatics

    CERN Document Server

    Pardalos, Panos M; Xanthopoulos, Petros

    2012-01-01

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

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

    Science.gov (United States)

    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.

  14. Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall.

    Science.gov (United States)

    Lowe, Daniel M; O'Boyle, Noel M; Sayle, Roger A

    2016-01-01

    Awareness of the adverse effects of chemicals is important in biomedical research and healthcare. Text mining can allow timely and low-cost extraction of this knowledge from the biomedical literature. We extended our text mining solution, LeadMine, to identify diseases and chemical-induced disease relationships (CIDs). LeadMine is a dictionary/grammar-based entity recognizer and was used to recognize and normalize both chemicals and diseases to Medical Subject Headings (MeSH) IDs. The disease lexicon was obtained from three sources: MeSH, the Disease Ontology and Wikipedia. The Wikipedia dictionary was derived from pages with a disease/symptom box, or those where the page title appeared in the lexicon. Composite entities (e.g. heart and lung disease) were detected and mapped to their composite MeSH IDs. For CIDs, we developed a simple pattern-based system to find relationships within the same sentence. Our system was evaluated in the BioCreative V Chemical-Disease Relation task and achieved very good results for both disease concept ID recognition (F1-score: 86.12%) and CIDs (F1-score: 52.20%) on the test set. As our system was over an order of magnitude faster than other solutions evaluated on the task, we were able to apply the same system to the entirety of MEDLINE allowing us to extract a collection of over 250 000 distinct CIDs. © The Author(s) 2016. Published by Oxford University Press.

  15. Multichannel biomedical time series clustering via hierarchical probabilistic latent semantic analysis.

    Science.gov (United States)

    Wang, Jin; Sun, Xiangping; Nahavandi, Saeid; Kouzani, Abbas; Wu, Yuchuan; She, Mary

    2014-11-01

    Biomedical time series clustering that automatically groups a collection of time series according to their internal similarity is of importance for medical record management and inspection such as bio-signals archiving and retrieval. In this paper, a novel framework that automatically groups a set of unlabelled multichannel biomedical time series according to their internal structural similarity is proposed. Specifically, we treat a multichannel biomedical time series as a document and extract local segments from the time series as words. We extend a topic model, i.e., the Hierarchical probabilistic Latent Semantic Analysis (H-pLSA), which was originally developed for visual motion analysis to cluster a set of unlabelled multichannel time series. The H-pLSA models each channel of the multichannel time series using a local pLSA in the first layer. The topics learned in the local pLSA are then fed to a global pLSA in the second layer to discover the categories of multichannel time series. Experiments on a dataset extracted from multichannel Electrocardiography (ECG) signals demonstrate that the proposed method performs better than previous state-of-the-art approaches and is relatively robust to the variations of parameters including length of local segments and dictionary size. Although the experimental evaluation used the multichannel ECG signals in a biometric scenario, the proposed algorithm is a universal framework for multichannel biomedical time series clustering according to their structural similarity, which has many applications in biomedical time series management. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  16. Extracting useful knowledge from event logs

    DEFF Research Database (Denmark)

    Djenouri, Youcef; Belhadi, Asma; Fournier-Viger, Philippe

    2018-01-01

    Business process analysis is a key activity that aims at increasing the efficiency of business operations. In recent years, several data mining based methods have been designed for discovering interesting patterns in event logs. A popular type of methods consists of applying frequent itemset mini...

  17. User Profiling and Knowledge Extraction For Tourism

    OpenAIRE

    Almeida, Diogo Miguel Rodrigues Soares de

    2015-01-01

    O sector do turismo é uma área francamente em crescimento em Portugal e que tem desenvolvido a sua divulgação e estratégia de marketing. Contudo, apenas se prende com indicadores de desempenho e de oferta instalada (número de quartos, hotéis, voos, estadias), deixando os indicadores estatísticos em segundo plano. De acordo com o “ Travel & tourism Competitiveness Report 2013”, do World Economic Forum, classifica Portugal em 72º lugar no que respeita à qualidade e cobertura da ...

  18. OntoGene web services for biomedical text mining.

    Science.gov (United States)

    Rinaldi, Fabio; Clematide, Simon; Marques, Hernani; Ellendorff, Tilia; Romacker, Martin; Rodriguez-Esteban, Raul

    2014-01-01

    Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical data within the pharmaceutical industry. Traditional architectures, based on monolithic applications, do not offer sufficient flexibility for a wide range of use case scenarios, and therefore open architectures, as provided by web services, are attracting increased interest. We present an approach towards providing advanced text mining capabilities through web services, using a recently proposed standard for textual data interchange (BioC). The web services leverage a state-of-the-art platform for text mining (OntoGene) which has been tested in several community-organized evaluation challenges,with top ranked results in several of them.

  19. Epidemiology and Reporting Characteristics of Systematic Reviews of Biomedical Research: A Cross-Sectional Study.

    Directory of Open Access Journals (Sweden)

    Matthew J Page

    2016-05-01

    Full Text Available Systematic reviews (SRs can help decision makers interpret the deluge of published biomedical literature. However, a SR may be of limited use if the methods used to conduct the SR are flawed, and reporting of the SR is incomplete. To our knowledge, since 2004 there has been no cross-sectional study of the prevalence, focus, and completeness of reporting of SRs across different specialties. Therefore, the aim of our study was to investigate the epidemiological and reporting characteristics of a more recent cross-section of SRs.We searched MEDLINE to identify potentially eligible SRs indexed during the month of February 2014. Citations were screened using prespecified eligibility criteria. Epidemiological and reporting characteristics of a random sample of 300 SRs were extracted by one reviewer, with a 10% sample extracted in duplicate. We compared characteristics of Cochrane versus non-Cochrane reviews, and the 2014 sample of SRs versus a 2004 sample of SRs. We identified 682 SRs, suggesting that more than 8,000 SRs are being indexed in MEDLINE annually, corresponding to a 3-fold increase over the last decade. The majority of SRs addressed a therapeutic question and were conducted by authors based in China, the UK, or the US; they included a median of 15 studies involving 2,072 participants. Meta-analysis was performed in 63% of SRs, mostly using standard pairwise methods. Study risk of bias/quality assessment was performed in 70% of SRs but was rarely incorporated into the analysis (16%. Few SRs (7% searched sources of unpublished data, and the risk of publication bias was considered in less than half of SRs. Reporting quality was highly variable; at least a third of SRs did not report use of a SR protocol, eligibility criteria relating to publication status, years of coverage of the search, a full Boolean search logic for at least one database, methods for data extraction, methods for study risk of bias assessment, a primary outcome, an

  20. International Symposium on Biomedical Engineering and Medical Physics

    CERN Document Server

    Katashev, Alexei; Lancere, Linda

    2013-01-01

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

  1. Time-Resolved Microfluorescence In Biomedical Diagnosis

    Science.gov (United States)

    Schneckenburger, Herbert

    1985-02-01

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

  2. Time Resolved Microfluorescence In Biomedical Diagnosis

    Science.gov (United States)

    Schneckenburger, Herbert

    1985-12-01

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

  3. Double-compression method for biomedical images

    Science.gov (United States)

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

    2017-08-01

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

  4. Research evaluation support services in biomedical libraries.

    Science.gov (United States)

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

    2018-01-01

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

  5. Biomedical engineering at UCT - challenges and opportunities.

    Science.gov (United States)

    Douglas, Tania S

    2012-03-02

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

  6. Welcome to Biomedical Research and Therapy

    OpenAIRE

    Phuc Van Pham

    2014-01-01

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

  7. Multiplicative calculus in biomedical image analysis

    NARCIS (Netherlands)

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

    2011-01-01

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

  8. Love troubles : human attachment and biomedical enhancements

    NARCIS (Netherlands)

    Nyholm, S.

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

  9. Usage of cell nomenclature in biomedical literature

    KAUST Repository

    Kafkas, Senay; Sarntivijai, Sirarat; Hoehndorf, Robert

    2017-01-01

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

  10. Biomedical composites materials, manufacturing and engineering

    CERN Document Server

    Davim, J Paulo

    2013-01-01

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

  11. Archives of Medical and Biomedical Research: Submissions

    African Journals Online (AJOL)

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

  12. Electrosprayed calcium phosphate coatings for biomedical purposes.

    NARCIS (Netherlands)

    Leeuwenburgh, S.C.G.

    2006-01-01

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

  13. Biomedical Engineering Education: A Conservative Approach

    Science.gov (United States)

    Niemi, Eugene E., Jr.

    1973-01-01

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

  14. Status of Research in Biomedical Engineering 1968.

    Science.gov (United States)

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

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

  15. Sierra Leone Journal of Biomedical Research: Submissions

    African Journals Online (AJOL)

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

  16. Thermoforming of film-based biomedical microdevices

    NARCIS (Netherlands)

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

    2011-01-01

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

  17. Biomedical Visual Computing: Case Studies and Challenges

    KAUST Repository

    Johnson, Christopher

    2012-01-01

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

  18. Journal of Medicine and Biomedical Research

    African Journals Online (AJOL)

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

  19. Nigerian Journal of Health and Biomedical Sciences

    African Journals Online (AJOL)

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

  20. Biomedical Visual Computing: Case Studies and Challenges

    KAUST Repository

    Johnson, Christopher

    2012-01-01

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

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

    Indian Academy of Sciences (India)

    G DEEP

    2018-03-10

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

  2. Europium enabled luminescent nanoparticles for biomedical applications

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-15

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

  3. Europium enabled luminescent nanoparticles for biomedical applications

    International Nuclear Information System (INIS)

    Syamchand, S.S.; Sony, G.

    2015-01-01

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

  4. Knowledge Sharing is Knowledge Creation

    DEFF Research Database (Denmark)

    Greve, Linda

    2015-01-01

    Knowledge sharing and knowledge transfer are important to knowledge communication. However when groups of knowledge workers engage in knowledge communication activities, it easily turns into mere mechanical information processing despite other ambitions. This article relates literature of knowledge...... communication and knowledge creation to an intervention study in a large Danish food production company. For some time a specific group of employees uttered a wish for knowledge sharing, but it never really happened. The group was observed and submitted to metaphor analysis as well as analysis of co...

  5. Special Issue: 3D Printing for Biomedical Engineering

    Directory of Open Access Journals (Sweden)

    Chee Kai Chua

    2017-02-01

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

  6. ZK DrugResist 2.0: A TextMiner to extract semantic relations of drug resistance from PubMed.

    Science.gov (United States)

    Khalid, Zoya; Sezerman, Osman Ugur

    2017-05-01

    Extracting useful knowledge from an unstructured textual data is a challenging task for biologists, since biomedical literature is growing exponentially on a daily basis. Building an automated method for such tasks is gaining much attention of researchers. ZK DrugResist is an online tool that automatically extracts mutations and expression changes associated with drug resistance from PubMed. In this study we have extended our tool to include semantic relations extracted from biomedical text covering drug resistance and established a server including both of these features. Our system was tested for three relations, Resistance (R), Intermediate (I) and Susceptible (S) by applying hybrid feature set. From the last few decades the focus has changed to hybrid approaches as it provides better results. In our case this approach combines rule-based methods with machine learning techniques. The results showed 97.67% accuracy with 96% precision, recall and F-measure. The results have outperformed the previously existing relation extraction systems thus can facilitate computational analysis of drug resistance against complex diseases and further can be implemented on other areas of biomedicine. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Knowledge Management.

    Science.gov (United States)

    1999

    The first of the four papers in this symposium, "Knowledge Management and Knowledge Dissemination" (Wim J. Nijhof), presents two case studies exploring the strategies companies use in sharing and disseminating knowledge and expertise among employees. "A Theory of Knowledge Management" (Richard J. Torraco), develops a conceptual…

  8. Building a biomedical ontology recommender web service

    Directory of Open Access Journals (Sweden)

    Jonquet Clement

    2010-06-01

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

  9. Biomedical technology prosperity game{trademark}

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-07-01

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

  10. Managing Knowledge

    OpenAIRE

    Connolly, Niall

    2013-01-01

    This paper provides a perspective on what knowledge is, why knowledge is important, and how we might encourage good knowledge behaviours. A knowledge management framework is described, and although the framework is project management-centric the basic principles are transferrable to other contexts. From a strategic perspective, knowledge can be considered an asset that has the potential to provide a competitive advantage provided that it has intrinsic value, it is not easily accessible by ...

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

    Science.gov (United States)

    Guo, Shijun; Lyu, Jie; Zhang, Peiming

    2017-08-01

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

  12. Introduction to applied statistical signal analysis guide to biomedical and electrical engineering applications

    CERN Document Server

    Shiavi, Richard

    2007-01-01

    Introduction to Applied Statistical Signal Analysis is designed for the experienced individual with a basic background in mathematics, science, and computer. With this predisposed knowledge, the reader will coast through the practical introduction and move on to signal analysis techniques, commonly used in a broad range of engineering areas such as biomedical engineering, communications, geophysics, and speech.Introduction to Applied Statistical Signal Analysis intertwines theory and implementation with practical examples and exercises. Topics presented in detail include: mathematical

  13. A novel end-to-end classifier using domain transferred deep convolutional neural networks for biomedical images.

    Science.gov (United States)

    Pang, Shuchao; Yu, Zhezhou; Orgun, Mehmet A

    2017-03-01

    Highly accurate classification of biomedical images is an essential task in the clinical diagnosis of numerous medical diseases identified from those images. Traditional image classification methods combined with hand-crafted image feature descriptors and various classifiers are not able to effectively improve the accuracy rate and meet the high requirements of classification of biomedical images. The same also holds true for artificial neural network models directly trained with limited biomedical images used as training data or directly used as a black box to extract the deep features based on another distant dataset. In this study, we propose a highly reliable and accurate end-to-end classifier for all kinds of biomedical images via deep learning and transfer learning. We first apply domain transferred deep convolutional neural network for building a deep model; and then develop an overall deep learning architecture based on the raw pixels of original biomedical images using supervised training. In our model, we do not need the manual design of the feature space, seek an effective feature vector classifier or segment specific detection object and image patches, which are the main technological difficulties in the adoption of traditional image classification methods. Moreover, we do not need to be concerned with whether there are large training sets of annotated biomedical images, affordable parallel computing resources featuring GPUs or long times to wait for training a perfect deep model, which are the main problems to train deep neural networks for biomedical image classification as observed in recent works. With the utilization of a simple data augmentation method and fast convergence speed, our algorithm can achieve the best accuracy rate and outstanding classification ability for biomedical images. We have evaluated our classifier on several well-known public biomedical datasets and compared it with several state-of-the-art approaches. We propose a robust

  14. Knowledge Sharing

    DEFF Research Database (Denmark)

    Holdt Christensen, Peter

    The concept of knowledge management has, indeed, become a buzzword that every single organization is expected to practice and live by. Knowledge management is about managing the organization's knowledge for the common good of the organization -but practicing knowledge management is not as simple...... as that. This article focuses on knowledge sharing as the process seeking to reduce the resources spent on reinventing the wheel.The article introduces the concept of time sensitiveness; i.e. that knowledge is either urgently needed, or not that urgently needed. Furthermore, knowledge sharing...... is considered as either a push or pull system. Four strategies for sharing knowledge - help, post-it, manuals and meeting, and advice are introduced. Each strategy requires different channels for sharing knowledge. An empirical analysis in a production facility highlights how the strategies can be practiced....

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

    Science.gov (United States)

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

    2016-07-01

    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

  16. Support patient search on pathology reports with interactive online learning based data extraction.

    Science.gov (United States)

    Zheng, Shuai; Lu, James J; Appin, Christina; Brat, Daniel; Wang, Fusheng

    2015-01-01

    more accurate knowledge to support biomedical research and clinical diagnosis. IDEAL-X provides a bridge that takes advantage of online machine learning based data extraction and the knowledge from human's feedback. By combining iterative online learning and adaptive controlled vocabularies, IDEAL-X can deliver highly adaptive and accurate data extraction to support patient search.

  17. Support patient search on pathology reports with interactive online learning based data extraction

    Directory of Open Access Journals (Sweden)

    Shuai Zheng

    2015-01-01

    tests. Conclusions: Extracting data from pathology reports could enable more accurate knowledge to support biomedical research and clinical diagnosis. IDEAL-X provides a bridge that takes advantage of online machine learning based data extraction and the knowledge from human′s feedback. By combining iterative online learning and adaptive controlled vocabularies, IDEAL-X can deliver highly adaptive and accurate data extraction to support patient search.

  18. Knowledge management

    DEFF Research Database (Denmark)

    Foss, Nicolai Juul; Mahnke, Volker

    2003-01-01

    Knowledge management has emerged as a very successful organization practice and has beenextensively treated in a large body of academic work. Surprisingly, however, organizationaleconomics (i.e., transaction cost economics, agency theory, team theory and property rightstheory) has played no role...... in the development of knowledge management. We argue thatorganizational economics insights can further the theory and practice of knowledge managementin several ways. Specifically, we apply notions of contracting, team production,complementaries, hold-up, etc. to knowledge management issues (i.e., creating...... and integrationknowledge, rewarding knowledge workers, etc.) , and derive refutable implications that are novelto the knowledge management field from our discussion....

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

    CERN Document Server

    Dhillon, Sarinder; Advances in biomedical infrastructure 2013

    2013-01-01

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

  20. Antimicrobial thin films based on ayurvedic plants extracts embedded in a bioactive glass matrix

    Science.gov (United States)

    Floroian, L.; Ristoscu, C.; Candiani, G.; Pastori, N.; Moscatelli, M.; Mihailescu, N.; Negut, I.; Badea, M.; Gilca, M.; Chiesa, R.; Mihailescu, I. N.

    2017-09-01

    Ayurvedic medicine is one of the oldest medical systems. It is an example of a coherent traditional system which has a time-tested and precise algorithm for medicinal plant selection, based on several ethnopharmacophore descriptors which knowledge endows the user to adequately choose the optimal plant for the treatment of certain pathology. This work aims for linking traditional knowledge with biomedical science by using traditional ayurvedic plants extracts with antimicrobial effect in form of thin films for implant protection. We report on the transfer of novel composites from bioactive glass mixed with antimicrobial plants extracts and polymer by matrix-assisted pulsed laser evaporation into uniform thin layers onto stainless steel implant-like surfaces. The comprehensive characterization of the deposited films was performed by complementary analyses: Fourier transformed infrared spectroscopy, glow discharge optical emission spectroscopy, scanning electron microscopy, atomic force microscopy, electrochemical impedance spectroscopy, UV-VIS absorption spectroscopy and antimicrobial tests. The results emphasize upon the multifunctionality of these coatings which allow to halt the leakage of metal and metal oxides into the biological fluids and eventually to inner organs (by polymer use), to speed up the osseointegration (due to the bioactive glass use), to exert antimicrobial effects (by ayurvedic plants extracts use) and to decrease the implant price (by cheaper stainless steel use).